Under-the-radar dengue virus infections in natural populations of Aedes aegypti mosquitoes

Sean M. Boyles; Carla N. Mavian; Esteban Finol; Maria Ukhanova; Caroline J. Stephenson; Gabriela Hamerlinck; Seokyoung Kang; Caleb Baumgartner; Mary Geesey; Israel Stinton; Kate Williams; Derrick K. Mathias; Mattia Prosperi; Volker Mai; Marco Salemi; Eva A. Buckner; John A. Lednicky; Adam R. Rivers; Rhoel R. Dinglasan

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.24.919282 doi: bioRxiv preprint 11 to and/or persistence in mosquito populations. Comparative selection and mutation analyses 119 revealed NS2A as a relatively strong region of potential selection for the Manatee County 120 genome. HyPhy algorithms were used to estimate non-synonymous (dN) to synonymous (dS) 121 codon substitution rate ratios (ω), with ω<1 indicating purifying/negative selection and ω>1 122 indicating diversifying/positive selection [33, 34] . Fast, unconstrained Bayesian approximation 123 (FUBAR) [35] was used for inferring pervasive selection, and the mixed effects model of 124 evolution (MEME) [36] (Fig. 1a) . 151 A full DENV4 genome (MN192436) was constructed with an overall genome coverage of ~11X 152 across the reads (Fig. 2) . We observed that the 2017 DENV4 signal was much lower than 168 After analyzing the metavirome, we investigated the genome of the DENV4 strain to determine 169 its likely source and assess the potential timeframe of introduction into Florida. Our first 170 analysis confirmed the phylogenetic signal and absence of nucleotide substitution saturation 171 ( Fig. S2a-b) . We subsequently explored Manatee County DENV4's phylogeny with a 234-172 genome DENV4 dataset constructed from GenBank sequences (Table S1) by maximum 173 likelihood (ML) phylogenetic inference (Fig. 3a) . The ML phylogeny showed three clades: two 174 Asian clades, and one American clade with two Senegalese strains (MF00438, KF907503) and 175 one Thai (KM190936) at the base (Fig. 3a) . Manatee DENV4 can be classified as DENV4 176 genotype IIb. The DENV4 genome obtained in Florida most closely clustered with two Haitian 177 isolates from 2014 (KT276273, KP140942) and a cluster of Puerto Rican isolates (Fig. 3a) . 178 Further back, a Haitian isolate (JF262782) collected 20 years earlier also clustered with the 179 Manatee-associated clade (Fig. 3a) .