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Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

ABSTRACT: Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

SUBMITTER: Grubaugh ND

PROVIDER: S-EPMC5536180 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh Nathan D ND Ladner Jason T JT Kraemer Moritz U G MUG Dudas Gytis G Tan Amanda L AL Gangavarapu Karthik K Wiley Michael R MR White Stephen S Thézé Julien J Magnani Diogo M DM Prieto Karla K Reyes Daniel D Bingham Andrea M AM Paul Lauren M LM Robles-Sikisaka Refugio R Oliveira Glenn G Pronty Darryl D Barcellona Carolyn M CM Metsky Hayden C HC Baniecki Mary Lynn ML Barnes Kayla G KG Chak Bridget B Freije Catherine A CA Gladden-Young Adrianne A Gnirke Andreas A Luo Cynthia C MacInnis Bronwyn B Matranga Christian B CB Park Daniel J DJ Qu James J Schaffner Stephen F SF Tomkins-Tinch Christopher C West Kendra L KL Winnicki Sarah M SM Wohl Shirlee S Yozwiak Nathan L NL Quick Joshua J Fauver Joseph R JR Khan Kamran K Brent Shannon E SE Reiner Robert C RC Lichtenberger Paola N PN Ricciardi Michael J MJ Bailey Varian K VK Watkins David I DI Cone Marshall R MR Kopp Edgar W EW Hogan Kelly N KN Cannons Andrew C AC Jean Reynald R Monaghan Andrew J AJ Garry Robert F RF Loman Nicholas J NJ Faria Nuno R NR Porcelli Mario C MC Vasquez Chalmers C Nagle Elyse R ER Cummings Derek A T DAT Stanek Danielle D Rambaut Andrew A Sanchez-Lockhart Mariano M Sabeti Pardis C PC Gillis Leah D LD Michael Scott F SF Bedford Trevor T Pybus Oliver G OG Isern Sharon S Palacios Gustavo G Andersen Kristian G KG

Nature 20170524 7658

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We s ...[more]

PMID: 28538723

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Project description: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.

Project description:The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median C t value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17-26 cycles), but after 10 days, the median C t value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.

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Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

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Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

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