Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

Black, Alison, Moncla, Louise H., Laiton-Donato, Katherine, Potter, Barney, Pardo, Lissethe, Rico, Angelica, Tovar, Catalina, Rojas Alvarez, Diana P., Longini, Ira M., Halloran, M. Elizabeth, Pelaez-Carvajal, Dioselina, Ramirez, Juan D., Mercado-Reyes, Marcela, and Bedford, Trevor (2019) Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC Infectious Diseases, 19. 963.

[img]
Preview
PDF (Published Version) - Published Version
Available under License Creative Commons Attribution.

Download (2MB) | Preview
View at Publisher Website: https://doi.org/10.1186/s12879-019-4566-...
 
9


Abstract

Background: Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.

Methods: We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.

Results: We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 – Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.

Conclusions: Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

Item ID: 61052
Item Type: Article (Research - C1)
ISSN: 1471-2334
Keywords: Colombia, genomic epidemiology, phylogeography, virus evolution, Zika virus
Copyright Information: Copyright © Black et al. 2019. his article is distributed under the terms of the Creative Commons Attribution 4.0 InternationalLicense (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in anymedium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commonslicense, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Funders: National Science Foundation (NSF), USA, National Institute of Health (NIH), Gobernación de Córdoba, sistema general de regalias (SGR) Colombia, Universidad del Rosario, Colombia
Projects and Grants: NSF DGE-1256082, Gobernación de Córdoba, sistema general de regalias (SGR) Colombia, Grant No. 754/2013, NIH R35 GM119774-01, NIH U54 GM111274
Date Deposited: 10 Dec 2019 03:53
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1117 Public Health and Health Services > 111706 Epidemiology @ 50%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 50%
SEO Codes: 92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920404 Disease Distribution and Transmission (incl. Surveillance and Response) @ 80%
92 HEALTH > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920109 Infectious Diseases @ 20%
Downloads: Total: 9
Last 12 Months: 9
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page