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Preprint ARTICLE | doi:10.20944/preprints202401.1014.v1

Brinjal Little Leaf Disease Epidemiology in Insect Proof Conditions

Mukesh Darabakula, Sri Tej Mateeti, Francesco Pacini, Assunta Bertaccini, Nicoletta Contaldo

Subject: Biology And Life Sciences, Horticulture Keywords: disease management; eggplant; DNA extraction; RFLP analysis; nested PCR amplification; sequencing, phylogeny

Online: 12 January 2024 (11:40:25 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0316.v1

Temporal Trend of the SARS-CoV-2 Omicron Variant and Res-Piratory Syncytial Virus in the Nasal Cavity and Accuracy of the Newly Developed Antigen-Detecting Rapid Diagnostic Test

Daisuke Tamura, Yuji Morisawa, Takashi Mato, Shin Nunomiya, Masaki Yoshihiro, Yuta Maehara, Shizuka Ito, Yasushi Ochiai, Hirokazu Yamagishi, Toshihiro Tajima, Takanori Yamagata, Hitoshi Osaka

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Omicron; rapid diagnostic test; RT-PCR; RSV; SARS-CoV-2; viral antigens

Online: 6 December 2023 (07:38:00 CET)

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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/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/preprints202404.0301.v1

Evaluation of Safety and Efficacy of Repeated Mesenchymal Stem Cell Transplantation in Patients with ALS by Investigating Patient's Specific MicroRNAs as Novel Biomarkers: A Retrospective Study

Zahraa Alkhazaali, Sajad Sahab-Negah, Amir Reza Boroumand, Najmeh Kaffash Farkhad, Mohammad Ali Khodadoust, Rashin Ganjali, Jalil Tavakol-Afshari

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: bone marrow-derived mesenchymal stem cells; ALS; microRNA; Mir206; Mir338-3p; RT -PCR.

Online: 3 April 2024 (14:25:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202403.1530.v1

Technical Advances in Circulating Cell-Free DNA Detection and Analysis for More Personalized Medicine in Patients’ Care

Monica Sorbini, Tullia Carradori, Gabriele Maria Togliatto, Tiziana Vaisitti, Silvia Deaglio

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cell-free DNA; Next-generation Sequencing; digital PCR; liquid biopsy; non-invasive diagnostics

Online: 26 March 2024 (06:40:21 CET)

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Preprint REVIEW | doi:10.20944/preprints202401.1268.v2

Limits of Detection Analysis of Advanced Technologies for Bacterial Detection in Food Samples: Review & Future Perspective

Xinyi Zhao, Abhijnan Bhat, Christine O’Connor, James Curtin, Baljit Singh, Furong Tian

Subject: Biology And Life Sciences, Food Science And Technology Keywords: limit of detection; bacterial detection; food sample; LFIA; PCR; electrochemical; multiplexing; food safety

Online: 20 February 2024 (06:30:15 CET)

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Foodborne illnesses can be infectious and dangerous and most of them are caused by bacteria. Some types of common food-related bacteria exist widely in nature and pose a serious threat to both humans and animals, and can cause poisoning, diseases, disabilities and even death. Rapid, reliable and cost-effective methods for bacteria detection are of paramount importance in food-safety and environmental monitoring. Polymerase chain reaction (PCR), lateral flow immunochromatographic assay (LFIA) and electrochemical method have been widely used in food-safety and environmental monitoring. In this paper, the recent developments (2013-2023) covering PCR, LFIA and electrochemical method for various bacteria detection (Salmonella, Listeria, Campylobacter, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli)) considering different foods types, analytical performances and the reported limit of detection (LOD) are discussed. It is found that the bacteria type and food sample type contribute significantly to the analytical performance and LOD. Detection by LFIA has higher average LOD (24 CFU/ml) than detection by electrochemical method (12 CFU/ml) and PCR (6 CFU/ml). Salmonella and E. coli in the Pseudomonadota domain usually have low LODs. LODs are usually lower for detection in fish and eggs. LFIA with gold and iron nanoparticles are prominent in the majority of articles of 26 CFU/ml and 12 CFU/ml respectively. Electrochemical method reveals that the average LOD is highest for cyclic voltammetry (CV) of 18 CFU/ml), followed by electrochemical impedance spectroscopy (EIS) of 12 CFU/ml and differential pulse voltammetry (DPV) of 8 CFU/ml. LOD usually decreases when replicate number increases until it remain unchanged. Exponential relations with (R²>0.95) between LOD of Listeria in milk by LFIA and electrochemical method with replicate number have been obtained. Finally, the review discusses the challenges and future perspectives (including the role of nanomaterials/advanced materials) to improve the analytical performance for bacterial detection.

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.

Preprint REVIEW | doi:10.20944/preprints201808.0266.v1

Microfluidic Advancements in Classical Biotechnology – A Review

Ishtiaq Ahmed, Zain Akram, Mohammed Hussen Bule, Hafiz M. N. Iqbal

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: microchannel; micro-array; microstructure; biofilms; polydimethylsiloxane; Micro-PCR; reynolds number; micro electro mechanical systems

Online: 15 August 2018 (05:37:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.2031.v1

Seasonal Variability of Cultivable Nitrate Reducing and Denitrifying Bacteria and Functional Gene Copy Number in a Fresh Water Lake

Jörg Böllmann, Marion Martienssen

Subject: Environmental And Earth Sciences, Ecology Keywords: denitrification; nitrite reductase; MPN; vbnc state; PCR; microscopical cell number; dimictic lake, epilimnion; hypolimnion; sediment

Online: 29 January 2024 (12:31:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0752.v1

Diagnostic Role of Cell-Free miRNAs in Identifying Placenta Accreta Spectrum during the First-Trimester Screening

Angelika V. Timofeeva, Ivan S. Fedorov, Yuliya V. Suhova, Alla M. Tarasova, Larisa S. Ezhova, Tatyana M. Zabelina, Oksana N. Vasilchenko, Tatyana Y. Ivanets, Gennady T. Sukhikh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: miRNA; NGS; real-time PCR; peripheral blood; placenta; myometrium; placenta accreta spectrum; first-trimester screening

Online: 12 December 2023 (05:46:17 CET)

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Abstract: Placenta accreta spectrum (PAS) is a severe complication of pregnancy associated with excessive invasion of cytotrophoblast cells at the sites of the endometrial-myometrial interface and the myometrium itself in cases of adherent (creta) and invasive (increta and percreta) forms, respectively. Despite advancements in ultrasound protocols and found associations of alpha-fetoprotein, PAPP-A, hCG, PLGF, sFlt-1, IL-8, and IL-33 peripheral blood levels with PAS, the condition remains undiagnosed before delivery because of the lacking clear evaluation criteria for each of the three grades of PAS. This leads to a high risk of massive blood loss, maternal hysterectomy, and preterm birth. While using deep sequencing, miRNA signatures of placental tissue, myometrium, and blood plasma from women with PAS in the third trimester of pregnancy, as well as miRNA profile in exosomes from the blood serum of women in the first trimester with physiologically progressing pregnancy, complicated by PAS or preeclampsia, were obtained. Two logistic regression models were constructed, both featuring statistically significant parameters related to the levels of miR-26a-5p, miR-17-5p, and miR-101-3p quantified by real-time PCR in native blood serum. These models demonstrated 100% sensitivity in detecting PAS during the first pregnancy screening. These miRNAs were identified as specific markers for PAS, showing significant differences in their blood serum levels during the first trimester in the PAS group compared to those in physiological pregnancies, early- or late-onset preeclampsia groups. Furthermore, these miRNAs exhibited differential expression in the PAS placenta and/or myometrium in the third trimester and, according to literature data, control angiogenesis. Significant correlations were found between extracellular hsa-miR-101-3p and nuchal translucency thickness, hsa-miR-17-5p and uterine artery pulsatility index, and hsa-miR-26a-5p and hsa-miR-17-5p with PLGF. The developed test system for early non-invasive PAS diagnosis based on the blood serum level of extracellular miR-26a-5p, miR-17-5p, and miR-101-3p can serve as an auxiliary method for 1st trimester screening pregnant women, subject to validation on independent test samples.

Preprint ARTICLE | doi:10.20944/preprints202311.0010.v1

EPD as LCA Quality Input Data. A Critical Analysis

María Seila Otero, Teresa Garnica, Soledad Montilla, Marta Conde, José A. Tenorio

Subject: Engineering, Architecture, Building And Construction Keywords: Environmental Product Declaration; Life Cycle Assessment; Generic databases; Environmental impacts; Uncertainty; Product category rules (PCR)

Online: 1 November 2023 (08:33:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.1532.v1

Molecular and Clinical Epidemiology of SARS-CoV-2 Infection Among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

José R. Mediavilla, Tara Lozy, Annie Lee, Justine Kim, Veronica W. Kan, Elizabeth Titova, Ashish Amin, Michael Zody, André Corvelo, Dayna M. Oschwald, Amy Baldwin, Samantha Fennessey, Jerry M. Zuckerman, Thomas Kirn, Liang Chen, Yanan Zhao, Kar Fai Chow, Tom Maniatis, David S. Perlin, Barry N. Kreiswirth

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; pandemic; variants; RT-PCR; sequencing; surveillance; vaccination; vaccine breakthrough; comorbidity.

Online: 21 July 2023 (13:55:29 CEST)

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New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOC) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5,007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOC, including Alpha (n =714), Delta (n =1,877), and Omicron (n =1,802). Omicron isolates were further sub-typed as BA.1 (n =899), BA.2 (n =853), and BA.4/BA.5 (n =50); the remaining 614 isolates were classified as “Other”. Approximately 31.5% (1,577/5,007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p <0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p <0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p <0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

Preprint ARTICLE | doi:10.20944/preprints202208.0143.v1

Molecular Epidemiology and Virulence of Non-Typhoidal Salmonella in Armenia

Anahit Sedrakyan, Zhanna Ktsoyan, Karine Arakelova, Zaruhi Gevorgyan, Magdalina Zakharyan, Shoghik Hakobyan, Alvard Hovhannisyan, Arsen Arakelyan, Rustam Aminov

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: non-typhoidal Salmonella; ERIC-PCR typing; WGS; virulence-related genes; SPIs; Salmonella virulence plasmids; prophages

Online: 8 August 2022 (10:07:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0040.v1

Augmented Sensitivity of At-Home Rapid SARS-CoV-2 Antigen Test (RAT) Kits with Computer Vision

Kim Miikki, Lars Miikki, Jenny Wiklund, Alp Karakoç

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; rapid antigen test; RT-PCR test; COVID-19; image processing; Raspberry Pi

Online: 2 March 2022 (08:06:49 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0045.v1

Kombucha Tea as a Reservoir of Cellulose Producing Bacteria: Assessing Diversity Among Komagataeibacter Isolates

Salvatore La China, Luciana De Vero, Kavitha Anguluri, Marcello Brugnoli, Dhouha Mamlouk, Maria Gullo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Kombucha tea; microbial diversity; bacterial cellulose; Komagataeibacter xylinus; repetitive elements sequence-based rep-PCR; typing

Online: 4 January 2021 (13:24:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202005.0076.v2

Effect of Instant Controlled Pressure Drop (DIC) Treatment on the Detection of Nut Allergens by Real Time PCR

Africa Sanchiz, Carmen Cuadrado, Joseph Haddad, Rosario Linacero

Subject: Biology And Life Sciences, Food Science And Technology Keywords: Real time PCR; tree nuts; allergen detection; processed foods; thermal processing; pressure processing; DIC processing

Online: 16 May 2020 (19:18:21 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0201.v1

Detecting the COVID-19

Pravin Pokhrel, Changpeng Hu, Hanbin Mao

Subject: Biology And Life Sciences, Virology Keywords: diagnosis; detection kits; RT-PCR; immunoassay; false negative; false positive; sensitivity; point-of-care (POC)

Online: 12 April 2020 (16:50:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0172.v1

RNA viruses of Amblyomma variegatum and Rhipicephalus microplus and Cattle Susceptibility in the French Antilles

Mathilde Gondard, Sarah Temmam, Elodie Devillers, Valerie Pinarello, Thomas Bigot, Delphine Chretien, Rosalie Aprelon, Muriel Vayssier-Taussat, Emmanuel Albina, Marc Eloit, Sara Moutaller

Subject: Biology And Life Sciences, Virology Keywords: ticks; cattle, rna viruses; next-generation sequencing; phylogeny; microfluidic real-time pcr technology; Caribbean; lips

Online: 12 December 2019 (12:29:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0287.v2

Engineering a Minimal Cloning Vector from a pUC18 Plasmid Backbone with an Extended Multiple Cloning Site

Jens Staal, Wouter De Schamphelaire, Rudi Beyaert

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: PCR; recombination; cloning; engineering; biotechnology; synthetic biology; synthetic nucleotide; plasmids; repository; minimalism; Escherichia coli; mutagenesis

Online: 15 October 2018 (09:22:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1548.v1

Thermotolerance and Hydrogen Production Potential of Salt-tolerant Microflora from Salt Fields

Tsuyoshi Imai, Gede Adi Wiguna Sudiartha, Jantima Teeka, Prapaipid Chairattanamanokorn, Alissara Reungsang, Yung-Tse Hung

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: halophilic bacteria; hydrogen production; thermotolerance; upper mesophilic temperature acclimation; PCR-DGGE; next-generation sequencing; salt fields

Online: 22 September 2023 (11:21:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1450.v1

Detection of Alpha- and Betacoronaviruses in Small Mammals in Western Yunnan Province, China

Fen-Hui Xu, Pei-yu Han, Jia-wei Tian, Li-dong Zong, Hong-min Yin, Jun-ying Zhao, Ze Yang, Wei Kong, Xing-Yi Ge, Yun-zhi Zhang

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Small mammalian coronavirus; Quantitative reverse transcription polymerase chain reaction (qRT-PCR); Tissue tropism; Cross-species transmission

Online: 22 August 2023 (02:55:29 CEST)

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The genetic diversity of coronavirus (CoV) is high, and its infection in animals has not yet been fully revealed. By RT-PCR detection of partial RNA dependent RNA polymerase (RdRp) gene of CoV, we screened a total of 502 small mammals belonging to 18 species in 12 genera and 4 orders collected in Dali and Nujiang Prefecture of Western Yunnan Province, China. The prevalence of β-CoV in Chevrieri's field mouse (Apodemus chevrieri) and Lancangjiang field mouse (A. ilex) were 3.54% (4/113) and 6.67% (6/90), respectively; the prevalence of α-CoV in White-footed Indochinese rat (Rattus nitidus) and long-tailed red-toothed shrew (Episoriculus leucops) was 75% (3/4) and 5.88% (1/17), respectively. The co-infection rates of β-CoV and α-CoV in Kachin red-backed vole (Eothenomys cachinus), Norway rat (R. norvegicus) were 2.22% (2/90), 3.85% (1/26) respectively. The identity of the partial RdRp genes obtained of 13 strains of β-CoV was 83.42%-99.23% at nucleotide level, and it is worth noting that the two strains from Kachin red-backed vole showed highly homology to BOV-36/IND/2015 from Indian bovine and DcCoV-HKU23 from one-humped camel (Camelus dromedarius) in Morocco, the nucleotide similarity between 97.86%-98.33%. Similarly, the identity of the 7 strains of α-CoV among the partial RdRp sequences was 94.00%-99.18% at nucleotide levels. The viral load in different tissues was measured by quantitative RT-PCR (qRT-PCR). The average CoV viral load in small mammalian intestinal tissue was 1.25×106copies/g, differently, the mean CoV viral load in liver, heart, lung, spleen and kidney tissue was from 1.29×103 to 4.02×103copies/g, which revealed that CoV has extensive tropism of intestinal tissue in small mammals (P < 0.0001). This result revealed the genetic diversity, epidemiology, and infective tropism of α-CoV and β-CoV in small mammals from Dali and Nujiang, which deepens the comprehending of the retention and infection of coronavirus in natural hosts.

Working Paper ARTICLE

Fast Detection of SARS-CoV-2 RNA Directly from Respiratory Samples Using a Loop-Mediated Isothermal Amplification (LAMP) Test

Olympia E. Anastasiou, Caroline Holtkamp, Miriam Schäfer, Frieda Schön, Anna Maria Eis-Hübinger, Andi Krumbholz

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; COVID-19; RT-PCR; nucleic acids; direct testing; loop-mediated isothermal amplification; LAMP

Online: 5 April 2021 (12:21:19 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints201812.0178.v2

Ecological Drivers of Species Distributions and Niche Overlap for Three Subterranean Termite Species in the Southern Appalachian Mountains, USA

Chaz Hyseni, Ryan Garrick

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: biodiversity; biogeography; competitive exclusion; ecological niche model; molecular taxonomic identification; PCR-RFLP; Reticulitermes; saproxylic; species richness

Online: 17 January 2019 (03:55:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.2035.v1

Quantification of Circulating Cell-Free DNA in Idiopathic Parkinson’s Disease Patients

Małgorzata Wojtkowska, Natalia Karczewska, Klaudia Pacewicz, Andrzej Pacak, Piotr Kopeć, Jolanta Florczak - Wyspiańska, Karolina Popławska - Domaszewicz, Tomasz Małkiewicz, Bartosz Sokół

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Parkinson`s disease; mitochondria; circulating cell free DNA (ccfDNA); mitochondrial (mtDNA); nuclear (ccfDNA); droplet digital PCR ddPCR

Online: 29 January 2024 (12:45:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0500.v1

Establishment of a Pilot Newborn Screening Program for Spinal Muscular Atrophy in Saint-Petersburg

Anton Kiselev, Marianna Maretina, Sofia Shtykalova, Haya Al-Hilal, Natalia Maslyanyuk, Maria Plokhih, Elena Serebryakova, Marina Frolova, Natalia Shved, Nadezhda Krylova, Arina Il'ina, Svetlana Freund, Natalia Osinovskaya, Iskender Sultanov, Anna Egorova, Anastasia Lobenskaya, Alexander Koroteev, Irina Sosnina, Yulia Gorelik, Olesya Bespalova, Vladislav Baranov, Igor Kogan, Andrey Glotov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: spinal muscular atrophy; newborn screening; SMN1; SMN2; real-time PCR; dried blood spots; SMA incidence; carrier frequency

Online: 28 February 2023 (03:45:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0203.v1

Cost-Effective PCR-Based Identification of Tunga penetrans (Siphonaptera) Larvae Extracted From Soil Samples Containing PCR Inhibitor-Rich Material

Billy L. Amugune, Abneel K. Matharu, Paul Ouma, Francis Mutebi, Lynne Elson, Ulrike Fillinger, Jürgen Krücken

Subject: Biology And Life Sciences, Insect Science Keywords: Tungiasis; Tunga penetrans; molecular entomology; DNA isolation; Phusion® polymerase; FIREpol® Taq polymerase; low-cost PCR,

Online: 10 November 2022 (11:19:42 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202105.0526.v1

Circulating SARS-CoV-2 Variants in Italy, October 2020-March 2021

Alessia Lai, Annalisa Bergna, Stefano Menzo, Gianguglielmo Zehender, Sara Caucci, Valeria Ghisetti, Francesca Rizzo, Fabrizio Maggi, Francesco Cerutti, Giorgio Giurato, Alessandro Weisz, Chiara Turchi, Bianca Bruzzone, Francesca Ceccherini-Silberstein, Nicola Clementi, Annapaola Callegaro, Fabio Sagradi, Daniela Francisci, Emmanuele Venanzi Rullo, Ilaria Vicenti, Massimo Clementi, Massimo Galli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 virus; complete genome sequencing; COVID-19 RT-PCR testing; Spike protein; vi-ral variants

Online: 21 May 2021 (15:12:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0526.v1

Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls

Avinash Premraj, Abi George Aleyas, Binita Nautiyal, Thaha Jamal Rasool

Subject: Biology And Life Sciences, Virology Keywords: COVID-19 testing; molecular diagnostics; immunological testing; RT-qPCR; ELISA; pool PCR; lateral flow assay; rapid assay

Online: 23 September 2020 (03:33:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0275.v1

Analysis of the Primary Presenting Symptoms and Hematological Findings of COVID-19 Patients in Bangladesh

Abu Taiub Mohammed Mohiuddin Chowdhury, Md Rezaul Karim, H.M. Hamidullah Mehedi, Mohammad Shahbaz, Md Wazed Chowdhury, Guo Dan, Shuixiang He

Subject: Medicine And Pharmacology, Hematology Keywords: SARS-CoV-2; COVID-19; real-time RT-PCR; COVID-19 symptoms; COVID-19 hematological findings; Bangladesh

Online: 21 June 2020 (14:47:03 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202002.0424.v1

Insufficient Sensitivity of RNA Dependent RNA Polymerase Gene of SARS-CoV-2 Viral Genome as Confirmatory Test using Korean COVID-19 Cases

Soyoun Kim, Dong-Min Kim, Baeckseung Lee

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: SARS-CoV-2; Korean COVID-19; Wuhan Corona virus; real time PCR Ct Value; Sensitivity; False Negative

Online: 28 February 2020 (12:03:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints201810.0495.v1

Field Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Platform for the Detection of Schistosoma japonicum Infection in Oncomelania hupemsis Snails

Zhi-Qiang Qin, Jing Xu, Ting Feng, Shan Lv, Yin-Jun Qian, Li-Juan Zhang, Yin-Long Li, Chao lv, Robert Bergquist, Shi-Zhu Li, Xiao-Nong Zhou

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Schistosoma japonicum; Oncomelania hupensis; snail; 28S ribosomal DNA; PCR; loop-mediated isothermal amplification (LAMP); pooled samples; China

Online: 22 October 2018 (12:30:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1390.v1

Suppression PCR-Based Selective Enrichment Sequencing for Pathogen and Antimicrobial Resistance Detection on Cell-Free DNA in Sepsis - A Targeted, Blood Culture Independent Approach for Rapid Pathogen and Resistance Diagnostics in Septic Patients

Mirko Sonntag, Vanessa K. Elgeti, Yevhen Vainshtein, Lucca Jenner, Jan Mueller, Thorsten Brenner, Sebastian O. Decker, Kai Sohn

Subject: Epidemiology And Infectious Diseases, Medicine And Pharmacology Keywords: sepsis; antimicrobial resistances; cell-free DNA; precision diagnostics; Next-Generation sequencing; suppression PCR; real-time diagnostics; nanopore sequencing

Online: 22 April 2024 (10:13:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0384.v1

How South Africa Used National Cycle Threshold (Ct) Values To Continuously Monitor SARS-CoV-2 Laboratory Test Quality

Lesley Erica Scott, Nei-yaun Hsiao, Graeme Dor, Lucia Hans, Puleng Marokane, Pedro Da Silva, Wolfgang Preiser, Heleen Vreede, Jonathan Tsoka, Koleka Mlisana, Wendy Susan Stevens

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: SARS-CoV-2; COVID19; Laboratory diagnostics; Cycle threshold; PCR platforms; median Ct; moving average; variants; continuous quality monitoring

Online: 6 June 2023 (05:35:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0971.v1

Diagnostic of Patients With COVID-19 Pneumonia Using Passive Medical Microwave Radiometry (MWR)

Berik Emilov, Aleksander Sorokin, Meder Seiitov, Tulegen Chubakov, Sergey Vesnin, Igor Goryanin

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: 2019-nCoV; COVID-19; RT-PCR; SARS-CoV-2; Community-acquired pneumonia; Chest CT; microwave radiometry; temperature measurement

Online: 26 April 2023 (08:02:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0184.v1

Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Result in a Decrease in PCR Efficiency

Olga A. Zasedateleva, Sergey A. Surzhikov, Viktoriya E. Kuznetsova, Valeriy E. Shershov, Victor E. Barsky, Alexander S. Zasedatelev, Alexander V. Chudinov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: C5-modified dUTPs; A and B family DNA polymerases; PCR amplification; X-ray structure; molecular modeling; non-covalent interactions

Online: 2 August 2023 (08:21:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0205.v1

Measuring Circularity and Impact Reduction Potential of Post-industrial and Post-consumer Recycled Plastics

Anna Schulte, Benjamin Kampmann, Christina Galafton

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Life cycle assessment; LCA; Circular Economy; Indicator; Polypropylene; Recycling; global warming impact; climate change; efficiency; effectiveness; PCR; PIR; environmental assessment

Online: 4 July 2023 (11:13:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1037.v1

Evaluation of Standard M10 Assay for Rapid Molecular Diagnosis of SARS-CoV-2, Influenza A/B virus and Respiratory Syncytial Virus (RSV)

Azwani Abdullah, I-Ching Sam, Yin Jie Ong, Chun Hao Theo, Muhammad Harith Pukhari, Yoke Fun Chan

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: respiratory syncytial virus; influenza A virus; influenza B virus; SARS-CoV-2; rapid RT-PCR; diagnostic accuracy; point-of-care testing

Online: 15 September 2023 (05:38:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1465.v1

Pfizer-BioNTech mRNA Vaccine Protection among Children and Adolescents Aged 12–17 Years against COVID-19 Infection in Qatar

Khadieja Osman Hassan Elhag, Jesha Mohammedali Mundodan, Juel Bikhash Chowdhry, Rejoice Puthuchira Ravi, Rekaya houda Baaboura, Jeevan Albuquerque, Bilal Riaz, Reem Yusuf Emran, Khatija Batoul, Abdul Mahmood Esameldin, Zinah Al Tabatabaee, Hayat Salaheldin Khogali, Soha Shawqi Albayat

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Adolescent; children; 12-17 years COVID-19 vaccine; fully vaccinated; partially vaccinated; vaccination status; RT-PCR-positive; Pfizer; BNT162b2; vaccine effectiveness

Online: 22 August 2023 (03:02:19 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202402.0581.v1

Detection of Booroola Polymorphism of Bone Morphogenetic Protein Receptor 1b and Embrapa Polymorphism of Growth Differentiation Factor 9 in Sheep in Thailand

Poothana Sae-Foo, Supawit Triwutanon, Theera Rukkwamsuk

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: bone morphogenetic protein receptor-1B (BMPR1B); fecundity (Fec); growth differentiation factor 9 (GDF9); polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP); sheep

Online: 9 February 2024 (19:15:18 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202204.0104.v1

Statistical Modelling and Experimental Design for the Validation of Droplet Digital PCR Methods

Steffen Uhlig, Christopher Weidner, Bertrand Colson

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Method validation; droplet digital PCR; orthogonal factorial design; variance components; Poisson assumption; cloglog model; target DNA copies per droplet; Monte Carlo; prediction interval

Online: 12 April 2022 (08:46:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0234.v1

Epidemiological Challenges in Pandemic Coronavirus Disease (COVID-19): Role of Artificial Intelligence

Abhijit Dasgupta, Abhisek Bakshi, Srijani Mukherjee, Kuntal Das, Soumyajeet Talukdar, Pratyayee Chatterjee, Sagnik Mondal, Puspita Das, Subhrojit Ghosh, Archisman Som, Pritha Roy, Rima Kundu, Akash Sarkar, Arnab Biswas, Karnelia Paul, Sujit Basak, Krishnendu Manna, Chinmay Saha, Satinath Mukhopadhyay, Nitai P. Bhattacharyya, Rajat K. De

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: SIRD; Twitter; GHSI; Pre-symptomatic; EHR; Contact tracing; On-line survey; qRT-PCR; X-ray; CT/HRCT; CNN; Autoencoder; Drug affinity; CPI; and Inflation.

Online: 14 May 2020 (11:25:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0172.v4

Protein-Encoding RNA-to-RNA Information Transfer in Mammalian Cells: Principles of RNA-Dependent mRNA Amplification

Vladimir Volloch

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: RNA-dependent amplification of mammalian mRNA; physiologically occurring intracellular PCR, iPCR; RNA-dependent RNA polymerase, RdRp; chimeric RNA; sense-strand RNA; antisense-strand RNA

Online: 12 June 2019 (12:21:59 CEST)

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The transfer of protein-encoding genetic information from DNA to RNA to protein, a process formalized as the “Central Dogma of Molecular Biology”, has undergone a significant evolution since its inception. It was amended to account for the information flow from RNA to DNA, the reverse transcription, and for the information transfer from RNA to RNA, the RNA-dependent RNA synthesis. These processes, both potentially leading to protein production, were initially described only in viral systems, and although RNA-dependent RNA polymerase activity was shown to be present, and RNA-dependent RNA synthesisfound to occur, in mammalian cells, its function was presumed to be restricted to regulatory. However, recent results, obtained with multiple mRNA species in several mammalian systems, strongly indicate the occurrence of protein-encoding RNA to RNA information transfer in mammalian cells. It can result in the rapid production of the extraordinary quantities of specific proteins as was seen in cases of terminal cellular differentiation and during cellular deposition of extracellular matrix molecules. A malfunction of this process may be involved in pathologies associated either with the deficiency of a protein normally produced by this mechanism or with the abnormal abundanceof a protein or of its C-terminal fragment. It seems to be responsible for some types of familial thalassemia and may underlie the overproduction of beta amyloid in sporadic Alzheimer’s disease. The aim of the present article is to systematize the current knowledge and understanding of this pathway. The outlined framework introduces unexpected features of the mRNA amplification such as its ability to generate polypeptides non-contiguously encoded in the genome, its second Tier, a physiologically occurring intracellular polymerase chain reaction, iPCR, a Two-Tier Paradox and RNA Dark Matter. RNA-dependent mRNA amplification represents a new mode of genomic protein-encoding information transfer in mammalian cells. Its potential physiological impact is substantial, it appears relevant to multiple pathologies and its understanding opens new venues of therapeutic interference, it suggests powerful novel bioengineering approaches and its further rigorous investigations are highly warranted.

Preprint ARTICLE | doi:10.20944/preprints202204.0091.v1

Evidence-Based Evaluation of PCR Diagnostics for SARS-Cov-2 and The Omicron Variants by Sanger Sequencing

Sin Hang Lee

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; SARS-CoV; RT-PCR; Sanger sequencing; RT-qPCR; receptor-binding domain (RBD); N-terminal domain (NTD); Omicron; multi-allelic SNPs; false-positive

Online: 12 April 2022 (03:57:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0415.v2

A Routine Sanger Sequencing Target Specific Mutation Assay For SARS-CoV-2 Variants Of Concern And Interest

Sin Hang Lee

Subject: Biology And Life Sciences, Virology Keywords: Delta variant; Variants of concern; Variants of interest; SARS-CoV-2; Spike protein; Nested RT-PCR; Sanger sequencing; Amino acid mutations; ACE2 RBD; N-terminal domain (NTD)

Online: 2 November 2021 (10:40:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.0001.v1

UTI Biomarkers in Symptomatic Patients are Significantly Elevated at Microbial Densities of 10,000 cells or CFUs per mL Indicating a Lower Microbial Density Threshold for Diagnosing UTIs

Laura Parnell, Natalie Luke, Mohit Mathur, Richard Festa, Emery Haley, Jimin Wang, Yan Jiang, Lori Anderson, David Baunoch

Subject: Medicine And Pharmacology, Urology And Nephrology Keywords: urinary tract infection (UTI); standard urine culture (SUC); multiplex polymerase chain reaction (M-PCR); urine biomarkers; diagnostic testing; neutrophil gelatinase-associated lipocalin (NGAL); interleukin (IL)-8, IL-1β

Online: 3 July 2023 (09:28:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1155.v1

Blood Plasma Small Non-Coding RNAs as Diagnostic Molecules of Progesterone Receptor-Negative Phenotype of Serous Ovarian Tumors

Angelika V. Timofeeva, Ivan S. Fedorov, Alexandra V. Asaturova, Maya V. Sannikova, Anna V. Tregubova, Oleg A. Mayboroda, Grigory N. Khabas, Vladimir E. Frankevich, Gennady T. Sukhikh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: miRNA; piRNA; mRNA; CA125; progesterone receptor (PGR); new-generation sequencing (NGS); quantitative RT-PCR; serous ovarian carcinoma; borderline cystadenoma; benign cystadenoma; formalin-fixed paraffin-embedded (FFPE) blocks; blood plasma; cytoreduction

Online: 18 July 2023 (09:58:12 CEST)

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Progesterone receptor (PGR) expression level determines biological characteristics of the serous ovarian carcinoma, and low PGR expression appears to be associated with chemoresistance and worse outcome. In this study, we aimed to find relationships between tumor progesterone receptor level and RNA-profile (miRNAs, piwiRNAs, and mRNAs), determining its biological characteristics and behavior. For this purpose, we applied next generation sequencing of small noncoding RNAs, quantitative RT-PCR, and immunohistochemistry to analyze FFPE and frozen tumor samples as well as blood plasma from patients with benign cystadenoma (BSC), serous borderline tumour (SBT), low-grade and high-grade serous ovarian carcinoma (LGSOC and HGSOC, respectively). We found significant upregulation of MMP7 and MUC16 and downregulation of PGR in LGSOC and HGSOC in comparison with BSC. The tissue content of miR-199a-5p, miR-214-3p, miR-424-3p, miR-424-5p, miR-125b-5p significantly inversely correlated with the expression level of MUC16 and blood serum CA125 concentration, and significantly directly correlated with the PGR expression level in tumor tissue. On the contrary, the tissue content of miR-16-5p, miR-17-5p, miR-20a-5p, miR-93-5p, responsible for epithelial-mesenchymal transition (EMT) of the cell, significantly directly correlated with the blood serum CA125 concentration and significantly inversely correlated with the PGR expression level in the tumor tissue. Levels of the EMT-associated miRNAs significantly directly correlated with the content of hsa_piR_022437, hsa_piR_009295, hsa_piR_020813, hsa_piR_004307, hsa_piR_019914 in tumor tissues. Among them, expression level of hsa_piR_004307 significantly inversly correlated with the PGR expression level in the tumor. Two optimal logistic regression models were developed based on the quantitation of hsa_piR_020813, miR-16-5p, hsa_piR_022437 or hsa_piR_004307, hsa_piR_019914, miR-93-5p in the tumor tissue, both of which significantly diagnose PGR-negative tumor phenotype with 93% sensitivity. According to FunRich3.1.3 functional enrichment analysis tool, 72 gene-targets of miRNA and piRNA identified here as markers of PGR-negative ovarian tumor phenotype were proven to be mutated in different cancers such as ovarian, breast, colorectal, liver, stomach, lung, endometrial, thyroid cancer. Among them, the blood plasma levels of miR-16-5p and hsa_piR_022437 can be used to diagnose PGR-negative tumor phenotype with 86% sensitivity before surgery and chemotherapy to choose the treatment strategy for this most aggressive type of ovarian cancer (for instance, neoadjuvant chemotherapy followed by cytoreduction in combination with hyperthermic intraperitoneal chemotherapy) to increase the effectiveness of treatment and longevity of the patient.

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