SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.
Downloads
References
Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20:533-4. https://doi.org/10.1016/S1473-3099(20)30120-1
World Health Organization-WHO. Rolling updates on coronavirus disease (COVID-19). Geneva: World Health Organization; 2020. Fecha de consulta: 31 de julio de 2020.
Disponible en: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-asthey-happen
Miller MJ, Loaiza JR, Takyar A, Gilman RH. COVID-19 in Latin America: Novel transmission dynamics for a global pandemic? PLoS Negl Trop Dis. 2020;14:e0008265. https://doi.org/10.1371/journal.pntd.0008265
United Nations. The impact of COVID-19 on Latin America and the Caribbean. New York: United Nations; 2020. p. 25.
Anderson RM, Heesterbeek H, Klinkenberg D, Hollingsworth TD. How will country-based mitigation measures influence the course of the COVID-19 epidemic? Lancet. 2020;395:931-4. https://doi.org/10.1016/S0140-6736(20)30567-5
Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: Lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci. 2017;1388:59-77. https://doi.org/10.1111/nyas.13273
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727-33. https://doi.org/10.1056/NEJMoa2001017
Quick J. nCoV-2019 sequencing protocol: protocols.io; 2020. Fecha de consulta: 2 de marzo de 2020. Disponible en: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w
Álvarez-Díaz DA, Franco-Muñoz C, Laiton-Donato K, Usme-Ciro JA, Franco-Sierra ND, Flórez-Sánchez AC, et al. Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia. Infect Genet Evol. 2020;84:104390. https://doi.org/10.1016/j.meegid.2020.104390
Franco-Muñoz C, Álvarez-Díaz DA, Laiton-Donato K, Wiesner M, Escandón P, Usme-Ciro JA, et al. Substitutions in spike and nucleocapsid proteins of SARS-CoV-2 circulating in South America. Infect Genet Evol. 2020;85:104557. https://doi.org/10.1016/j.meegid.2020.104557
Gasque P, Bandjee MC, Reyes MM, Viasus D. Chikungunya pathogenesis: From the clinics to the bench. J Infect Dis. 2016;214(Suppl.5):S446-S8. https://doi.org/10.1093/infdis/jiw362
Flórez-Lozano K, Navarro-Lechuga E, Llinas-Solano H, Tuesca-Molina R, Sisa-Camargo A, Mercado-Reyes M, et al. Spatial distribution of the relative risk of Zika virus disease in Colombia during the 2015-2016 epidemic from a Bayesian approach. Int J Gynaecol Obstet. 2020;148(Suppl.2):55-60. https://doi.org/10.1002/ijgo.13048
Pollett S, Fauver JR, Maljkovic Berry I, Meléndrez M, Morrison A, Gillis LD, et al. Genomic epidemiology as a public health tool to combat mosquito-borne virus outbreaks. J Infect Dis. 2020;221(Suppl.3):S308-18. https://doi.org/10.1093/infdis/jiz302
Laiton-Donato K, Usme-Ciro JA, Rico A, Pardo L, Martínez C, Salas D, et al. Análisis filogenético del virus del chikungunya en Colombia: evidencia de selección purificadora en el gen E1. Biomédica. 2016;36:25-34. https://doi.org/10.7705/biomedica.v36i0.2990
Laiton-Donato K, Álvarez DA, Peláez-Carvajal D, Mercado M, Ajami NJ, Bosch I, et al. Molecular characterization of dengue virus reveals regional diversification of serotype 2 in Colombia. Virol J. 2019;16:62. https://doi.org/10.1186/s12985-019-1170-4
Black A, Moncla LH, Laiton-Donato K, Potter B, Pardo L, Rico A, et al. Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC Infect Dis. 2019;19:963. https://doi.org/10.1186/s12879-019-4566-2
Laiton-Donato K, Villabona-Arenas CJ, Usme-Ciro JA, Franco-Muñoz C, Álvarez-Díaz DA, Villabona-Arenas LS, et al. Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia. Emerg Infect Dis. 2020;26. https://doi.org/10.1101/2020.06.26.20135715
Ramírez JD, Muñoz M, Hernández C, Flórez C, Gómez S, Rico A, et al. Genetic diversity among SARS-CoV2 strains in South America may impact performance of molecular detection. Pathogens. 2020;9:580. https://doi.org/10.3390/pathogens9070580
Resende PC, Delatorre E, Gräf T, Mir D, Motta FdC, Appolinario LR, et al. Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil. bioRxiv. 2020. https://doi.org/10.1101/2020.06.17.158006
Zhang L, Jackson CB, Mou H, Ojha A, Rangarajan ES, Izard T, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv. 2020. https://doi.org/10.1101/2020.06.12.148726
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020;182:812-27. https://doi.org/10.1016/j.cell.2020.06.043
Kim SJ, Nguyen VG, Park YH, Park BK, Chung HC. A novel synonymous mutation of SARSCoV-2: Is this possible to affect their antigenicity and immunogenicity? Vaccines (Basel).2020;8:220. https://doi.org/10.3390/vaccines8020220
Jesus JG, Sacchi C, Candido DDS, Claro IM, Sales FCS, Manuli ER, et al. Importation and early local transmission of COVID-19 in Brazil, 2020. Rev Inst Med Trop Sao Paulo. 2020;62:e30. https://doi.org/10.1590/s1678-9946202062030
Candido DS, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science. 2020;369:1255-60. https://doi.org/10.1126/science.abd2161
Xavier J, Giovanetti M, Adelino T, Fonseca V, Barbosa da Costa AV, Ribeiro AA, et al. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: Insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerg Microbes Infect. 2020;9:1824-34. https://doi.org/10.1080/22221751.2020.1803146
López-Álvarez D, Parra B, Cuéllar WJ. Genome sequence of SARS-CoV-2 isolate Cali-01, from Colombia, obtained using Oxford Nanopore MinION Sequencing. Microbiol Resour Announc. 2020;9:e00573-20. https://doi.org/10.1128/MRA.00573-20
Paniz-Mondolfi A, Muñoz M, Flórez C, Gómez S, Rico A, Pardo L, et al. SARS-CoV-2 spreadacross the Colombian-Venezuelan border. medRxiv. 2020. https://doi.org/10.1101/2020.07.09.20149856
Castillo AE, Parra B, Tapia P, Acevedo A, Lagos J, Andrade W, et al. Phylogenetic analysis of the first four SARS-CoV-2 cases in Chile. J Med Virol. 2020;92:1562-6. https://doi.org/10.1002/jmv.25797
Márquez S, Prado-Vivar B, Guadalupe JJ, Gutiérrez Granja B, Jibaja M, Tobar M, et al. Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador. medRxiv. 2020. https://doi.org/10.1101/2020.06.11.20128330
Garcés-Ayala F, Araiza-Rodríguez A, Mendieta-Condado E, Rodríguez-Maldonado AP,Wong-Arambula C, Landa-Flores M, et al. Full genome sequence of the first SARS-CoV-2 detected in México. Arch Virol. 2020;165:2095-8. https://doi.org/10.1007/s00705-020-04695-3
Franco D, González C, Abrego LE, Carrera JP, Díaz Y, Caisedo Y, et al. Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama. medRxiv. 2020. https://doi.org/10.1101/2020.07.31.20160929
Padilla-Rojas C, Lope-Pari P, Vega-Chozo K, Balbuena-Torres J, Cáceres-Rey O, Bailón-Calderón H, et al. Near-complete genome sequence of a 2019 novel coronavirus (SARSCoV-2) strain causing a COVID-19 case in Perú. Microbiol Resour Announc. 2020;9:e00303-20. https://doi.org/10.1128/MRA.00303-20
Padilla-Rojas C, Vega-Chozo K, Galarza-Pérez M, Calderón HB, Lope-Pari P, Balbuena-Torres J, et al. Genomic analysis reveals local transmission of SARS-CoV-2 in early pandemic phase in Perú. bioRxiv. 2020. https://doi.org/10.1101/2020.09.05.284604
Juscamayta-López E, Tarazona D, Valdivia F, Rojas N, Carhuaricra D, Maturrano L, et al. Phylogenomic reveals multiple introductions and early spread of SARS-CoV-2 into Perú. bioRxiv. 2020. https://doi.org/10.1101/2020.09.14.296814
Poterico JA, Mestanza O. Genetic variants and source of introduction of SARS-CoV-2 in South America. J Med Virol. 2020;92:2139-45. https://doi.org/10.1002/jmv.26001
Salazar C, Díaz-Viraqué F, Pereira-Gómez M, Ferrés I, Moreno P, Moratorio G, et al. Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay. bioRxiv. 2020. https://doi.org/10.1101/2020.05.09.086223
Díaz FJ, Aguilar-Jiménez W, Flórez-Álvarez L, Valencia G, Laiton-Donato K, Franco-Muñoz, et al. Aislamiento y caracterización de una cepa temprana de la epidemia de SARS-CoV-2 de 2020 en Medellín, Colombia. Biomédica. 2020;40(Supl.2):148-58. https://doi.org/10.7705/biomedica.5834
Some similar items:
- Yesika del Carmen Rojas, Helena Brochero, Hallazgo de Aedes aegypti (Linnaeus 1762), en el casco urbano del corregimiento de La Pedrera, Amazonas, Colombia , Biomedica: Vol. 28 No. 4 (2008)
- Luz Elena Velásquez, Catalina Gómez, Erika Valencia, Laura Salazar, Eudoro Casas, Paragonimosis in the peri-urban zone of Medellín, Antioquia , Biomedica: Vol. 28 No. 3 (2008)
- José Alejandro Martínez-Ibarra, Jorge Alejandro Martínez-Grant, Miguel Roberto Verdugo-Cervantes, Rafael Bustos-Saldaña, Benjamín Nogueda-Torres, Monitoring triatomid bug (Hemiptera: Reduviidae) presence by sentinel chicken coops in Southern Jalisco State, México , Biomedica: Vol. 30 No. 1 (2010)
- Sandra Milena Arias, Lina Marcela Salazar, Eudoro Casas, Alexandra Henao, Luz Elena Velásquez, Paragonimus sp. in crabs and awareness of the educational community to aquatic ecosystems in La Miel and La Clara, Caldas, Antioquia , Biomedica: Vol. 31 No. 2 (2011)
- Marylin Hidalgo, Claudia Santos, Carolina Duarte, Elizabeth Castañeda, Clara Inés Agudelo, Increase in erythromycin-resistant Streptococcus pneumoniae in Colombia, 1994-2008 , Biomedica: Vol. 31 No. 1 (2011)
- Myrtha Arango, Elizabeth Castañeda, Clara Inés Agudelo, Catalina De Bedout, Carlos Andrés Agudelo, Angela Tobón, Melva Linares, Yorlady Valencia, Ángela Restrepo, The Colombian Histoplasmosis Study Group, Histoplasmosis: results of the Colombian National Survey, 1992-2008 , Biomedica: Vol. 31 No. 3 (2011)
- Jaiberth Cardona-Arias, Luz Peláez-Vanegas, Juan López-Saldarriaga, Marcela Duque-Molina, Oscar Leal-Álvarez, Health related quality of life in adults with HIV/AIDS in Colombia , Biomedica: Vol. 31 No. 4 (2011)
- Pablo Chaparro, Edison Soto, Julio Padilla, Daniel Vargas, Estimation of the underreporting of malaria measurement in ten municipalities of the Pacific coast of Nariño during 2009 , Biomedica: Vol. 32 (2012): Suplemento 1, Malaria
- Jorge Andrés Cuellar, Alejandro Hernández, Enrique Villegas, Jorge Enrique Gómez, Efficiency of in vitro culture of Toxoplasma gondii in THP1 and Vero cell lines , Biomedica: Vol. 32 No. 3 (2012)
- Yiby Forero, Gina E. Morales, Edgar Benítez, Comparison of two methodologies used for determining metabolic syndrome in adult population , Biomedica: Vol. 33 No. 2 (2013)
| Article metrics | |
|---|---|
| Abstract views | |
| Galley vies | |
| PDF Views | |
| HTML views | |
| Other views | |
