key: cord-1049319-q5rm5tdk
authors: Singh, Ishwar; Vetrivel, Umashankar; Harish, D. R.; Chattophadhyay, Debprasad
title: Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation
date: 2021-02-11
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00016-21
sha: b5928209a12cb974960de2a3a35e13d2f3043d52
doc_id: 1049319
cord_uid: q5rm5tdk

We announce the coding-complete genome sequences of two isolates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from two coronavirus disease 2019 (COVID-19)-positive samples (RNA isolated from nasopharyngeal swabs) from Belagavi District, Karnataka State, India. Mutational analysis revealed the presence of the D614G substitution in both the isolates.

of 29,854 bp (GC content, 38%), with an average sequence depth of 3,587.38Â and 99.83% genome coverage.

Mutational analysis of NITMA1086 revealed 15 mutations, of which 8 were found to cause amino acid substitutions. In the case of NITMA1139, of the 16 mutations identified, 8 were found to cause substitutions. In both of the isolates, the P314L (ORF1b), D614G (S), R203K (N), G50N (ORF14), and G204R (N) substitutions were found in common (Table 1) . Of these variations, D614G is reported to be highly prevalent worldwide and is associated with higher viral load and titers of pseudoviruses (6) .

Phylogenetic comparison of these two genome sequences with globally detected viral strains was performed using the Nextstrain tool (with an inbuilt global data set from GISAID) (7) . This analysis revealed that both isolates belong to clade 20B, a subclade of 20A, which emerged in the European outbreak and evolved from the 19A Wuhan strain (Fig. 1 ). In the current scenario, 20B has been reported to be more common in the Indian population and is considered a major basis of disease transmission in India (8) . Common sharing and collating of whole-genome sequences during viral outbreaks are essential as a crucial part of outbreak response (9) . Thus, the genome sequences of these isolates will aid in studying the evolution and epidemiology of the virus and its transmission dynamics in Belagavi, as well as throughout India.

Data availability. These genome sequences have been deposited in the NCBI GenBank database under the accession numbers MW425563.1 and MW425837.1 for NITMA1086 and NITMA1139, respectively. The raw reads were also submitted to the NCBI SRA under the accession numbers SRX9766878 and SRX9766838 for NITMA1086 and NITMA1139, respectively. C241T

a Bold indicates the mutations leading to amino acid substitutions commonly observed in NITMA1086 and NITMA1139; italic indicates the other synonymous/intergenic variants commonly observed in NITMA1086 and NITMA1139. b SNP, single nucleotide polymorphism.

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FIG 1 Phylogenetic tree displaying sequenced SARS-CoV-2 strains (with reference to GISAID global data set), in accordance to the clades assigned for the virus during phylogenetic analysis using the Augur toolkit (with default parameters) run through the Nextstrain server. Augur implements the FastTree algorithm, which infers the maximum-likelihood method for building phylogenetic trees from alignments of nucleotide or protein sequences (7, 10)

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We acknowledge the director general of the Indian Council of Medical Research, Balram Bhargava, and the divisions of Basic Medical Sciences (BMS) and Epidemiology and Communicable Diseases (ECD) of ICMR for support and funding. We also acknowledge the Belagavi Institute of Medical Sciences (BIMS) and the district health authority of Belagavi, Karnataka State.