Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a ‘hot spot’ of virus transmission in Chicago, IL, USA.
Duplicate reads were removed using Dedupe (Gregg and Eder 2015). Deduplicated reads were assembled and analyzed using CLC Genomics Workbench v8.5 (CLC Bio, Aarhus, Denmark). Low-quality bases (phred quality score <30) and short reads (<50 nt) were discarded, and PCR primers were trimmed. To obtain consensus sequences from each sample, WNV genomes were assembled by aligning (‘mapping’) reads to a WNV reference sequence, BSL173-08 (GenBank accession JF957173). Consensus sequences were then aligned using the ClustalW algorithm (Larkin et al. 2007).