Genome Sequences of Chikungunya Virus Isolates from Bolivia Caio M. B. França, a Roxana Loayza, b Yelin Roca, b Ana Maria Montaño Arias, b Freddy Tinajeros, c Jose R. Loaiza, d,e,f Anshule Takyar, g Robert H. Gilman, h Matthew J. Miller i a Department of Biology, Southern Nazarene University, Bethany, Oklahoma, USA b U.F. Biología Molecular, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz, Bolivia c Asociación Benéfica PRISMA, Santa Cruz, Bolivia d Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City, Republic of Panama e Smithsonian Tropical Research Institute, Balboa, Republic of Panama f Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panama City, Republic of Panama g Department of Public Health and Department of Microbiology, University of Oklahoma, Norman, Oklahoma, USA h Bloomberg School of Public Health, John Hopkins University, Baltimore, Maryland, USA i Sam Noble Museum of Natural History, University of Oklahoma, Norman, Oklahoma, USA ABSTRACT We generated nine coding-complete chikungunya virus genome sequences from blood samples collected during the early 2015 outbreak in Bolivia. Relative to other publicly available chikungunya sequences, the Bolivian samples represent a monophyletic group, suggesting that a single lineage was widely circulating in the country between February and May 2015. A mong the Andean nations of South America, Bolivia has had the highest incidence of chikungunya and postinfection chronic disease (1). In Bolivia, chikungunya virus was first detected in early 2015, with cases of disease peaking between March and May 2015 (Fig. 1). Here, we report nine chikungunya (Togaviridae: Alphavirus) genome sequences for isolates from Bolivia. Febrile patients were screened for chikungunya virus at the Cenetrop national tropical medicine laboratory. We selected nine archived samples (maximum of 1 passage) for sequencing; samples were selected at random (Table 1). All isolates came from blood-extracted RNA (QIAamp viral RNA minikit; Qiagen) with unambiguously positive quantitative PCR (qPCR) tests (Pan American Health Organization [PAHO] diagnostic kits). Seven of the nine samples were from Santa Cruz de la Sierra. We also included one sample from Cochabamba and one sample from Trinidad. We generated cDNA using random hexamers via reverse transcriptase PCR (RT-PCR) (TaqMan reverse transcription reagents; Applied Biosystems). We amplified the chikungunya genome using a multiplex tiled amplicon approach (2). All samples were pooled and sequenced on a single Oxford Nanopore MinION R9.4 flow cell, generating 2,776,384 reads. Base calling was done in real time using Albacore v2.3.1, which implements quality filtering (QC), using only QC-passed reads in subsequent analyses. We demultiplexed and trimmed adapters and barcodes using qcat v1.1.0 (https://github.com/nanoporetech/qcat), which detected barcodes in 2,538,578 reads (91%) and assigned only 80 out of 2,538,578 (0.0004%) reads to barcodes BC10 to BC12 (not used in this study, but assignable in the qcat demultiplexing algorithm). This suggests negligible read misas- signment during demultiplexing. The average read length for QC-passed reads was 325.4 bp (range, 100 to 3,727 bp). For our highest read count sample (4866-15), we error corrected, trimmed, and de novo assembled reads in Canu v1.9 (3). The resulting assembly was fragmented, so we selected the largest contig to identify the closest whole chikungunya genome on GenBank using BLAST (2 March 2020) (4) to guide reference-based assembly. The BLAST Citation França CMB, Loayza R, Roca Y, Montaño Arias AM, Tinajeros F, Loaiza JR, Takyar A, Gilman RH, Miller MJ. 2020. Genome sequences of chikungunya virus isolates from Bolivia. Microbiol Resour Announc 9:e00230-20. https://doi.org/10.1128/MRA.00230-20. Editor Simon Roux, DOE Joint Genome Institute Copyright © 2020 França et al. This is an open- access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Matthew J. Miller, mjmiller@ou.edu. Received 8 March 2020 Accepted 24 March 2020 Published 16 April 2020 GENOME SEQUENCES crossm Volume 9 Issue 16 e00230-20 mra.asm.org 1 on July 22, 2020 by guest http://mra.asm.org/ Downloaded from