key: cord-0943374-7kvk1bik
authors: Ramírez, Juan David; Florez, Carolina; Muñoz, Marina; Hernández, Carolina; Castillo, Adriana; Gomez, Sergio; Rico, Angelica; Pardo, Lisseth; Barros, Esther C.; Castañeda, Sergio; Ballesteros, Nathalia; Martínez, David; Vega, Laura; Jaimes, Jesús E.; Cruz‐Saavedra, Lissa; Herrera, Giovanny; Patiño, Luz H.; Teherán, Aníbal A.; Gonzalez‐Reiche, Ana S.; Hernandez, Matthew M.; Sordillo, Emilia Mia; Simon, Viviana; van Bakel, Harm; Paniz‐Mondolfi, Alberto
title: The arrival and spread of SARS‐CoV‐2 in Colombia
date: 2020-08-13
journal: J Med Virol
DOI: 10.1002/jmv.26393
sha: d9cf622df774943f26ca857436a491cee471a33d
doc_id: 943374
cord_uid: 7kvk1bik

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus‐2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high‐risk areas.

The number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is rapidly increasing throughout South America. The To assess the genetic diversity and origins of SARS-CoV-2 in Colombia, we sequenced and assembled viral genomes from total RNA extracted from NP-VTM clinical specimens. Sample preparation for sequencing was done using whole-genome amplification with custom designed tiling primers and the Artic Consortium protocol (Figure 1 ). We performed univariate analysis to determine whether certain lineages were associated with a health-care worker status, hospital exposure (including intensive care unit admission), or a travel history to high-risk areas. A significant association (P = .033) was only found between infection with B.1 lineage and a travel history to high-risk areas. In conclusion, Pangolin lineage B.1 was associated with prior travel to high-risk areas.

We further constructed a time-scaled ML phylogeny using TreeTime and specimen collection date constraints. 8 In addition, the unfeasibility of complying with quarantine measures due to concern over loss of income or loosing employment, as well as the lack of water and inappropriate wastewater treatment may favor transmission and halt potential mitigation efforts needed for containment of the virus. This is why alongside strengthening public health capabilities there is an urgent need to better understand and address the main drivers influencing the epidemic spread in this The displayed time tree was inferred under a strict clock model with a fixed substitution rate of 0.8 × 10 −3 , based on previous rate value estimates. 5 TreeTime analyses were run for a total of six iterations and marginal date estimates of ancestral states are shown with 90% confidence intervals. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2 United States, Canada, Chile, and Iceland lineages (Figure 1) . That is the case of lineages A.5, B.1.3, B.1.11, B.1.5.1, and B.1.25 . Interestingly, the third most common lineage in the country was the B lineage, which has been reported worldwide in returning travelers from China, and which may suggest an independent introduction in the country of the ancestral SARS-CoV-2 lineage. This is also the case for other Latin-American countries, such as Uruguay, which has reported the occurrence of B, B.1 and A.1a lineages, 12 Chile that has reported B and A.2a lineages 13 and Brazil with the largest genomic epidemiology study so far in the region. 14 It is well known that mutational events in the S and N genes of coronaviruses may affect its pathogenicity. 15 In fact, it has been demonstrated that both of these genes are undergoing episodic selection as the virus is transmitted amongst humans. 16 More recently, the description of several mutations in the spike glycoprotein of SARS-CoV-2 capable of inducing a missense mutation has suggested the possibility for increased viral infectivity and virulence. 9,17 Also, illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions and increase infectivity in coronaviruses. To date there are few studies that have associated the SARS-CoV-2 lineage with the infection severity 18 and differential diagnosis. 19 In our case, we identified the key mutation D614G in most of the Colombian genomes which has been associated with increased infectivity, 9 future studies should unveil its clinical consequences and impact in South America and its regional particularities.

In conclusion, this represents the first genomic epidemiology study of SARS-CoV-2 in Colombia. Future studies in the country and elsewhere in South America, including sequencing of viral genomes as the predicted epidemic peak approaches, and of contact cases and spread clusters, may help to better identify transmission routes and inform potential prevention measures. Our study supports the relevance of genomic surveillance and the critical need to establish coordinated efforts to generate genomic data in South America that will enable integrative analyses to uncover SARS-CoV-2 dynamics at the continental level.

The authors thank Dirección de Investigación e Innovación from Universidad del Rosario for funding this study. Funding was provided by the 

The data are available in GISAID nextstrain.

http://orcid.org/0000-0002-1344-9312

COVID-19 in Latin America: the implications of the first confirmed case in Brazil

Ministerio de salud y protección social

Resumen: consenso colombiano de atención, diagnóstico y manejo de la infección por SARS-COV-2/COVID-19 en establecimientos de atención de la salud-recomendaciones basadas en consenso de expertos e informadas en la evidencia

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR 2020

Introductions and early spread of SARS-CoV-2 in the New York City area. Science

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus

Unipro UGENE: a unified bioinformatics toolkit

COVID-19 in Latin America: novel transmission dynamics for a global pandemic

Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo

Tracing new clinical manifestations in patients with COVID-19 in Chile and its potential relationship with the SARS-CoV-2 divergence

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Episodic evolution mediates interspecies transfer of a murine coronavirus

The 2019-new coronavirus epidemic: evidence for virus evolution

Patient-derived mutations impact pathogenicity of SARS-CoV-2

Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study

Viral and host factors related to the clinical outcome of COVID-19

The arrival and spread of SARS-CoV-2 in Colombia