More Florida Zika Sequences Expand Sub-clade

[niman]

Trevor Bedford has posted a phylogenetic tree with 11 Zika sequences from Florida that appear to be generated by USAMRIID.  

Most or all of these sequences appear to be distinct from sequences released by Scripps and Broad, but all 11 fall onto the same two branches defined by prior Florida sequences

 

http://virological.org/t/zikv-sequence-from-florida/364/10

Edited October 12, 2016 by niman

[niman]

[niman]

New Florida sequences on upper branch = FLUR001, FLUR002, FLUR005, FLUR006, FLUR007, FLUR008, FLUR009, FLUR013, FLUR015.

Lower branch = FLUR011,  FLUR022.

[niman]

jtladner

10d

1 

 

In collaboration with the Florida Department of Health, we (Center for Genome Sciences, USAMRIID) have generated 11 Zika virus (ZIKV) genomes from urine samples collected from patients in Florida with locally acquired ZIKV infections. All genomes were sequenced using Illumina in combination with RNA Access targeted enrichment. Illumina reads were aligned to BeH819015 (KU365778.1 with missing terminal UTR regions filled with sequence from MR766) and new consensus sequences were generated. A minimum of 3x read depth (in support of the consensus base) was required to make a consensus call. Across the different samples, genome coverage ranged from 57% to 99.8%. All samples were collected from patients in the Miami region during July 28 – August 31 2016.

All of these sequences form a phylogenetic clade together with the 4 Florida-derived genomes generated by the Andersen Lab [1 from a locally acquired human infection (http://andersen-lab.com/zika-sequence-local-florida-transmission/) and 3 from Aedes aegypti mosquitoes (http://andersen-lab.com/zika-sequences-miami-mosquitoes/)], 1 genome generated from a patient in Florida with a history of travel to Cuba (also from the Andersen Lab; http://andersen-lab.com/travel-related-cases-florida/) and 1 genome from a patient in Guadeloupe (Atkinson et al.; https://www.ncbi.nlm.nih.gov/nuccore/KX673530). However, the genomes generated from the locally acquired cases in Florida form two distinct subclades within this group, which are separated from each other by 18 substitutions. Ten human cases and two mosquito isolates belong to subclade #1 and two human cases and one mosquito isolate belong to subclade #2. The genome from Guadeloupe is basal to subclade #2, while the genome from the patient with a history of travel to Cuba is basal to subclade #1 in the MCC BEAST tree, but nested within subclade #1 in the ML tree.

Based on epidemiological data combined with tMRCA estimates, we believe that these results are most consistent with at least two introductions resulting in local transmission in Florida. Under this hypothesis, we estimate that both introductions likely occurred during the first half of 2016 (median estimates during April 2016). Alternatively, there could have been a single introduction followed by diversification within Florida (and export from Florida). However, based on the molecular clock analysis, this would require an introduction to Florida sometime in 2015 (median estimate during July 2015).

http://virological.org/t/zikv-sequence-from-florida/364/3