Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2021 Jan 8

PMID 33414350

Citations 3

Authors

Franklin Romulo Aguilar-Gamboa

Luis Alberto Salcedo-Mejia

Luis Miguel Serquen-Lopez

Marco Enrique Mechan-Llontop

Percy Omar Tullume-Vergara

Juan Jose Bonifacio-Briceno

Ramses Salas-Asencios

Heber Silva Diaz

Juan P Cardenas

Affiliations

Soon will be listed here.

Abstract

Here, we report the genomic sequences of five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from nasopharyngeal samples from five tested coronavirus disease 2019 (COVID-19)-infected patients from the Lambayeque region in Peru during early April 2020.

Citing Articles

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

Aguilar-Martinez S, Sandoval-Pena G, Molina-Mora J, Tsukayama-Cisneros P, Diaz-Velez C, Aguilar-Gamboa F Trop Med Infect Dis. 2024; 9(2).

PMID: 38393135 PMC: 10892787. DOI: 10.3390/tropicalmed9020046.

Introduction of SARS-CoV-2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil.

Kashima S, Slavov S, Giovanetti M, Rodrigues E, Patane J, Viala V J Med Virol. 2021; 94(3):1206-1211.

PMID: 34647634 PMC: 8662236. DOI: 10.1002/jmv.27389.

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

Coolen J, Wolters F, Tostmann A, van Groningen L, Bleeker-Rovers C, Tan E J Clin Virol. 2021; 144:104993.

PMID: 34619382 PMC: 8487099. DOI: 10.1016/j.jcv.2021.104993.

References

Danecek P, McCarthy S . BCFtools/csq: haplotype-aware variant consequences. Bioinformatics. 2017; 33(13):2037-2039. PMC: 5870570. DOI: 10.1093/bioinformatics/btx100. View

Hadfield J, Megill C, Bell S, Huddleston J, Potter B, Callender C . Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018; 34(23):4121-4123. PMC: 6247931. DOI: 10.1093/bioinformatics/bty407. View

Rambaut A, Holmes E, OToole A, Hill V, McCrone J, Ruis C . A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020; 5(11):1403-1407. PMC: 7610519. DOI: 10.1038/s41564-020-0770-5. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

Otto T, Dillon G, Degrave W, Berriman M . RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res. 2011; 39(9):e57. PMC: 3089447. DOI: 10.1093/nar/gkq1268. View

Juscamayta-Lopez E, Carhuaricra D, Tarazona D, Valdivia F, Rojas N, Maturrano L . Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru. J Med Virol. 2021; 93(10):5961-5968. PMC: 8426889. DOI: 10.1002/jmv.27167. View

Haas B, Papanicolaou A, Yassour M, Grabherr M, Blood P, Bowden J . De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8(8):1494-512. PMC: 3875132. DOI: 10.1038/nprot.2013.084. View

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

10.

Ilmjarv S, Abdul F, Acosta-Gutierrez S, Estarellas C, Galdadas I, Casimir M . Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Sci Rep. 2021; 11(1):13705. PMC: 8249556. DOI: 10.1038/s41598-021-91662-w. View