Primeras seis secuencias del genoma completo de SARS-CoV-2 por NGS en El Salvador
Keywords:
SARS-CoV-2, D614G, NGS, 2019-nCoV, COVID-19Abstract
Introduction. This work describes the first complete SARS-CoV-2 genome sequencies from samples of Salvadorean patients. Objective. To report the first six complete SARS-CoV-2 genome sequencies of six indigenous cases of COVID-19 detected in El Salvador, from nasopharyngeal discharge samples. Methodology. An NGS next generation sequencing was performed from indigenous samples in the Illumina platform MiniSeq Results. The phylogenetic analysis showed that these isolated belong to the clade 20C secondary of 20A, which have in common the S: D614G variant; the D614G mutation of the spike glycoprotein was found in the six sequencies of the SARS-CoV-2 genome. Using the GISAID platform, the sequencies were found to belong to the clade GH lineage pangolin B.1.2 y B.1.370, both present in the United States. Conclusion. The phylogenetic analysis showed that these six samples belong to clade 20C, a secondary clade of 20A, which has in common the variant of the spike glycoprotein D614G mutation
Downloads
References
Harcourt J, Tamin A, Lu X, Kamili S, Sakthivel SK, Murray J, et al. Severe acute respiratory syndrome coronavirus 2 from patient with coronavirus disease, United States. Emerging Infectious Diseases. 2020;26(6):1266-1273. DOI:10.3201/EID2606.200516
Holshue ML, DeBolt C, Lindquist S, Lofv K.H, Wiesman J, Bruce H, et al. First Case of 2019 Novel Coronavirus in the United States. New England Journal of Medicine. 2020;382(10):929- 936. DOI:10.1056/ nejmoa2001191
World Health Organization. Weekly Epidemiological Update on COVID-19. World Health Organization. 2020. Disponible en: https://www.who.int/publications/m/ item/weekly-epidemiological- update---3- november-2020
Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-269. DOI:10.1038/ s41586- 020-2008-3
Van Dorp L, Richard D, Tan CC, Shaw L, Acman M, Balloux F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nature Communications. 2020. DOI:10.1101/2020.05.21.108506
Jackson CB, Zhang L, Farzan M, Choe H. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Biochemical and Biophysical Research Communications. 2020. DOI:10.1016/j. bbrc.2020.11.026
Korber B, Fischer WM, Gnanakaran S, Better K, Yoon H, Theiler J, et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020;182(4):812-827.e19. DOI:10.1016/j. cell.2020.06.043
Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quilan BD, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nature Communications. 2020:1- 9. DOI:10.1038/ s41467-020-19808-4
Zhang L, Jackson C, Mou H, Ojha M, Rangarajan E.S, Izard T, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv. 2020. DOI:10.1101/2020.06.12.148726
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D.K.W, et al. Detection of 2019 -nCoV by RT-PCR. Euro Surveill. 2020;25(3):1-8. Disponible en: https://www. who.int/docs/ default-source/coronaviruse/wuhan-virus-assay v1991527e- 5122341d99287a1b17c111902.pdf?sfvrsn=d381fc88_21
Klempt P, Brož P, Kašný M, Novotný A, Kvapilová K, Kvapil P. Performance of targeted library preparation solutions for SARSCoV- 2 whole genome analysis. Diagnostics. 2020;10(10):1-12. DOI:10.3390/diagnostics10100769
Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, et al. Evaluation of NGS- based approaches for SARSCoV- 2 whole genome characterisation. Virus Evolution. 2020. DOI:10.1093/ve/veaa075
GISAID - phylodynamics of pandemic coronavirus in Latin America and the caribbean. GISAID. 2020. Fecha de consulta: 22 de diciembre de 2020. Disponible en: isaid.org/ epiflu-applications/ phylodynamics/
Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges. 2017;1(1):33-46. DOI:10.1002/ gch2.1018
Rambaut A, Holmes EC, Hill V, O’Toole Á, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology. 2020;5(11):1403-1407. DOI:10.1038/s41564-020-0770-5
Toyoshima Y, Nemoto K, Matsumoto S, Nakamura Y, Kiyotani K. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Journal of Human Genetics. 2020;65(12):1075- 1082. DOI:10.1038/s10038-020-0808-9
Hodcroft EB, Zuber M, Nadeau S, Candelas F, Standler T, Neher RA, et al. Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. medRxiv.2020. DOI: 10.1101/2020.10.25.20219063
Pfefferle S, Günther T, Kobbe R, Czech-Sioli M, Indenbirken D, Robitaille A, et al. SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany. Clinical Microbiology and Infection. 2020. DOI:10.1016/j. cmi.2020.09.034
Ministerio de Ciencia y Economía; Instituto de Salud Carlos III. Informe del Grupo de Análisis Científico de Coronavirus del ISCIII (GACC-ISCIII). Madrid. Instituto Carlos III. 2020. 8 p. Disponible en: https://fundadeps. org/wp-content/ uploads/2020/04/ TRANSMISIÓN-DEL-VIRUS_1.pdf
Downloads
Published
How to Cite
Issue
Section
License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Los textos académicos y científicos que se publican en la Revista La Universidad están protegidos bajo la licencia CC BY NC SA 4.0, esta permite usar una obra para crear otra obra o contenido, modificando o no la obra original, siempre que se cite al autor, la obra resultante se comparta bajo el mismo tipo de licencia y no tenga fines comerciales (https://creativecommons.org/licenses/by-nc-sa/4.0/deed.es) . El autor es el único que pose los derechos de publicación y la Revista La Universidad posee los derechos de difusión.