Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

Sergio Luis Aguilar-Martinez
,
Gustavo Adolfo Sandoval-Peña
ORCID logo ,
José Arturo Molina-Mora
ORCID logo ,
Pablo Tsukayama-Cisneros
ORCID logo ,
Cristian Díaz-Vélez
ORCID logo ,
Franklin Rómulo Aguilar-Gamboa
,
D. Katterine Bonilla-Aldana
* ORCID logo ,
Alfonso J. Rodriguez-Morales
Version 1 : Received: 22 November 2023 / Approved: 23 November 2023 / Online: 23 November 2023 (11:07:09 CET)

A peer-reviewed article of this Preprint also exists.

Aguilar-Martinez, S.L.; Sandoval-Peña, G.A.; Molina-Mora, J.A.; Tsukayama-Cisneros, P.; Díaz-Vélez, C.; Aguilar-Gamboa, F.R.; Bonilla-Aldana, D.K.; Rodriguez-Morales, A.J. Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru. Trop. Med. Infect. Dis. 2024, 9, 46. Aguilar-Martinez, S.L.; Sandoval-Peña, G.A.; Molina-Mora, J.A.; Tsukayama-Cisneros, P.; Díaz-Vélez, C.; Aguilar-Gamboa, F.R.; Bonilla-Aldana, D.K.; Rodriguez-Morales, A.J. Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru. Trop. Med. Infect. Dis. 2024, 9, 46.

Abstract

Objective: To identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. Methods: nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which have been considered mild, moderate and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. Results: it was determined that during the period December 2020 and January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, B.1.111 circulated, lineage C.14 the most predominant with 76.7% (n=23/30), these lineages were classified in clade 20D mainly and also within clade 20B and 20A. On the contrary, the variants found in the second batch of samples of the period September – October 2021 were Delta Variant (72.7%), Gamma (13.6%), Mu (4.6%), Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J and 21I. Conclusions: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

Keywords

SARS-CoV-2; genome; sequencing; phylogenetic analysis; Peru

Subject

Medicine and Pharmacology, Tropical Medicine

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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