Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh

Published time: 11 June 2020

Keywords: geneome, nasopharyngeal, SARS-CoV-2, betacoronavirus.

Abstract

The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported. Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which belongs to the family Coronaviridae and the genus Betacoronavirus. In Bangladesh, the first three cases were detected on 8 March 2020. By 14 May 2020, more than 18,000 cases and 280 deaths had been reported in the country. The Child Health Research Foundation (CHRF) has been a testing center for COVID-19 since 29 March 2020 and uses quantitative PCR (qPCR)- based SARS-CoV-2 detection in nasopharyngeal or oropharyngeal swab samples (1). Here, we report the complete sequence of a SARS-CoV-2 isolate from a patient who tested positive in a qPCR test. All protocols were approved by the National Research Ethics Committee, Bangladesh Medical Research Council, and the ethical review board of the Bangladesh Institute of Child Health. Samples from suspected COVID-19 patients were collected for clinical care and diagnostic testing at the discretion of the attending health care providers and were received and tested at the CHRF with the permission of the Director General Health Services, Government of Bangladesh. For this study, a nasopharyngeal specimen from a symptomatic patient with COVID-19 was collected on 18 April 2020. The specimen was tested for SARS-CoV-2 using qPCR at the CHRF and had a low cycle threshold value (CT 15). Extraction of the viral nucleic acid from the nasopharyngeal specimen was performed using the QuickRNA/DNA microprep extraction kit (product no. D7005; Zymo) according to the manufacturer’s protocol. cDNA was converted to Illumina libraries using the NEBNext Ultra II RNA library preparation kit (product no. E7770; NEB) according to the manufacturer’s protocol. Targeted enrichment of the SARS-CoV-2 sequence using 73 tiling primers at a 20:1 molar ratio of random primers to tiled primers was adapted from viral genome recovery methods described previously (2, 3). External RNA Controls Consortium Collection spike-in control mix (product no. 4456740; Thermo Fisher Scientific) was used as a marker of potential library preparation errors and for input RNA mass calculation. The library was sequenced on an Illumina.

Reference: https://doi.org/10.1128/MRA.00568-20