Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Abstract

C oronavirus disease (COVID-19) is a life-threatening respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an emerging zoonotic virus first identified in Wuhan, China (1). The first confirmed cases of COVID-19 were reported on January 12, 2020, from patients who had respiratory symptoms during December 8, 2019-January 2, 2020 (2). Despite early containment and mitigation measures (3), the high infectiousness, presymptomatic transmission, and prolonged transmissibility of SARS-CoV-2 (4,5) combined with other factors, such as globalization, led to the rapid spread of COVID-19 across the world. Rigorous contact-tracing and physical distancing measures implemented in different countries have been effective in delaying the epidemic during the contention phase (6-9). However, ensuing lockdowns and travel restrictions to minimize the burden on healthcare systems have led to a decline in wellbeing and an economic downturn and have had profound impacts in low-to-middle income countries (10). The contention phase in Colombia started on March 6, 2020, when the Instituto Nacional de Salud (INS; National Institute of Health) confirmed the first case of COVID-19 from a person returning to Colombia from Italy on February 26, 2020 (11). On March 23, a total 314 cases had been confirmed, which prompted the closure of all the country borders to contain the outbreak. On March 31, >10% of confirmed cases were among persons with no known exposure to a COV-ID-19 patient (12), presumably due to extensive community transmission. Colombia then implemented the mitigation phase, which included physical distancing as the main strategy to limit virus spread. By June 18, a total of 57,046 confirmed cases and 1,864 deaths had been reported in Colombia (13). The unprecedented global health and societal emergency posed by the COVID-19 pandemic urged data sharing and faster-than-ever outbreak research developments that are reflected in the >37,000 complete SARS-CoV-2 genomes made available through

Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama

“…We obtained complete genome coverage for samples using reverse transcription PCR cycle threshold values <25 (Appendix 2 Figure 6, panel B) and found circulation of >10 virus lineages (Figure 2, panel A; Appendix 2 Figure 7) (6). The most frequently identified was A.2 (71.2%), followed by B.1 (16.7%) and A.1 (3.5%), in contrast to other studies in Latin America, where B-like lineages largely predominate (7,8). Lineages A.3, B, and B.1.5 were identified in 79 cases detected early on in the epidemic, 11 (13.9%) of the cases imported (Figure 2, panel A; Appendix 2 Figure 7).…”

The unfurl of the coronavirus and its thwack on humans and the environment: a review

“…[ 35 ].The accessibility of SARS-CoV-2 genomes empowered us to distinguish a quickly creating variety, exhibiting that the genomic epidemic is a ground-breaking approach for describing the outburst. Genomic epidemic depends on phylogenetic examination and has empowered scientists across the world to identify SARS-CoV-2 increase in people, to uncover the importation and nearby transmission chains not recognized by movement history and conventional contact-following procedures, and follow the geographic spread and predominance of strains bearing explicit transformations of epidemiologic pertinence [ 36 ].…”

Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K

“…This amino acid change located at the RBD of the spike protein has been found to have a negative effect on neutralization by monoclonal antibodies (10), as well as vaccine-induced (11) and polyclonal antibodies resulting from natural infection with circulating lineages (12). In Colombia, SARS-CoV-2 genomic surveillance was established early during the pandemic, leading to the identification of the importation of at least 12 lineages before international flight cancellation and during lockdown (13). A high percentage (48%) of SARS-CoV-2 sequences were assigned to the B.1 parental lineage with little or no shared mutations accumulated during the early local transmission inside the country.…”

“…In Colombia, SARS-CoV-2 genomic surveillance was established early during the pandemic, leading to the identification of the importation of at least 12 lineages before international flight cancellation and during lockdown ( 13 ). A high percentage (48%) of SARS-CoV-2 sequences were assigned to the B.1 parental lineage with little or no shared mutations accumulated during the early local transmission inside the country.…”