key: cord-0737135-1anmoyaj
authors: Paulino-Ramirez, Robert; Calderon, Victor Virgilio; Vallejo Degaudenzi, Alejandro
title: Genome Sequences of Community SARS-CoV-2 B.1.526 and P.1 Variants Circulating in the Dominican Republic
date: 2021-10-07
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00744-21
sha: 5abeca744c0842d13d9a28382edb87f80c8cc01c
doc_id: 737135
cord_uid: 1anmoyaj

Nearly complete genome sequences were obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern and two variants of interest from nasopharyngeal swab samples obtained during surveillance activities in urban communities, among individuals with no previous travel history, in Santo Domingo, Dominican Republic.

pipeline (https://github.com/artic-network/fieldbioinformatics), ensuring further read filtering, primer trimming, amplicon coverage normalization, variant calling, and consensus building. Genomes obtained were visually curated with the IGV genome browser (6) . Consensus genomes obtained from these processes were compared using the Nextstrain clade tool (7), with which the proper clade was identified. To perform phylogenetic analysis, other relevant genomes were downloaded from the GISAID database, the genomes were aligned with MAFFT v7 (https://mafft.cbrc.jp/alignment/server), and a phylogenetic tree was constructed (Fig. 1B) with a maximum likelihood algorithm based on the GTR model using MEGA X v7.0.26 (https://www.megasoftware.net). We used default parameters for all software.

Two genomes of these three viral samples correspond to the B.1.526 (Iota, 20C) lineage, which was first described in the New York region (8) , and one to P.1 (Gamma, 20J/ 501Y.V3), which was detected first in Japan and later in Brazil, where it has become the dominant circulating variant (9) . Genomic characteristics are presented in Table 1 . The development of variants of SARS-CoV-2 is and will be quintessential as a result of natural selection; therefore, variant surveillance is of utmost importance to strengthen nonpharmaceutical interventions and to envision the negative impact on vaccines campaigns in low-and middle-income countries. Data availability. Sequences of the SARS-CoV-2 variants were deposited in the NCBI database (GenBank accession numbers MZ645039, MZ576192, and MZ621913 and BioSample accession numbers SAMN21197472, SAMN21197473, and SAMN21197474) and the GISAID database (https://www.gisaid.org) (accession numbers EPI_ISL_2601034, EPI_ISL_2601037, and EPI_ISL_2601038). The raw reads were deposited in the NCBI Sequence Read Archive (SRA) database (SRA accession numbers SRR15697814, SRR15697813, and SRR15697812). b NSP, nonstructural protein.

Seroprevalence of specific antibodies against SARS-CoV-2 from hotspot communities in the Dominican Republic

COVID-19 weekly epidemiological bulletin 20

Emerging variants of SARS-CoV-2 and its public health implications

Whole genome sequence of a SARS-CoV-2 isolate from Dominican Republic. GenBank accession number PRJNA691021

The proximal origin of SARS-CoV-2

Nextstrain: real-time tracking of pathogen evolution

SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape

Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings

This work is part of the Observatory of Pandemics and Emerging Pathogen initiative at the IMTSAG-UNIBE in Santo Domingo, DR.We thank the IMTSAG-UNIBE molecular laboratory team for their dedication and constant support throughout the COVID-19 pandemic response.