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The copyright holder for this preprint (which was not peer-reviewed) is the .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 the 2K peptide, NS4B, and NS5) (Fig. 4a) . The protein-coding regions of Manatee DENV4 215 were compared to four Haitian DENV4 genomes from 1994-2015 and a 1981 Senegalese 216 DENV4 genome. These were analyzed for all amino acid substitutions between strains, and a 217 dN/dS analysis was conducted comparing the Senegalese DENV4 genome with Manatee 218 DENV4 ( Fig. 4a and Table S2 ). The highest proportions of amino acid substitution were seen 219 in NS2A and the 2K peptide; simultaneously, the highest dN/dS values occurred for the NS2A 220 gene, to a point of weak positive selection (dN/dS > 1) that covered a V1238T mutation 221 discussed further herein. We then calculated dN/dS ratios for DENV4 altogether, genotype II, 222 genotype IIa, and genotype IIb with all sequences available, as well as within the Haiti-Florida 223 clade and the Haiti-Florida-Puerto-Rico clades (Fig. 4b) . Purifying selection, which occurs 224 when non-synonymous mutations are deleterious, dominated, but we found weaker purifying 225 selection in NS2A and 2K peptide genes, correlating to the Manatee-to-Senegal dN/dS 226 analysis conducted previously. Values of dN/dS for these genes increased relative to those for 227 flanking genes for genotype IIb and Caribbean/Florida-specific groups as well (Fig. 4b) .