key: cord-0753102-s82wgtvt
authors: Narayanan, S.; Patil, G.; More, S.; Saliki, J. T.; Kaul, A.; Ramachandran, A.
title: First detection and report of SARS-CoV-2 Spike protein N501Y mutations in Oklahoma USA
date: 2021-01-29
journal: nan
DOI: 10.1101/2021.01.26.21250584
sha: 6510004a324a63d12882ace232b2c60ad57b432b
doc_id: 753102
cord_uid: s82wgtvt

We describe the detection of SARS-CoV-2 (VOC )B.1.1.7 lineage in Oklahoma, USA. Various mutations in the S gene and ORF8 with similarity to the genome of B.1.1.7 lineage were detected in 4 of the 6 genomes sequenced and reported here. The sequences have been made available in GISAID. Presence of novel lineages indicate the need for frequent whole genome sequencing to better understand pathogen dynamics in different geographical locations.

We describe the detection of SARS-CoV-2 (VOC )B.1.1.7 lineage in Oklahoma, USA. Various mutations in the S gene and ORF8 with similarity to the genome of B.1.1.7 lineage were detected in 4 of the 6 genomes sequenced and reported here. The sequences have been made available in GISAID. Presence of novel lineages indicate the need for frequent whole genome sequencing to better understand pathogen dynamics in different geographical locations.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

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Since the start of the COVID-19 pandemic in December 2019, several lineages/variants of SARS-CoV-2 have been identified based on whole genome sequencing. As of January 21, 2021 approximately 420,000 whole genome sequences have been deposited in the GISAID database (https://www.gisaid.org/) (1,2). Recently a novel SARS-CoV-2 lineage (B 1.1.7.) was identified in Kent and Greater London in the United Kingdom (3) and is reported to have enhanced transmissibility. Infections by the B.1.1.7 lineage has since been reported from several other countries including the United States (4). We report the identification of B.1.1.7 in Oklahoma, USA.

COVID-19 was first reported in Oklahoma on March 6 th 2020 (5). As of January 19 th, 2021, a total of 358,374 cases and 3,037 deaths have been registered in the state (6). Six clinical samples, from different counties in the state, collected between January 1 st and 8 th , 2021, were sequenced for this report. RNA was extracted using a commercial kit (MVP, ThermoFisher) and viral presence was detected by real-time PCR using TaqPath COVID-19 kit (Thermofisher, MA, USA) that targets the S gene, N gene and ORF 1ab. The S gene target of all the samples selected for sequencing either failed to amplify or had Ct values that were higher when compared to N gene and ORF1ab. Sequencing was performed using the MinION platform (Oxford Nanopore Technologies, UK ) following the ARTIC protocol (7).

Sequenced genomes were assembled using canu (8) . Reference assisted consensus assemblies were generated using minimap2 (9) and nanopolish (10), SARS-CoV-2 reference genome Wuhan-Hu-1 (GenBank ID: MN908947.3) was used for reference assembly. Individual genes were annotated using VIGOR (11) . Annotated genes and the whole genomes were aligned using MUSCLE aligner in MEGA-X (12) . The genome sequences were submitted to GISAID (1) and their GISAID classification and PANGO lineages (13) are shown in table 1. Four of the six samples sequenced carried SNPs similar to those described in the B.1.1.7 lineage (20I/501Y.V1 Variant of Concern (VOC) 202012/01) (4), including N501Y, 69/70 deletion, Y144 deletion, A570D, P681H, T716I, S982A, D1118H mutations. Q27Stop mutation in ORF 8 was detected in 3 out of these 4 samples. N501Y and the previously described D614G mutations (14, 15) were detected in all 6 samples ( Table 2) . Frequent whole genome sequencing is critical to monitor mutations in the viral genome. The evolution of highly transmissible strains of SARS-CoV-2 and its global spread underlines the need to remain vigilant and continue practicing necessary social measures to prevent further disease spread.

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted January 29, 2021. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted January 29, 2021. ;

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