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Preprint ARTICLE | doi:10.20944/preprints202005.0440.v1

Clinical Performance Analysis and Evaluation of Quantitative Real Time PCR for Diagnosis of Scrub Typhus in North East India

Diptanu Paul, W Valarie Lyngdoh, Himesh Barman, Clarissa Jane Lyngdoh, Kryshanlang Lynrah, Elantamilan Durairaj

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Scrub typhus; qRT PCR; Quantitative PCR; real time PCR; IgM ELISA; North-East India

Online: 27 May 2020 (07:51:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.1257.v1

Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis

Daniella Van der Walt, Emma Steenkamp, Brenda D. Wingfield, P. Markus Wilken

Subject: Biology And Life Sciences, Life Sciences Keywords: Ceratocystis; hybridization; PCR RFLP

Online: 30 April 2023 (04:34:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0520.v1

Prevalence of Human Herpesviruses (HHV1-7), and its Clinical Significance in Middle Eastern Pediatric Leukemia Patients Using 2 Independent PCR Assays

Waleed Seif ElDin Mohamed, Hisham Abid Aldabbagh, Hussein Ali Aldughmani, Zeinab Fathy Abdullah, Sara Ahmed Kassem, Iman Adel Abdel-Almoniem, Mohamed Fawzy Ibrahim

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Multiplex PCR; Real time PCR; Human herpes viruses; clinical significance; Pediatric Leukemia patients

Online: 30 August 2022 (10:30:06 CEST)

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Objectives: Human herpes viruses can cause life-threatening diseases in immunocompromised children, especially leukemic patients. Therefore, the aim of this study is to detect the human herpes viruses (HHV1-7) and to investigate its clinical significance in Middle Eastern Pediatric Leukemia Patients by using 2 Independent PCR assays. Methods: Detection of human herpes virus DNA has been done in blood samples of 200 pediatric leukemia patients in addition to 90 blood donors as a control group using multiplex PCR assays. When a ‘‘positive’’ result was observed, real-time PCR was performed to measure the viral load. Results: The most frequent herpes virus infection in Middle Eastern Pediatric Leukemia cases was CMV, followed by EBV, then HHV6, VZV, HHV7, HSV1, and HSV2, where they were 92/200 (46%), 76/200 (38%), 72/200 (36%), 48/200 (24%), 12/200 (6%), 8/200 (4%), and 2/200 (1%) respectively. Also, there was a statistically significance difference between leukemic patients and their controls regarding CMV, EBV, HHV6, and VZV (P <0.05). Correlation between percentage of co-infection, and clinical parameters for the 7 herpes viruses has been studied, and there is an increase in absolute neutrophilic count (ANC), total leukocyte count (TLC) and duration of fever and neutropenia in age group 6-11 years for HHV6/CMV, then in age group 12-18 years especially for EBV/CMV and CMV/HHV6. Also, our results show that multiplex PCR assay is close to single PCR assay in relation to specificity and sensitivity which in turn prove its validity for early diagnosis of herpes viral infection. Conclusions: Adopting multiplex PCR technique is helpful in screening of virus infections. It will save time, effort, cost effective and will assist in rapid diagnosis. However, the clinical relevance of the virus infection needs to be evaluated by quantitative real-time PCR which in turn will help patient's management by using appropriate antiviral treatment.

Preprint ARTICLE | doi:10.20944/preprints202309.0323.v1

utPCR: A Strategy for Highly Specific and Absolutely Quantitative Detection of Single Molecules within Only Minutes

Rui Wang, Ying Liu, Shuaiwei Chen, Linlin Bai, Kaiming Guo, Yanan Pang, Feng Qian, Yongfang Li, Li Ding, Yongming Wang

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Ultrafast PCR; droplet digital PCR (ddPCR); single-molecule detection; bloodstream infection; absolute quantification; molecular diagnosis

Online: 6 September 2023 (04:20:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0688.v1

Direct Quantitation of SARS-CoV-2 Using Droplet Digital PCR in Suspected Samples With Very Low Viral Load

Michela Deiana, Chiara Piubelli, Antonio Mori, Gian Paolo Chiecchi, Giulia La Marca, Martina Leonardi, Davide Treggiari, Anna Beltrame, Lucia Moro, Zeno Bisoffi, Elena Pomari

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: droplet digital PCR; real time RT-PCR; SARS-CoV-2; false negative; viral load; diagnosis

Online: 26 April 2021 (20:09:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1650.v1

The Molecular Characterization of Lineage-IV Peste Des Petits Ruminants Virus and the Development of In-House IELISA for Its Rapid Detection

Tahira Kamal Rana, Saeed-ul-Hassan Khan, Fariha Hassan, Aamer Bin Zahur, Aman Ullah, S. Murtaza Hassan Andrabi, Ghulam Muhammad Ali

Subject: Biology And Life Sciences, Virology Keywords: IELISA; PPRV; RT-PCR; Cost-effective

Online: 23 August 2023 (10:08:12 CEST)

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Peste des Petits Ruminants (PPR), a highly contagious viral disease, causes significant economic losses in sheep and goats. Laboratory diagnosis is crucial to disease control and eradication. Since PPRVs have recently adopted new hosts, genetic diversity within isolates of the same lineage is more likely than if they were host-specific, sheep and goats most often. ELISA detects antibodies and antigens in serology. However, mishandling, environmental conditions (temperature and humidity), storage, and sensitivity issues of commercially available ELISA kits prevent rapid PPR virus detection in third-world countries like Pakistan. In the 2020-21 outbreaks in Pakistan, 325 blood samples, 19 swabs, and 6 virus tissue samples of sheep and goats were collected from Gilgit, Islamabad, and Fateh Jang. These virus isolates were submitted to NCBI for partial N gene sequencing. Antigen was prepared from indigenous virus Using semi-purified antigen from PPRV, an indirect ELISA for the detection of PPR antibodies in goat and sheep serum was developed using MW600922 grown in Vero cells. Dilutions of 1:200 serums and 1:32 antigens improve antibody detection. The N-gene-based analysis revealed a better understanding of PPRV genetic characterization. This study develops an RT-PCR assay to detect PPRV by targeting the N-protein gene. This assay offers an accurate and affordable diagnostic tool for PPRV and partial genome sequencing. Results described that PPRV isolates from the current study have 99.73% and 99.4% similarity to previously published Lahore and Faisalabad isolates from Pakistan, respectively. Compared to previous isolates from NCBI data, the virus showed high divergence rates with the Turkish strain. The comparative analysis between Commercial kit (c-ELISA) and I-ELISA revealed that the former had a high sensitivity of 90.60% and specificity of 85.23% compared with the cELISA kit. By comparing I-ELISA and VNT, we find that the current assay is 100% specific and 82.14 % sensitive. Based on these results, serological surveys for PPR antibodies, on a larger scale, in small ruminants can be conducted with indirect ELISA rather than competitive ELISA. Furthermore, the cost and storage efficiency was highly significant because the currently developed method has a low production cost, which is much lesser than the commercially available kit. Our findings demonstrated a significant breakthrough in terms of cost-effectiveness and storage efficiency, and they are highly recommended for developing countries.

Preprint ARTICLE | doi:10.20944/preprints202211.0030.v1

PCR-based Detection of Typhoidal Salmonella from Human Clinical Samples and Evaluation of Traditional PCR, Nested-PCR and Widal Test in Pune, India

Abas O. Hadi, Hussein Alburkat, Taisir Abdulelah Kadhim, Ammar M S Al-Helli, Mustafa Hamza Ghazi, Yasir Abdulameer N. Aldabbagh, Reem Numaan Talib, Sama Hussein Ali, Noor Hameed Imran, Ruaa Almohsen, Turki Muftin Saad, Pallavi Mandave

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: PCR; Salmonella Typhi; Widal Test; BHI

Online: 1 November 2022 (12:43:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0061.v1

Handheld Ultra-Fast duplex PCR assays and Lateral flow detection and identification of Leishmania parasites for cutaneous leishmanisis diagnosis

Insaf Bel Hadj Ali, Yusr Saadi Ben Aoun, Zeineb Hammami, Oumayma Rhouma, Ahmed Sahbi Chakroun, Ikram Guizani

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Cutaneous leishmaniases; Molecular diagnosis; Point of care; Leishmania; Molecular target; Palm PCR; Duplex PCR; Lateral Flow immunoassay

Online: 2 October 2023 (09:43:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0284.v1

Designing and Validation of a Droplet Digital PCR Procedure for Diagnosis and Accurate Quantification of Nervous Necrosis Virus

Sandra Souto, José G. Olveira, Carmen López-Vázquez, Isabel Bandín, Carlos P. Dopazo

Subject: Biology And Life Sciences, Virology Keywords: VNNV; Diagnosis; Validation; dPCR; droplet digital PCR.

Online: 3 August 2023 (10:44:12 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202212.0429.v1

Hidden Pitfalls of Using Onion Pollen in Molecular Research

Majd Mardini, Aleksey Ermolaev, Ludmila Khrustaleva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: onion; PCR inhibition; pollenkitt; wetted pollen; pollination

Online: 22 December 2022 (12:58:49 CET)

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Working Paper ARTICLE

Chip-Based Digital Pcr Improves the Detection of Low-Rate pik3ca Mutations in Breast Cancer Patients

Stefano Giannoni-Luza, Oscar Acosta Conchucos, Alexis Germán Murillo Carrasco, Pierina Danos, José Manuel Cotrina Concha, Henry Guerra Miller, Joseph A. Pinto, Alfredo Aguilar Cartagena, Jhajaira M. Araujo, Ricardo Fujita, José Luis Buleje Sono

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Breast cancer; PIK3CA; digital PCR; Sanger sequencing

Online: 5 July 2021 (14:00:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0597.v1

Surveillance for COVID-19 in the English Football League 2019-2020

Subhashis Basu, Richard Higgins, Aneil Malhotra, Imtiaz Ahmad

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: Surveillance; COVID; Football; Infection; Professional; PCR; Elite

Online: 26 February 2021 (08:59:29 CET)

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Preprint ARTICLE | doi:10.20944/preprints202010.0221.v1

Canine Filariasis Outbreak in Southwestern Colombia: A Molecular and Epidemiological Study

Nathaly Espinosa, Angelo Rosero, Claudia Lucia Villegas, Isabel Cristina Garcia, Tania Gaviria-Cantin, Alejandra Peña, Beatriz Eugenia Ferro, Luisa Maria Nieto Ramirez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Dogs; Microfilariae; Acanthocheilonema; PCR-RFLP; Cali; Zoonosis

Online: 12 October 2020 (10:18:10 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202005.0193.v1

Added Value of Chest CT in Suspected COVID-19: An Analysis of 239 Patients

Daniel A. Korevaar, Ruud S. Kootte, Loek P. Smits, Joost G. van den Aardweg, Peter I. Bonta, Janke Schinkel, Rene M. Vigeveno, Inge A.H. van den Berk, Maeke J. Scheerder, Bregtje A. Lemkes, Abraham Goorhuis, Ludo F.M. Beenen, Jouke T. Annema

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; diagnostic accuracy; CT; RT-PCR

Online: 11 May 2020 (12:35:08 CEST)

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Introduction: Clinicians have been struggling with the optimal diagnostic approach of patients with suspected COVID-19. We evaluated the added value of chest CT over RT-PCR alone. Methods: Consecutive adult patients with suspected COVID-19 presenting to the emergency department (Academic Medical Center, Amsterdam University Medical Centers, the Netherlands) from March 16^th to April 16^th were retrospectively included if they required hospital admission and underwent chest CT and RT-PCR testing for SARS-CoV-2 infection. The CO-RADS classification was used to assess the radiological probability of COVID-19, where a score of 1-2 was considered as negative, 3 as indeterminate, and 4-5 as positive. CT results were stratified by initial RT-PCR results. For patients with a negative RT-PCR but a positive CT, serology or multidisciplinary discussion after clinical follow-up constituted the final diagnosis. Results: 258 patients with suspected COVID-19 were admitted, of which 239 were included because they had both CT and RT-PCR testing upon admission. Overall, 112 patients (46.9%) had a positive initial RT-PCR, and 14 (5.9%) had a positive repeat RT-PCR. Of 127 patients with a negative or indeterminate initial RT-PCR, 38 (29.9% [95%CI 21.3-39.3%]) had a positive CT. Of these, 13 had a positive RT-PCR upon repeat testing, and 5 had positive serology. The remaining 20 patients were assessed in a multidisciplinary consensus meeting, and for 13 it was concluded that COVID-19 was ‘very likely’. Of 112 patients with a positive initial RT-PCR result, CT was positive in 104 (92.9% [95%CI 89.3-97.5%]). Conclusion: In a high-prevalence emergency department setting, chest CT showed high probability of COVID-19 (CO-RADS 4-5) in 29.9% of patients with a negative or indeterminate initial RT-PCR result. As the majority of these patients had proven or ‘very likely’ COVID-19 after follow-up, we believe that CT helps in the identification of patients who should be admitted in isolation.

Preprint REVIEW | doi:10.20944/preprints202005.0142.v1

COVID-19 Clinical and Laboratory Diagnosis Overview

Rania Zayed, Dalia Omran, Abeer Zayed

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; serology; RT-PCR; lab; clinical

Online: 8 May 2020 (12:26:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0039.v1

Genetic Diversity of Lowbush Blueberry throughout its U.S. Native Range in Managed and Non-managed Populations

Lee Beers, Jeannie Rowland, Francis Drummond

Subject: Biology And Life Sciences, Horticulture Keywords: EST-PCR; Vaccinium angustifolium; geographic range; domestication

Online: 6 May 2019 (08:43:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0680.v1

Symbiont Diversity in Imidacloprid-Resistant and Imidacloprid-Susceptible Populations of Nilaparvata lugens (Hemiptera: Delphacidae)

Juefeng Zhang, Fang Li, Haiying Zhong, Jianming Chen

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: imidacloprid; Nilaparvata lugens; PCR-DGGE; insecticide resistance; neonicotinoids

Online: 12 September 2023 (04:11:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0313.v1

Epidermal growth factor receptor T790M Mutation Testing in Non-small Cell Lung Cancer: An International Collaborative Study to Assess Molecular EGFR T790M Testing in Liquid Biopsy

Martin Filipits, Verena Kainz, Viktor Sebek, Herwig Zach

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Liquid biopsy; EGFR; NSCLC; T790M mutation; NGS; PCR

Online: 5 June 2023 (11:06:11 CEST)

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Background: The detection of the EGFR T790M (T790M) mutation in non-small cell lung cancer (NSCLC) patients who progressed under treatment with first- or second-generation EGFR-tyrosine kinase inhibitors (TKIs) is important to offer a subsequent therapy with a third-generation EGFR-TKI. Liquid biopsy is a powerful tool to determine the T790M mutation status. Several liquid biopsy platforms with varying degrees of accuracy are available to test for T790M mutations and sensitivities may differ among these methods. Methods: As no standard exists for the testing of T790M mutation in liquid biopsy, we performed a collaborative study to describe and compare the sensitivity of different in-house liquid biopsy platforms for the detection of the T790M mutation, EGFR exon 19 deletion (del19) and EGFR L858R mutation (L858R) across multiple participating laboratories in seven Central and Eastern European countries. Results: Of the 25 invited laboratories across Central and Eastern Europe, 21 centers participated and received 10 plasma samples spiked with cell-line DNA containing the T790M, del19, or L858R mutation in different concentrations. In-house PCR-based and NGS-based methods were used accordingly, and results reported as in routine clinical practice. Two laboratories, which used the AmoyDx® EGFR 29 Mutations Detection Kit (AmoyDx) with Cobas® cfDNA Sample Preparation Kit and QX200 Droplet Digital PCR (ddPCR) with the QIAamp Circulating Nucleic Acid Kit identified all ten samples correctly. Cobas® EGFR Mutation Test v2 (Cobas), the NGS methods, and the IdyllaTM detection method used in this study performed within the known sensitivity range of each detection method. Conclusions: If a negative result was obtained from methods with lower sensitivity (e.g. Cobas), repeated liquid biopsy testing and/or tissue biopsy analysis should be performed whenever possible, with the aim of identifying T790M-positive patients to allow them to receive the optimal second-line treatment with a third-generation EGFR TKI.

Preprint ARTICLE | doi:10.20944/preprints202210.0199.v1

Improvement, Standardization, and Validation of A Novel Genomic DNA Extraction Method for Human Breastmilk

Mario Iván Alemán-Duarte, Blanca Rosa Aguilar-Uscanga, Guadalupe García-Robles, Felipe de Jesús Ramírez-Salazar, Israel Benítez-García, Edgar Balcázar-López, Josué Raymundo Solís-Pacheco

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: human milk; DNA extraction; PCR; DNA quality, microbiota

Online: 14 October 2022 (03:19:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0526.v1

Circulating Phylotypes of White Spot Syndrome Virus in Bangladesh and Their Virulence

Mehedi Mahmudul Hasan, M. Nazmul Hoque, Firoz Ahmed, Md. Inja-Mamun Haque, Munawar Sultana, M. Anwar Hossain

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: VP28; WSSV; real-time PCR; viral load; apoptosis

Online: 29 November 2021 (11:55:17 CET)

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White Spot Syndrome Virus (WSSV) has emerged as one of the most prevalent and lethal viruses globally, and infects both shrimps and crabs in the aquatic environment. This study aimed to investigate the occurrence of WSSV in different ghers of Bangladesh and the virulence of the circulating phylotypes. We collected 360 shrimp (Penaeus monodon) and 120 crab (Scylla sp.) samples from the South-East (Cox’s Bazar) and South-West (Satkhira) coastal regions of Bangladesh. The VP28 gene-specific PCR assays and sequencing revealed statistically significant (p < 0.05, Kruskal Wallis test) differences in the prevalence of WSSV in shrimps and crabs between the study areas (Cox’s Bazar and Satkhira), and over the study periods (2017-2019). The mean Log load of WSSV varied from 8.40 (Cox’s Bazar) to 10.48 (Satkhira) per gram of tissue. The mean values for salinity, dissolved oxygen, temperature and pH were 14.71±0.76 ppt, 3.7±0.1 ppm, 34.11±0.38˚C and 8.23±0.38, respectively in the WSSV-positive ghers. The VP28 gene-based phylogenetic analysis showed an amino-acid substitution (E→G) at 167th position in the isolates from Cox’s Bazar (referred to as phylotype BD2) compared to the globally circulating one (BD1). Shrimp PL artificially challenged with BD1 and BD2 phylotypes with filtrates of tissue containing 0.423 X 109 copies of WSSV per mL resulted a median LT50 value of 73 hrs and 75 hrs, respectively. The in-vivo trial showed higher mean Log WSSV copies (6.47±2.07 per mg tissue) in BD1 challenged shrimp PL compared to BD2 (4.75±0.35 per mg tissue). Crabs infected with BD1 and BD2 showed 100% mortality within 48 hrs and 62 hrs of challenge, respectively with mean Log WSSV copies of 12.06±0.48 and 9.95±0.37 per gram tissue, respectively. Moreover, shrimp antimicrobial peptides (AMPs) penaeidin and lysozyme expression was lower in BD1 challenged group compared to BD2 challenged shrimps. These results collectively demonstrated that relative virulence properties of WSSV based on mortality rate, viral load and expression of host immune genes in artificially infected shrimp PL could be affected by single aa substitution in VP28.

Preprint ARTICLE | doi:10.20944/preprints202109.0224.v1

Drought Stress Described by Transcriptional Responses of Picea Abies under Pathogen Heterobasidion Parviporum Attack

Xenia Hao-Yi Yeoh, Blessing Durodola, Kathrin Blumenstein, Eeva Terhonen

Subject: Biology And Life Sciences, Forestry Keywords: Drought; Norway spruce; Heterobasidion; RNA-seq; qRT-PCR

Online: 14 September 2021 (08:19:04 CEST)

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The major threats to the sustainable supply of forest tree products are adverse climate, pests and diseases. Climate change, exemplified by increased drought, poses a unique threat to global forest health. This is attributed to the unpredictable behavior of forest pathosystems, which can favor fungal pathogens over the host under persistent drought stress conditions in the future. Currently, the effects of drought on tree resistance against pathogens are hypothetical, thus research is needed to identify these correlations. Norway spruce (Picea abies) is one of the most economically important tree species in Europe, and is considered highly vulnerable to changes in climate. Dedicated experiments to investigate how disturbances will affect the Norway spruce - Heterobasidion sp. pathosystem are important, in order to develop different strategies to limit the spread of H. annosum s.l. under the predicted climate change. Here, we report a transcriptional study to compare Norway spruce gene expressions to evaluate the effects of water availability and the infection of Heterobasidion parviporum. We performed inoculation studies of three-year-old saplings in a greenhouse (purchased from a nursery). Norway spruce saplings were treated in either high (+) or low (-) water groups: high water group received double the water amount than the low water group. RNA was extracted and sequenced. Similarly, we quantified gene expression levels of candidate genes in biotic stress and jasmonic acid (JA) signaling pathways using qRT-PCR, through which we discovered a unique preferential defense response of H. parviporum-infected Norway spruce under drought stress at the molecular level. Disturbances related to water availability, especially low water conditions can have negative effects on the tree host and benefit the infection ability of the pathogens in the host. From our RNA-seq analysis, 114 differentially expressed gene regions were identified between high (+) and low (-) water groups under pathogen attack. None of these gene pathways were identified to be differentially expressed from both non-treated and mock-control treatments between high (+) and low (-) water groups. Finally, only four genes were found to be associated with drought in all treatments.

Preprint ARTICLE | doi:10.20944/preprints202010.0379.v1

Evaluation of Reference Genes for qRT-PCR Normalization in Angelica decursiva under Various Experimental Conditions

Yuedong He, Yuan Zhong, Zhenzhen Bao, Weiqi Wang, Xiaoqing Xu, Yanan Gai, Jie Wu

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: qRT-PCR; reference gene; Angelica decursiva; expression stability

Online: 19 October 2020 (12:25:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0663.v1

Molecular Characterization and Phylogenetic Analysis of Orf Virus Isolated From Goats in Sokoto Metropolis, Nigeria

Nafiu Lawal

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ORFV; PCR; Sanger method; B2L gene; Phylogenetic analysis

Online: 27 September 2020 (04:58:03 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202007.0279.v1

COVID19 PCR Testing and the Unprecedented Institutional Response in a Low-Resource Setting

Akintunde Orunmuyi, Olukemi Adekanmbi, Adeola Fowotade, Akindele Adebiyi, Adekunle Adeniji, Olukemi Amodu, E. Oluwabunmi Olapade-Olaopa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID19; sub-Sahara Africa; PCR testing; Capacity building

Online: 13 July 2020 (06:32:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201810.0383.v1

Pathologic Complete Response (pCR) and Survival of Women with Inflammatory Breast Cancer (IBC): An Analysis Based on Biologic Subtypes and Demographic Characteristics

Tithi Biswas, Charulata Jindal, Timothy Fitzgerald, Jimmy Efird

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Biologic subtypes; diagnosis; inflammatory breast cancer; pCR; survival

Online: 17 October 2018 (11:08:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.0363.v1

Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection

Nazar A. Shapoval, Alexander V. Kir’yanov, Anatoly V. Krupitsky, Roman V. Yakovlev, Anna E. Romanovich, Jing Zhang, Qian Cong, Nick V. Grishin, Margarita G. Kovalenko, Galina N. Shapoval

Subject: Biology And Life Sciences, Insect Science Keywords: Colias; DNA barcoding; Lepidoptera; molecular taxonomy; PCR screening; Wolbachia

Online: 6 November 2023 (14:54:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1937.v1

Effects of Clothianidin Pesticide Application on the Honey Bees Colony Strength and Stress-Related Genes in the Vicinity of Rice Fields

Minwoong Son, Ji Soo Kim, Dongwon Kim, Chang-Hoon Lee, Peter Njukang Akongte, Daegeun Oh, Yong-Soo Choi, Bo-Sun Park

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: neonicotinoids; pollinator; rice field; qRT PCR; toxicity stress-genes

Online: 31 October 2023 (02:46:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1446.v1

Genetic Association of UMOD Gene Variant (16:20353266A>G) and Bioinformatics Analyses of the Uromodulin Protein in CKD Patients of Pakistani Origin

Mehmoona Zahid, Rashid Saif, Amna Younus, Mehnaz Ghulam Hussain, Sadia Jabeen, Hooria Younas

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: UMOD; CKD; Creatinine; Urea; eGFR; Uromodulin; Genotyping; ARMS-PCR

Online: 22 August 2023 (02:34:34 CEST)

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Chronic Kidney Disease (CKD) is one of the worldwide health threats, kidneys may be affected by internal pathologies and environmental factors as well as a number of genes are also involved in the kidney dysfunctioning, so UMOD is one of these genes which has significant effect in regulating urea and creatinine level in blood and decreased excretion of uric acid which causes interstitial damages in kidney and may result CKD. Hence, the present study is envisaged to observe the association of this gene locus (r.1264T>C) with CKD in Pakistani population using ARMS-PCR genotyping, for the purpose, a total of 75 samples were investigated, out of which 45 were found homozygous wild-type, 21 heterozygous and 09 homozygous mutants. PLINK data analysis toolset showed that our sampled population does not obeys Hardy-Weinberg Equilibrium by χ² (2, N = 75) = 18.87, p = and Chi-square statistics with p = 1.40×10^-005showing a significant genotypic association with the subject phenotype with an alternative allele frequency of 0.15 and 0.48 within cases & controls respectively. Furthermore, an odds-ratio of 0.2 predicts that the risk of wild-type allele (A) is 0.8 times higher in patient as compared to controls and mutant allele is 0.2 times preventive in patients. Additionally, a few bioinformatics tools e.g., ProtParam, PsiPred, TMHMM-2.0, Motif Scan, ScanProsite, NetPhos3.1, GPS PAIL2.0, NetOGlyc4.0, PRmePRed, PDB-RCSB and STRING were applied to predict different characteristics of Uromodulin protein including physicochemical properties, secondary/transmembrane structures, protein conserved domains and posttranslational modifications respectively. This pilot scale study provided a comprehensive insight of the association of aforementioned genetic variant with CKD to identify and evaluate the genetic risk factors along with functional effects of the subject variant which may be used as CKD prevention by adopting DNA screening and genetic counselling recommendations.

Preprint ARTICLE | doi:10.20944/preprints202307.1387.v1

ToBRFV Mexican Strain: Seed Transmission Rate, Efficacy of Seed Disinfection Treatment, and Rapid Sensitive Detection in Seed Lots

Erika Janet Zamora-Macorra, Daniel Lobardo Ochoa-Martínez, Claudia Yaritza Chavarín-Camacho, Rosemarie W Hammond, Katia Aviña-Padilla

Subject: Biology And Life Sciences, Virology Keywords: seed transmission; tobamovirus; diagnostic method; natural hosts; RT-PCR

Online: 20 July 2023 (07:26:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0319.v1

Study on the Prevalence of Pneumocystis jirovecii as a Causative Agent of Lung Pathology in People with Different Immune Status

Rumen Harizanov, Nina Tsvetkova, Aleksandra Ivanova, Raina Enikova, Mihaela Videnova, Iskra Rainova, Eleonora Kaneva, Iskren Kaftandjiev, Dimitar Strashimirov, Nina Yancheva-Petrova, Ivan Simeonovski, Viktoria Levterova, Nikolai Yanev

Subject: Public Health And Healthcare, Primary Health Care Keywords: Pneumocystis pneumonia; immune status; real-time PCR; staining methods

Online: 5 June 2023 (12:55:05 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202211.0436.v1

Multiplex PCR Detects Respiratory Viruses at A Much Higher Rate in Kawasaki Disease

Masayuki Nagasawa, Teruyoshi Shimoyama, Sayuri Hashimoto, Ryuichi Nakagawa, Haruna Yokoyama, Mari Okada, Tomohiro Udagawa, Akihiro Oshiba

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Kawasaki disease; febrile convulsions; respiratory virus; filmarray; multiplex PCR

Online: 23 November 2022 (07:02:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0449.v1

Dysregulated Expression of Ion Channels in Sensory Neurons Enhances Action Potential Afterhyperpolarization in Patients with Chronic Kidney Disease–Associated Pruritus

Akishi Momose, Michihiro Yabe, Shigetoshi Chiba, Kenjirou Kumakawa, Yasuo Shiraiwa, Hiroki Mizukami

Subject: Medicine And Pharmacology, Dermatology Keywords: CKD-aP; ion channels; action potential; hyperpolarization; RT-PCR

Online: 29 July 2022 (04:50:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0122.v1

Alternative Approaches for Uncovering Phytoplasma Biodiversity and Vector Associations

Valeria Trivellone, Yanghui Cao, Christopher H. Dietrich

Subject: Biology And Life Sciences, Plant Sciences Keywords: anchored hybrid enrichment; biodiversity, biorepository; nested PCR; Sanger sequencing

Online: 8 June 2022 (09:57:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0208.v1

Probiotic Lactobacilli in Fermented Dairy Products: Selective Detection, Enumeration and Identification Scheme

Nasim Farahmand, Labia Irene Ouoba, Shahram Naghizadeh Raeesi, Jane P Sutherland, Hamid B. Ghoddusi

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Probiotic; Lactobacilli; Fermented dairy product; Identification; enumeration; Rep-PCR

Online: 10 May 2021 (15:11:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0450.v2

False-negative Molecular Diagnosis of SARS-CoV-2 in Samples with Amplification Inhibitors

Marcelo Fruehwirth, Açucena Veleh Rivas, Andressa Faria Rahyn Fitz, Aline Cristiane Cechinel Assing Batista, Cleypson Vinicius Silveira, Robson Michael Delai

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; rRT-PCR; dilution; viral diagnosis; RNA extraction

Online: 16 October 2020 (11:48:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0749.v1

Fatal Interstitial Pneumonia Caused by Bovine Coronavirus in Cows from Southern Italy

Maria Grazia Amoroso, Giuseppe Lucifora, Barbara Degli Uberti, Francesco Serra, Alessandro Di Domenico, Maria Concetta Cuomo, Giovanna De Luca, Francesca Bove, Giorgio Galiero, Giovanna Fusco

Subject: Biology And Life Sciences, Virology Keywords: Bovine coronavirus; intersititial pneumonia; phylogenetic analysis; Real time PCR

Online: 31 July 2020 (13:46:21 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0316.v1

Diagnostics and Monitoring of COVID-19 Infection – Current Understanding

Martina Bergant, Ario de Marco

Subject: Biology And Life Sciences, Virology Keywords: RT-PCR; seroconversion; serum biomarkers; SARS-CoV2; neutralizing antibodies

Online: 20 May 2020 (04:10:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0038.v1

Isolation of Naegleria spp. from a Brazilian Water Source

Natália Karla Bellini, Ana Letícia Moreira da Fonseca, María Reyes-Batlle, Jacob Lorenzo-Morales, Odete Rocha, Otavio Henrique Thiemann

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Naegleria spp.; free-living amoeba; PCR; Monjolinho River; Brazil

Online: 4 December 2019 (04:27:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints201909.0148.v1

Identification of Candida Species from Clinical Samples in a Honduran Tertiary Hospital

Kathy Montes, Bryan Ortiz, Celeste Galindo, Isis Figueroa, Sharleen Braham, Gustavo Fontecha

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Candida spp.; PCR-RFLP; Honduras; HardyCHROM®; MicroScan®

Online: 15 September 2019 (03:30:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0108.v1

Fusarium species and Fusarium mycotoxins in grain of wheat in Poland in 2009 and 2010

Tomasz Góral, Piotr Ochodzki, Linda Kærgaard Nielsen, Dorota Walentyn-Góral

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: biomass, Fusarium head blight, real-time PCR, trichothecenes, zearalenone

Online: 10 September 2019 (11:24:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0037.v1

Characterization and Antimicrobial Efficacy of Bovine Dermcidin, a Novel Antimicrobial Peptide Gene

Nevien Sabry, Tarek Moussa

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bos taurus; skin; bovine dermcidin; RT-PCR; antimicrobial activity

Online: 6 May 2019 (08:35:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0285.v1

Detection of Transgenes in Gene Delivery Model Mice by Adenoviral Vector Using ddPCR

Takehito Sugasawa, Kai Aoki, Koichi Watanabe, Koki Yanazawa, Tohru Natsume, Tohru Takemasa, Kaori Yamaguchi, Yoshinori Takeuchi, Yasuko Yoshida, Katsuyuki Tokinoya, Nanami Sekine, Kaoru Takeuchi, Haruna Ueda, Yasushi Kawakami, Satoshi Shimizu, Kazuhiro Takekoshi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: gene doping; gene therapy; droplet digital PCR; adenoviral vector

Online: 25 April 2019 (12:45:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0189.v1

Optimisation of DNA Extraction from Individual Sand Flies for PCR Amplification

Lorena G. Caligiuri, Adolfo E. Sandoval, Jose C. Miranda, Felipe A. Pessoa, María S. Santini, Oscar D. Salomón, Nagila F. C. Secundino, Christina McCarthy

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Sand fly; DNA extraction; Calcium; PCR, lysis buffer, Lutzomyia

Online: 17 December 2018 (10:41:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0395.v1

Rapid Diagnosis of Capnocytophaga canimorsus Septic Shock in an Immunocompetent Individual Using Real-Time Nanopore Sequencing

Seweryn Bialasiewicz, Tania P.S. Duarte, Son H. Nguyen, Vichitra Sukumaran, Alexandra Stewart, Sally Appleton, Miranda E. Pitt, Arnold Bainomugisa, Amy V. Jennison, Rikki Graham, Lachlan J.M. Coin, Krispin Hajkowicz

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: nanopore sequencing; droplet digital PCR; Capnocytophaga canimorsus; diagnosis; sepsis

Online: 16 November 2018 (09:45:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201805.0144.v1

ISSR-Markers Assisted Genetic Diversity Assessment of Acid Lime [Citrus aurantifolia (Christm.) Swingle] Germplasm of Eastern Nepal

Nabin Narayan Munankarmi, Neesha Rana, Tribikram Bhattarai, Ram Lal Shrestha, Bal Krishna Joshi, Bikash Baral, Sangita Shrestha

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: citrus breeding; diversity; genetic similarity; Lime; molecular markers; PCR

Online: 9 May 2018 (11:05:37 CEST)

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Acid lime [Citrus aurantifolia (Christm.) Swingle] is a fruit crop, enriched with high commercial value and is cultivated in 60 out of 75 districts representing all geographical landscapes of Nepal. Lack of high yielding cultivars is probably one of the main reason for its extremely reduced productivity which warrants a deep understanding of genetic diversity in existing germplasm. Hereby, we aim to access the genetic diversity of acid lime germplasm cultivated at 3-different ecological gradients of eastern Nepal employing PCR-based Inter-Simple Sequence Repeats markers (ISSR). Altogether, 21 polymorphic ISSR markers were used to assess the genetic diversity in 60 acid lime cultivars sampled from different geographical locations. Analysis of binary data matrix was performed on the basis of bands obtained, scoring of the data was done accordingly, and principal coordinate analysis and phenogram were constructed using different computer algorithms. ISSR profiling yielded 234 amplicons, of which 87.18% were found to be polymorphic. The number of amplified fragments ranged from 7-18 with amplicon size ranging from 250-3200 bp. The NTSYS based Cluster analysis using UPGMA algorithm taking Dice Similarity coefficient separated 60 accessions into 2-major and 3-minor clusters. The genetic diversity analysis revealed the highest for Terai and the lowest for High-hill zone. Cluster I comprised of accessions from High-hill and Mid-hill regions revealing the close genetic relationship, whereas cluster II comprised of accessions from all three agro-ecological zones and the exotic varieties. Furthermore, our results revealed the accessions harvested from different geographical gradients were not genetically distinct, but highest diversity was observed in Terai accessions in comparison to the regions belonging to the High and Mid-hills. Thus, our data indicate that the ISSR provides a better option for evaluating the genetic diversity of Nepalese Acid Lime cultivars and furnished significant information, assisting parental selection in current and future breeding programs and germplasm conservation which ultimately may help to provide a technological breakthrough for the farmers of the developing country like Nepal.

Preprint ARTICLE | doi:10.20944/preprints202308.1264.v1

Investigating the Significance of Non-Jejuni/Coli Campylobacter Strains in Patients with Diarrhea

Nermin Teksoy, Mehmet Ilktac, Betigul Ongen

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Campylobacter spp.; C. concisus; gastroenteritis; multiplex PCR; non-jejuni/coli

Online: 17 August 2023 (08:02:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1718.v1

Persistent Infections of Ostreid Herpesvirus 1 in Adult Pacific Oysters, Crassostrea gigas

Konstantin Divilov, Xisheng Wang, Gary B Fleener, Blaine Schoolfield, Christopher Langdon, Ling Jin

Subject: Biology And Life Sciences, Virology Keywords: Pacific oysters; OsHV-1; latent; persistent; qPCR; nested PCR; hemocytes

Online: 25 June 2023 (05:24:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0008.v1

Comparative Analysis of Plant Morphological Features and Molecular Genetic Data for Polymorphism Study in Genus Tulipa L. and Determining the Tulip Species

Maria V. Semenova, Ludmila S. Olekhnovich, Olga L. Enina

Subject: Biology And Life Sciences, Horticulture Keywords: Tulipa; tulip; species; identification; DNA; PCR; ISSR analysis; morphological features

Online: 1 June 2023 (03:06:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.1164.v1

Feasibility, Uptake, and Results of COVID-19 Antigen Rapid Diagnostic Tests Among Refugees and Migrants in a Pilot Project in Northwest Syria

Hassan Ghawji, Mohamad Nihad ALYOUSFI, Srinath Satyanarayana, Nevin Wilson, Laila Tomeh, Hussam Alkhellov, Sali Hasan, Sanjay Sarin, Kekeletso Kao

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID-19; rapid diagnostic tests; refugees; prevention; Ag-RDTs; PCR

Online: 28 April 2023 (10:33:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0196.v1

SARS-CoV-2 PCR Persistence and Duration of COVID-19 Symptoms in Health Professionals

Tatiana Schäffer Gregianini, Ludmila Fiorenzano Baethgen, Richard Steiner Salvato, Ivone Andreatta Menegolla, CEVS COVID-19 Team, Ana Beatriz Gorini da Veiga

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; PCR persistent positive; respiratory infection; COVID-19

Online: 12 December 2022 (09:04:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202208.0509.v1

Using FTA Cards as a Rapid and Field Tool for Detection and Serotyping of Foot-and-mouth Disease Virus in Libya

Fadila Abosrer, Elfurgani Kraim, Emiliana Brocchi, Giulia Pezzoni, Santina Grazioli, Abdunaser Dayhum, Ibrahim Eldaghayes

Subject: Biology And Life Sciences, Virology Keywords: FTA cards; foot-and-mouth disease; RT-PCR; field; sequence

Online: 30 August 2022 (05:45:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0466.v1

Analysis of the virulence and inflammatory markers elicited by Enteroaggregative Escherichia coli isolated from clinical and non-clinical sources in an experimental infection model, India

Vinay Modgil, ChanderDeo Narayan, Harpreet Kaur, Vivek kumar Yadav, Naveen Chaudhary, Vishal Kant, Balwinder Mohan, Alka Bhatia, Neelam Taneja

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Keywords: Enteroaggregative Escherichia coli, virulence, inflammatory markers, Phylogeny, Multiplex PCR.

Online: 29 August 2022 (04:49:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0442.v1

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples

Karen Marcela Jiménez, Dora Janeth Fonseca-Mendoza, Adrien Morel, Oscar Ortega-Recalde, Nora Contreras, Camilo Andres Velandia-Piedrahita, Adriana Steevens, Luisa Caldas, Juan Pablo Ribón, Martha Sanchez, Carlos Martín Restrepo, Rodrigo Cabrera

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; molecular diagnostic; SARS-CoV-2; Real-time PCR

Online: 29 July 2022 (03:10:47 CEST)

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Working Paper ARTICLE

Detection of Peanut Allergen by Real Time PCR: Looking For the Suitable Detection Marker as Affected by Processing

Africa Sanchiz, Paulina Sánchez-Enciso, Carmen Cuadrado, Rosario Linacero

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Real-time PCR; peanut; food allergen; chloroplast marker; DNA isolation

Online: 16 June 2021 (11:33:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0285.v1

Quantitative Fluorescent Polymerase Chain Reaction for Prenatal Diagnosis and Its Application in Vietnam: A Literature Review

Thuan Phan

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: QF-PCR; cytogenetics; prenatal diagnosis; aneuploidy; chromosome abnormalities; screening test

Online: 10 June 2021 (09:17:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0299.v1

Optimizing Droplet Digital PCR for Environmental Samples

Vasilis Kokkoris, Eric Vukicevich, Andrew Richards, Corrina Thomsen, Miranda Hart

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ddPCR, droplet digital PCR, environmental samples, environmental DNA, soil microbiology

Online: 12 April 2021 (12:48:11 CEST)

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Working Paper BRIEF REPORT

Are we on the Right Way after 200 Days of COVID-19 in Morocco?

Issam Bennis, Amina Nasri Sahraoui, Moulay Mustapha Alaoui

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; RT-PCR; control strategy; Morocco

Online: 5 November 2020 (10:40:41 CET)

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Historically, 2020 will be remembered as the year of COVID-19 pandemic, that limited people move and their social habits. This virus, becomes the first daily tracked public health burden that leads to more than 1,2 million deaths in the World by the end of October 2020, and until now no countries' best control strategies are cited as the example of long term success.Since March 2^nd, 2020, date of the first SARS-COV-2 detected case in Morocco; many decisions were adopted as COVID-19 control strategies. If the first period of COVID-19 noticed a few numbers of cases and deaths, the second half from July is marked with an exponential increase of the number of cases and a spread in almost all provinces with more intensive care needs and more deaths. The policy analysis approach was followed as a method to define the pitfalls themes and to compare with the updated available international information any significant similarities or divergences. Thus, this report has the aim to present an overview of how the COVID-19 pandemic was dealt in Morocco during these 200 days, by highlighting some discrepancies with corrective advice provided in the first version of the manuscript to be confronted by a Moroccan health policymaker’s community, then to notice the decisions adopted during another one month by the MoH to get better future control results against COVID-19.Unfortunately, despite the MoH decision to increase the diagnostic facilities for molecular tests, the overall number of laboratory tests do not go further than 21000 tests per day. The actual insidious transmission is a dangerous blind threat that dissipates the collaborating efforts, due to this limited number of confirmation and follows up tests.Accurate, standardised and up to ten times per day tests of molecular biology represented by RT-qPCR, to interpret results following the time progress of cycle quantification values is the primary action to be done to enhance the overall control strategy.

Preprint ARTICLE | doi:10.20944/preprints202007.0265.v1

Identification and Differences in Antimicrobial Susceptibility of Lactococcus garvieae from Farmed Grey Mullet ( Mugil cephalus ) and Non-Grey Mullet in Southern Taiwan

Jian-Lin Lee, Shu-Yung Chiu, Che-Chun Chen, Chishih Chu, Jiann-Hsiung Wang

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lactococcus garvieae; Grey Mullet (Mugil cephalus); Multiplex PCR; Antibiotic Susceptibility

Online: 12 July 2020 (15:41:52 CEST)

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Working Paper BRIEF REPORT

Positive Rate Is Useful to Evaluate the Sufficiency of RT-PCR Test Availability for COVID-19

Sadao Suzuki

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; RT-PCR test; pre-test probability; positive rate

Online: 5 May 2020 (06:04:41 CEST)

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Working Paper BRIEF REPORT

Natural Latent Toxoplasmosis in Wild and Captivity-born Olive Baboons (Papio Anubis) in Kenya

David Kamau, John Kagira, Muturi Karanja, Maina Ngotho, Maina Naomi, John Mokua

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Toxoplasmosis; Toxoplasma gondii; nested PCR; non-human primates; Olive baboons

Online: 26 November 2019 (11:47:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202205.0403.v1

Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta africana) and Rhinoceros (Ceratotherium simum, Diceros bicornis) in South Africa

Wynand J. Goosen, Charlene C. Clarke, Léanie Kleynhans, Tanya J. Kerr, Peter Buss, Michele A. Miller

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: African elephants; broncholoalveolar lavage; Hain CMdirect V1.0; ku PCR; Mycobacterium tuberculosis complex; non-tuberculous mycobacteria; rhinoceros; rpoB PCR; trunk wash; Xpert MTB/RIF Ultra

Online: 30 May 2022 (16:33:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0132.v1

Detection of Toxoplasma gondii in Sylvatic Rodents in Poland Using Molecular and Serological Methods

Joanna Nowicka, Daniela Antolová, Anna Lass, Beata Biernat, Karolina Baranowicz, Aleksander Goll, Martyna Krupińska, Bartłomiej Ferra, Aneta Strachecka, Jerzy M. Behnke, Anna Bajer, Maciej Grzybek

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Toxoplasma gondii; rodents; rodent-borne diseases; environment contamination; biomonitoring; wildlife; molecular detection; PCR assay; nested-PCR assay prevalence; serological detection; agglutination test; ELISA method; seroprevalence

Online: 7 March 2023 (09:38:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0183.v1

Genetic Structure of Daphnia cucullata SARS, 1862 Native Population in Boreal Lakes

Aija Brakovska, Nataļja Škute

Subject: Biology And Life Sciences, Life Sciences Keywords: Cladocera; Daphnia cucullata; genetic diversity; microsatellite-PCR; Boreal biogeographical region lakes

Online: 4 October 2023 (13:07:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0989.v1

Lightweight Network DCR-YOLO for Surface Defect Detection on Printed Circuit Boards

Yuanyuan Jiang, MengNan Cai, Dong Zhang

Subject: Computer Science And Mathematics, Computer Vision And Graphics Keywords: DCR-YOLO; Defect detection; Printed circuit board; SDDT-FPN; PCR; C5ECA

Online: 14 July 2023 (11:07:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.2110.v1

Research on the Device of Micro Droplet PCR in Microfluidic Chip Based on Constant Pressure Regulation

Luyang Duanmu, Yuanhua Yu, Xiangkai Meng

Subject: Engineering, Control And Systems Engineering Keywords: Constant Pressure Regulation; Micro droplet Digital PCR; Fluorescence Detection; Quantitative Detection

Online: 30 May 2023 (10:31:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0337.v1

Screening and Validation of Internal Reference Genes for Quan-Titative Real-Time PCR Analysis of Leaf Color Mutants in Den-Drobium Officinale

Hua Cao, Han Li, Lin Lu, Yulu Ji, Lulin Ma, Shenchong Li

Subject: Biology And Life Sciences, Plant Sciences Keywords: Dendrobium officinale; leaf color; qRT-PCR; reference gene; leaf color mutant

Online: 5 May 2023 (09:34:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0077.v1

Chikungunya (Togaviridae) and Dengue 2 (Flaviviridae) Viruses Isolated from Aedes aegypti Mosquitoes by qRT-PCR Technique: Xenosurveillance for Arboviruses Circulating in Burkina Faso

Aristide Sawdetuo Hien, Ibrahim Sangaré, Eric L. Parfait Ouattara, Simon P. Sawadogo, Diloma D. Soma, Maiga Hamidou, Abdoulaye Diabaté, Emmanuel Bonnet, Valéry Ridde, Florence Fournet, Carina Kaupra, Jérémy Bouyer, Adly M.M. Abd-Alla, Frances M. Hawkes, Roch K. Dabiré

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: arboviruses; Dengue; Chikungunya; molecular biology; qRT-PCR; Aedes aegypti; Burkina Faso

Online: 3 August 2021 (12:48:01 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202105.0342.v1

RNA Extraction Alternative Method for SARS-CoV-2 Molecular Diagnosis

Elisa Bianchini, Francesco Rossignolo, Melissa Perfranceschi, Chiara Cazzin, Ronaldo Silva, Fabio Formenti, Francesca Perandin, Cristiana Griffante, Rosaria Remelli, Michela Padovani, Salvatore Scarso, Martina Leonardi, Chiara Piubelli

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: COVID-19; SARS-CoV-2; nasopharyngeal swab; RNA extraction; RT-PCR

Online: 14 May 2021 (14:46:42 CEST)

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Working Paper ARTICLE

Overexpression of GmRIQ2-like (Glyma.04G174400) Enhances the Tolerance of Strong Light Stress and Reduces Photoinhibition in (Glycine max L. Merr.)

Jing Deng, Huayi Yin, Li Ma, Jiukun Zhang, Dongmei Li, Bibin Zhang

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: soybean (Glycine max L.); NPQ; photoinhibition; bioinformatics; subcellular localization; qRT-PCR

Online: 10 February 2020 (09:47:05 CET)

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Preprint ARTICLE | doi:10.20944/preprints201901.0212.v1

One-tube RT-PCR for the Simultaneous Detection and Typing Duck Hepatitis A Virus Subtypes 1 and 3

Xueming Chen, Yuhuan Chen, Chunguo Liu, Xiaojun Li, Hongyu Liu, Xiaofei Bai, Ming Liu, Yun Zhang

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: DHAV-1; DHAV-3; Phylogenetic analysis; One-tube RT-PCR; Simultaneously

Online: 22 January 2019 (11:08:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints201805.0169.v1

The Presence of Toxic and Non-toxic Cyanobacteria in the Sediments of the Limpopo River Basin: Implications for Human Health

Murendeni Magonono, Paul Johan Oberholster, Shonhai Addmore, Makumire Stanley, Jabulani Ray Gumbo

Subject: Environmental And Earth Sciences, Environmental Science Keywords: cyanobacteria; cyanotoxins; nutrient enrichment; akinetes; harmful algal blooms; PCR; phylogenetic analyses

Online: 10 May 2018 (15:37:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0173.v1

Molecular and Biochemical Characterization of Calmodulin from Echinococcus granulosus

Ning Wang, Xiu-Qin Zhong, Xing-Ju Song, Xiao-Bin Gu, Wei-Ming Lai, Yue Xie, Xue-Rong Peng, Guang-You Yang

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Echinococcus granulosus; Calmodulin; Ca2+-binding protein; Immunohistochemical localization; Quantitative RT-PCR

Online: 24 May 2017 (08:07:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201703.0162.v1

Evaluation of the Effects of Airborne Particulate Matter on Bone Marrow-Mesenchymal Stem Cells (BM-MSCs): Cellular, Molecular and Systems Biological Approaches

Muhammad Abu-Elmagd, Mansour A Alghamdi, Magdy Shamy, Mamdouh I Khoder, Max Costa, Mourad Assidi, Roaa Kadam, Haneen Alsehli, Mamdooh Gari, Peter Natesan Pushparaj, Gauthaman Kalamegam, Mohammed Al-Qahtani

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Particulate matter; BM-MSCs; cell proliferation; cell death; qRT-PCR; IPA

Online: 20 March 2017 (16:33:56 CET)

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Preprint OPINION | doi:10.20944/preprints201608.0016.v1

Dark Side of Molecular Techniques: How to Fix It ?

Vikash Bhardwaj

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: parallel DNA; antiparallel DNA; PCR; CRISPR; nucleic acid hybridization; microarray; siRNA

Online: 2 August 2016 (10:42:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1505.v1

Diagnostic Accuracy of Multiplex PCR in Early Onset Neonatal Sepsis

Anja Stein, Daniel Soukup, Peter-Michael Rath, Ursula Felderhoff-Müser

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: neonatal sepsis; early onset sepsis; multiplex PCR; infection; neonate; diagnosis; pathogen detection

Online: 24 October 2023 (08:11:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1620.v1

Identification of Reference Genes for Precise Expression Analysis during Germination in Chenopodium quinoa Seeds under Salt Stress

ESTEFANIA CONTRERAS, Lucía Martín-Fernández, Arafet Manaa, Jesús Vicente-Carbajosa, RAQUEL IGLESIAS-FERNANDEZ

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Chenopodium quinoa; Germination sensu stricto; Reference gene; quantitative PCR; Salt stress; Seed

Online: 26 September 2023 (02:51:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.2272.v1

The Hypocholesterolemic Potential of the Edible Algae Fucus Vesiculosus: Proteomic and Quantitative PCR Analysis

Rebeca André, Rita Pacheco, Ana Catarina Alves, Hugo M. Santos, Mafalda Bourbon, Maria-Luísa Serralheiro

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Fucus vesiculosus; cholesterol synthesis; cholesterol excretion; , Ezetimibe; , NPC1L1; ABCG5; qRT-PCR; mRNA

Online: 31 May 2023 (14:54:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1348.v1

Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness

Pallavi Upadhyay, Jairus Reddy, Teddie Proctor, Oceane Sorel, Harita Veereshlingam, Manoj Gandhi, Vijay Singh

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Respiratory tract infections; COVID-19; influenza-like illness; multiplex PCR; syndromic panels

Online: 18 May 2023 (14:10:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0501.v1

Risk Factors of Breast Cancer Recurrence in Pathologic Complete Response Achieved by Patients Following Neoadjuvant Chemotherapy

Joon Young Choi, Doyoun Woen, Sung Yoon Jang, Hyunjun Lee, Dong Seung Shin, Youngji Kwak, Byung Joo Chae, Jonghan Yu, Jeong Eon Lee, Seok Won Kim, Seok Jin Nam, Jai Min Ryu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Breast Neoplasm; Neoadjuvant Chemotherapy (NAC); pathologic Complete Response (pCR); Risk Factor; recurrence

Online: 29 March 2023 (03:52:14 CEST)

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Background: Pathologic complete response (pCR) of breast cancer after neoadjuvant chemotherapy (NAC) is highly related to molecular subtypes. Patients who achieved tumor pCR after NAC have a better prognosis. However, despite of better prognosis, pCR patients have a potential for recurrence. There is little evidence of risk factors of recurrence in patients with pCR. We aim to analyze factors associated with tumor recurrence in patients who achieved pCR. Methods: This study retrospectively reviewed the data of patients diagnosed with breast cancer who achieved pCR after receiving NAC between January 2009 and December 2018 in Samsung Medical Center. pCR was defined as no residual invasive cancer in the breast and axillary nodes even if there is residual ductal carcinoma in situ (ypT0 or ypTis with ypN0). Breast cancers are classified into 4 subtypes based on hormone receptors (HR) and human epithelial growth factor receptor 2 (HER2) status. Patients who had bilateral breast cancer, inflammatory breast cancer, distant metastasis, unknown subtype, and histologically unique case were excluded from the study. Results: In total 483 patients were included in this study except for patients who corresponded to the exclusion criteria. The median follow-up duration was 59.0 months (range, 0.5-153.3 months). Breast cancer recurred in 4.1% of patients (20 of 483). There was a significant difference in clinical T (p = .004) and clinical N (p = .034) stage in the Kaplan-Meier curve for disease-free survival. Molecular subtypes (p = .573), Ki67 (p = 1.000), and breast surgery type (p = .574) were not associated with tumor recurrence in patients who achieved pCR after NAC. In the clinical T stage and clinical N stage, there was a significant difference between recurrence and no-recurrence groups (clinical T stage; p = .045, clinical N stage; p = .002). Univariable Cox regression revealed statistical significance in the clinical T stage (p = .049) and clinical N stage (p = .010), while multivariable Cox regression demonstrated non-significance in the clinical T stage (p = .320) and clinical N stage (p = .073). Conclusion: Results in this study showed that clinical T, clinical N stage, and molecular subtypes were not statistically significant predictors of recurrence in patients who achieved pCR after NAC. It is hypothesized that a multicenter-based study would lead to the identification of factors as predictors of recurrence after achieving pCR.

Preprint ARTICLE | doi:10.20944/preprints202303.0219.v1

SARS-CoV-2 Positivity and Viral Load during Three Viral Waves in Mumbai, India

Chaitali Nikam, Wilson Suraweera, Sze Hang Fu, Patrick E Brown, Nico Nagelkerke, Prabhat Jha

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2 pandemic; PCR positivity; Aleph Delta Omicron waves; Mumbai; India

Online: 13 March 2023 (06:31:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0279.v1

Quantification of DNA of Fusarium culmorum and Trichothecene Genotypes 3ADON and NIV in the Grain of Winter Wheat

Tomasz Góral, Jarosław Przetakiewicz, Piotr Ochodzki, Barbara Wiewióra, Halina Wiśniewska

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chemotype; 3ADON; DNA; Fusarium; Fusarium head blight; NIV; real-time PCR; wheat

Online: 15 November 2022 (07:09:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202204.0090.v1

IL-1R8 Downregulation and Concomitant TLR7 and TLR9 Up-Regulation Are Related to the Pathogenesis of Canine Diffuse Large B-Cell Lymphoma

Federica Riva, Joel Filipe, Antonella Fanelli, Laura Marconato, Alessia Inglesi, Eugenio Scanziani, Sabina Soldati, Luca Licenziato, Stefano Comazzi, Lucia Minoli, Luca Aresu

Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: dog; diffuse large B-cell lymphoma; IL-1R8; TLR7; TLR9; qRT-PCR

Online: 11 April 2022 (09:15:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0548.v1

Transfer Learning for the Detection and Diagnosis of Types of Pneumonia Including Pneumonia Induced by the COVID-19 from Chest X-Ray Images

Yusuf Brima, Marcellin Atemkeng, Stive Tankio Djiokap, Jaures Ebiele, Franklin Tchakounté

Subject: Engineering, Automotive Engineering Keywords: ANN; COVID-19; CT; mRNA; MRI; RT-PCR; SARS-CoV-2; XCR

Online: 23 July 2021 (15:02:40 CEST)

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Working Paper ARTICLE

Silica Nanoparticle Effect on Population Parameters and Gene Expression of an Internal Feeder, American Serpentine Leafminer

Ahmad F. Thabet, Ola A. Galal, Midori Tuda, Magdy F.M. El–Samahy, Ryusuke Fujita, Masato Hino

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Silica nanoparticles; Liriomyza trifolii; Phaseolus vulgaris; qRT-PCR; Oxidative stress; Dose dependency

Online: 7 December 2020 (11:26:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0740.v1

Speeding Up COVID-19 Detection Using Shaker-Mill Homogenization and a Direct-to-PCR Workflow

Zachary P Morehouse, Caleb M Proctor, Gabriella L Ryan, Rodney J Nash

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; Virus Detection; Viral Diagnostics; Diagnostics; SARS-CoV-2; Coronavirus; PCR

Online: 31 July 2020 (09:31:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0374.v2

Global Comparison of Changes in the Number of Test-Positive Cases and Deaths by Coronavirus Infection (COVID-19) in the World

Akihiro Hisaka, Hideki Yoshioka, Hiroto Hatakeyama, Hiromi Sato, Yoshihiro Onouchi, Naohiko Anzai

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; coronavirus; infectious disease; infection management; PCR test; mortality; kinetic analysis

Online: 3 June 2020 (05:10:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0147.v1

Whole Genome Alignment Based Development of Molecular Marker for Detecting Leptosphaeria maculans and Leptosphaeria biglobosa, the Causal Agent of Blackleg Disease in Brassicas

Mostari Jahan Ferdous, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Jong-In Park, Hee-Jeong Jung, Hoy-Taek Kim, Ill-Sup Nou

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR

Online: 13 October 2019 (16:08:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0142.v1

Chronic Kidney Disease–Associated Pruritus is Caused by Dysregulated Ion Channels in Sensory Neurons

Akishi Momose, Michihiko Yabe, Shigetoshi Chiba, Kenjirou Kumakawa, Yasuo Shiraiwa, Hiroki Mizukami

Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: uremic pruritus; ion channels; cell signaling; Cav3.2 calcium channel; RT-PCR; skin

Online: 14 September 2019 (19:00:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1033.v2

Designing Microfluidic PCR Chip Device Using CFD Software for the Detection of Malaria

Meynard R. Austria, Jon Patrick T. Garcia, Lemmuel L. Tayo, Alvin R. Caparanga, Bonifacio Jr T. Doma

Subject: Engineering, Bioengineering Keywords: polymerase chain reaction (PCR); Computational Fluid Dynamics (CFD); Plasmodium falciparum; microfluidic chip design

Online: 10 August 2023 (10:30:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0816.v1

Overcoming the Challenges of Lyme Disease Diagnosis: The Role of Phage-based Testing

Jinyu Shan, Ying Jia, Tatjana Mijatovic, Louis Teulières, Martha Clokie

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Tick-borne diseases; Lyme disease; Diagnostic methods; PCR; Bacteriophages (phages); Borrelia; Detection limit

Online: 12 June 2023 (10:05:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0234.v1

The Effects of Antiperspirant Aluminum Chlorohydrate on the Development of Antibiotic Resistance in Staphylococcus epidermidis

Ayse Aras, Suna Sibel Rizvanoglu, Elif Seren Tanriverdi, Basar Karaca, Mujde Eryilmaz

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: aluminum chlorohydrate; antibiotic resistance; minimum inhibitory concentration; quantitative reverse transcriptase-PCR; Staphylococcus epidermidis

Online: 13 March 2023 (14:04:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0320.v1

Performance Characteristics of Real-time PCRs for African Swine Fever Virus Genome Detection – comparison of Twelve Kits to an OIE Recommended Method

Jutta Pikalo, Tessa Carrau, Paul Deutschmann, Melina Fischer, Kore Schlottau, Martin Beer, Sandra Blome

Subject: Biology And Life Sciences, Virology Keywords: African swine fever virus; laboratory diagnosis; commercial real-time PCR; performance; sensitivity; specificity

Online: 21 December 2021 (09:24:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0538.v1

Health Screening of the Reef Forming Scleractinian Cold-Water Corals Lophelia pertusa and Madrepora oculata in a Remote Submarine Canyon on the European Continental Margin, NE Atlantic

John Appah, Sharon Lynch, Aaron Lim, Ruth O'Riordan, Luke O'Reilly, Larissa de Oliveira, Andrew James Wheeler

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Lophelia pertusa; Haplosporidia; Vibrio; Rickettsiales-like organisms; Histology; PCR; Pathogen; Cold-water corals

Online: 24 May 2021 (08:20:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0481.v1

Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance

Warish Ahmed, Stuart Simpson, Paul Bertsch, Kyle Bibby, Aaron Bivins, Linda Blackall, Silvia Bofill-Mas, Albert Bosch, Joao Brandao, Phil Choi, Mark Ciesielski, Erica Donner, Nishita D'Souza, Andreas Farnleitner, Daniel Gerrity, Raul Gonzalez, John Griffith, Pradip Gyawali, Charles Haas, Kerry Hamilton, Chanditha Hapuarachchi, Valerie Harwood, Rehnuma Haque, Greg Jackson, Stuart Khan, Wesaal Khan, Masaaki Kitajima, Asja Korajkic, Giuseppina La Rosa, Blythe Layton, Erin Lipp, Sandra McLellan, Brian McMinn, Gertjan Medema, Suzanne Metcalfe, Wim Meijer, Jochen Mueller, Heather Murphy, Colleen Naughton, Rachel Noble, Sudhi Payyappat, Susan Petterson, Tarja Pitkanen, Veronica Rajal, Brandon Reyneke, Fernando Roman, Joan Rose, Marta Rusinol, Michael Sadowsky, Laura Sala-Comorera, Yin Xiang Setoh, Samendra Sherchan, Kwanrawee Sirikanchana, Wendy Smith, Joshua Steele, Rosalie Sabburg, Erin Symonds, Phong Thai, Kevin Thomas, Josh Tynan, Simon Toze, Janelle Thompson, Andy Whiteley, Judith Wong, Daisuke Sano, Stefan Wuertz, Irene Xagoraraki, Qian Zhang, Amity Zimmer-Faust, Orin Shanks

Subject: Environmental And Earth Sciences, Waste Management And Disposal Keywords: COVID-19; SARS-CoV-2; Wastewater; Surveillance; False-positive; False-negative; RT-PCR

Online: 19 April 2021 (13:08:13 CEST)

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Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence and/or prevalence and trends of coronavirus disease-19 (COVID-19). Surveillance of SARS-CoV-2 in wastewater may provide an early-warning signal of COVID-19 infections in a community. The capacity of the world’s environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is rapidly increasing. However, there are no standardized protocols nor harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can lead to false-positive and -negative errors in the surveillance of SARS-CoV-2, culminating in recommendations and strategies that can be implemented to identify and mitigate these errors. Recommendations include, stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, amplification inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly during a low incidence of SARS-CoV-2 in wastewater. Corrective and confirmatory actions must be in place for inconclusive and/or potentially significant results (e.g., initial onset or reemergence of COVID-19 in a community). It will also be prudent to perform inter-laboratory comparisons to ensure results are reliable and interpretable for ongoing and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance was demonstrated during this global crisis. In the future, wastewater will play an important role in the surveillance of a range of other communicable diseases.

Preprint ARTICLE | doi:10.20944/preprints201911.0293.v1

Identification of Cryptic Species of Four Candida Complexes in a Culture Collection

Gustavo Fontecha, Kathy Montes, Bryan Ortiz, Celeste Galindo, Sharleen Braham

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Candida spp; cryptic species; Honduras; PCR-RFLP; hwp1 gene; gpi gene; C. auris

Online: 24 November 2019 (16:05:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1430.v1

Polyphasic Characterization of Brucella spp. in Livestock Slaughtered from Abattoirs in Eastern Cape, South Africa

Koketso Desiree Mazwi, Francis B Kolo, Ishmael Festus Jaja, Charles Byaruhanga, Ayesha Hassim, Henriette Van Heerden

Subject: Public Health And Healthcare, Other Keywords: Brucellosis; Livestock; Tissue samples; culture positive; AMOS-PCR; Brucella abortus; Brucella melitensis; South Africa

Online: 23 November 2023 (17:32:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0621.v1

Occurrence of Picobirnavirus in Domestic and Wild Animals from Three Cities of Brazilian Amazon

Elaine Hellen Nunes Chagas, Julia Rezende Da Silva, Bruno de Cássio Veloso de Barros, José Wandilson Barboza Duarte Júnior, Fabiolla da Silva dos Santos, Edivaldo Costa Sousa Júnior, Delana Andreza Melo Bezerra, Helder Henrique Costa Pinheiro, Ceyla Maria Oeiras de Castro, Yashpal Singh Malik, Joana D’Arc Pereira Mascarenhas

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: enteric virus; picobirnavirus; brazilian animals; page, rt-pcr; rdrp gene; phylogenetic analysis; genogroup I

Online: 9 November 2023 (11:24:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202103.0292.v1

Ke Zhou, Audrey Blanc-Lapierre, Valérie Seegers, Michèle Boisdron-Celle, Frédéric Bigot, Marianne Bourdon, Hakim Mahammedi, Aurélien Lambert, Mario Campone, Martine Bellanger, Jean-Luc Raoul

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: cancer; COVID-19; symptoms; healthcare workers; anosmia; dysgeusia; ageusia; France; serological test; RT-PCR

Online: 10 March 2021 (16:17:48 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0284.v1

Factors Affecting SARS-CoV-2 (COVID-19) Pandemic, including Zoonotic, Human Transmission and Chain of Infection. Reducing Public Health Risk by Serum Antibody Testing, Avoiding Screening in Unhygienic Places and False PCR Reporting. A Scientific Review

Kamran Mahmood Ahmed Aziz, Abdullah Othman, Waleed Alqahtani, Sumaiya Azhar

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; RT-PCR; antibody; zoonotic; animal transmission; genomics; asymptomatic fraction; herd immunity

Online: 23 June 2020 (13:30:11 CEST)

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Since December 2019, a rapid increase in the number of SARS-CoV-2 (COVID-19) cases was reported worldwide, despite strict infection control and lock down measures. Current paper investigated the actual facts behind this rapid increase in the number of cases. Study of genomic sequence reveals that domestic and wild animals were likely ancestors and zoonotic source for SARS-CoVs, MERS-CoVs, and SARS-CoV-2. Strong evidence suggest that these viruses already existed and replicated in animals and humans during past several decades, exhibiting diverse mutations, evolutions and self-limiting diseases, except during outbreaks. Serious zoonotic reservoir investigations are required to investigate animal transmission of SARS-CoVs and SARS-CoV-2 to limit current pandemic. This might be the reason of increasing number of cases via animals. SARS-CoV-2 has been retrospectively isolated in different studies in August 2019, several months before Wuhan announced. Hence, there is a possibility that viruses existed, went undetected, infecting subclinically, in past several years, and SARS-CoV-2 antigens and neutralizing antibodies may have been present in humans since long time. This might be another reason of increasing number of cases by screening as mass screening and antigen or antibody testing was not carried out in the past years. Randomized controlled trials are required to investigate human to human transmission by touch, as the current evidence is limited with conflicting results. As all SARS-CoVs are basically respiratory viruses, droplet precautions and infection control measures are essential, especially for hospital staff. Increased number of SARS-CoV-2 asymptomatic, or subclinical cases are detected worldwide. This silent phase of transmission can be beneficial for humans. Lack of symptoms eventually lessen virus transmission and reduce the pathogen's long-term survival and provide humoral herd immunity up to several years. Hence, seropositivity with diverse antibodies develops against mutating SARS-CoVs which will confer strong immunity during epidemics. Strategies such as identification, contact tracing and quarantine are costly and practically difficult. Hence, asymptomatic persons can continue their work with droplet precautions and standard infection control procedures, while symptomatic or sick persons can isolate themselves in their homes without the need for strict quarantine until clinical recovery, with reduced hospital visits and minimizing chances of hospital acquired infections. RT-PCR has low sensitivity and specificity, carries a high risk of handling live virus antigens, and requires difficult protocols. As viral load also sharply declines after few days of onset of infection, this technique might overlook infection. Furthermore, SARS-CoV-2 infection may be present in blood when oropharyngeal swabs are negative by RT-PCR. Additionally, RT-PCR usually gives false negative and false positive results and must be interpreted cautiously. This might be again a reason of increasing number of cases by false positive RT-PCR reporting. Moreover, antibodies against SARS-CoVs develop robustly in serum even by reduced amount of antigens. In contrast to RT-PCR, ELISA for diagnosing antibodies against SARS-CoV-2 demonstrates 100% specificity and 100% sensitivity, even in clinically asymptomatic individuals. These antibodies can be used for serologic surveys, monitoring and screening. However, screening tests for SARS-COV-2 should be avoided in unhygienic public places by nasopharyngeal swabs, which carry a high risk of further transmission, co-infection or superinfection. Such highly infectious virus must be isolated and tested in highly sterilized laboratory. Further strict international laws and policies are required to stop the possible spread of experimental viruses, biological warfare and bioterrorism.

Preprint ARTICLE | doi:10.20944/preprints202006.0032.v1

Emergence of RBD and D614G Mutations in Spike Protein: An Insight from Indian SARS-CoV-2 Genome Analysis

VINAYAGAM SAMYUKTHA, VENKATESAN NAVEEN KUMAR

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Spike protein; COVID-19; Mutation; hACE2 Receptor; Real-time PCR; Vaccine

Online: 4 June 2020 (08:48:03 CEST)

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Currently, entire world is crumbled due to COVID-19 caused by novel SARS-CoV-2. Globally, over 5 million people are infected by SARS-CoV-2 with 6% fatality rate. The surface spike (S) protein plays a key role in the pathogenesis of SARS-CoV-2 by mediating viral entry through human angiotensin converting enzyme 2 (hACE2) receptors on the host cell and there is a big global race to find viral neutralizing antibodies and vaccine against S protein of SARS-CoV-2. Since SARS-CoV-2 evolved into 10 different clades in a very short span, a study on sipke protein mutation is essential to have effective vaccine coverage globally. Based on the mutation analysis of S protein from 166 Indian SARS-CoV-2 genome, a total of 40 different SNPs comprising of 14 synonymous and 26 non-synonymous mutations were observed, and notably, Indian S protein diverged into two major clusters, D614 and G614, with 11 different types. Majority of Indian strains fall in A2a and O clusters. Alarmingly, we have observed six SNPs at RBD and notably two of them at RBM (S438F and S494P). S494P SNP, similar to Bat–SARS like-CoV, may indicate a low ACE2 binding affinity. Interestingly 38% of Indian strains harbor a characteristic D614G SNP which was found predominantly in A2a cluster, mostly comprising USA and European strains with high disease severity. The association of disease severity with D614G SNP is well-correlated in states with high death rate except Maharashtra. Notably, more than 50% of D614G mutation were observed in Northern part of India and 14% in Southern part but not in Kerala and Tamil Nadu strains. Highly conserved motif, D614 (608-VAVLYQDVNCT-618) in upstream and also few downstream, of S1/S2 furin cleavage site may indicate specific key role in efficient interaction with host proteases in pathogenesis. Further studies are warranted to clarify the impact of SD614G SNP association to disease severity . Interestingly, C2367T (Y789Y) synonymous SNP is observed in 37% of Indian strains and notably similar SNPs with degeneracy bases were observed which is a key indication for the possibility of misdiagnosis by Real-Time PCR and revised strategies are needed for the precise diagnosis. Circulation of high number of signature SNPs [D614G and C2367T (Y789Y)] in certain states may be an early indication of emergence of community transmission in India. Further large genome sequence data from India will aid in deep understanding on the diversity of circulating SASR-Cov-2 and its impact on disease severity, origin of imported cases to India, community spread, effect on diagnosis and vaccine coverage.

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