Dataset Information

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

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.

SUBMITTER: Black A

PROVIDER: S-EPMC6852897 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Black Allison A Moncla Louise H LH Laiton-Donato Katherine K Potter Barney B Pardo Lissethe L Rico Angelica A Tovar Catalina C Rojas Diana P DP Longini Ira M IM Halloran M Elizabeth ME Peláez-Carvajal Dioselina D Ramírez Juan D JD Mercado-Reyes Marcela M Bedford Trevor T

BMC infectious diseases 20191112 1

<h4>Background</h4>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.<h4>Methods</h4>We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the tempora ...[more]

PMID: 31718580

Similar Datasets

Project description:Genomic surveillance and epidemiology have shed light on the viral diversity driving coronavirus disease 2019 (COVID-19) outbreaks and are important during waves of highly transmissible and immune-escaping variants of interest or of concern (VOCs). We analyzed the epidemiological data of the understudied country of Malta and related the patterns observed with viral genetic sequences obtained through the surveillance system headed by the Mater Dei Hospital and the University of Malta. We reconstructed the evolutionary history and spatiotemporal dynamics of Maltese severe acute respiratory syndrome coronavirus 2 viruses using a phylodynamics framework. Our findings suggest that the number of cases associated with B.1.1.7/Alpha, B.1.617.2.X/Delta, and B.1.1.529.X/Omicron VOCs was nine times higher than those associated with wild-type variants. The positivity rates in Malta remained low to moderate (<10%). A combination of public health interventions appeared to have allowed Malta to mitigate the impact of COVID-19. Our phylodynamic reconstruction traced most of the 173 viral introductions inferred to countries in Northern Europe, which is consistent with flight connectivity patterns. We also observed prolonged periods of cryptic transmission (median = 102 days) until expansion into larger outbreaks. These larger outbreaks were more easily detected by the intermittent genomic surveillance in Malta, characterized by periods of sequencing hiatus. Our study demonstrates that integrating epidemiological and genomic data are crucial for uncovering the COVID-19 dynamics of understudied locations, particularly when genomic surveillance is suboptimal. Accordingly, strengthening the genomic surveillance system in Malta should help in the earlier detection of introductions and minimize viral expansion in the country while informing public health interventions. IMPORTANCE Our study provides insights into the evolution of the coronavirus disease 2019 (COVID-19) pandemic in Malta, a highly connected and understudied country. We combined epidemiological and phylodynamic analyses to analyze trends in the number of new cases, deaths, tests, positivity rates, and evolutionary and dispersal patterns from August 2020 to January 2022. Our reconstructions inferred 173 independent severe acute respiratory syndrome coronavirus 2 introductions into Malta from various global regions. Our study demonstrates that characterizing epidemiological trends coupled with phylodynamic modeling can inform the implementation of public health interventions to help control COVID-19 transmission in the community.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets