Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains in Bangladesh

Abstract

Here, we report the coding-complete genome sequences of 40 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains of the newly emerged recombinant Omicron variants XBB, XBB.1, and XBB.2. The strains were isolated from nasopharyngeal swab samples that had been collected from symptomatic patients in Bangladesh between September and October 2022 and were sequenced using an Oxford Nanopore Technologies (ONT) system.

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

“…OQ075381) or XBB.2 variant (accession no. OQ075400) (Habib et al 2023). Interestingly, we also recently pinpointed round 400 147 RWMD spike insertion mutants in US patients (Chakraborty, 2023a).…”

The severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) omicron sub-variants in Bangladesh cause mild COVID-19 and associate with similar antibody responses irrespective of natural infection or vaccination history

“…Although there are gaps in our survey between June 17 and July 28, 2022, we assume that XBB emerged in Bangladesh during July 2022, indicating approximately two months prior to the XBB omicron infections reported in India and Singapore [ 23 ] and the 40 SARS CoV-2 omicron XBB variants isolated between September and October 2022 in Bangladesh [ 28 ]. The XBB.1 mutant EPI_ISL_17268137 carrying L368I and missing F486P mutation and the rare omicron sequence patterns of CJ.1 EPI_ISL_17268138, BL.1/BA.2.75.1 EPI_ISL_17268140 and the BA.5.2.26 EPI_ISL_17268139 all associated with mild COVID-19 symptoms, predominantly body ache and loss of smell.…”

Emergence of SARS-CoV-2 Omicron sub-lineage JN.1 in Bangladesh

“…Bangladesh reported the first confirmed case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on 8 March 2020, and as of 3 February 2024, the country reported 2 million COVID-19 (coronavirus disease 2019) confirmed cases ( 1 ). Between October 2022 and May 2023, the circulating strains were Omicron sub-lineages, XBB.1.16, XBB.2.3, FL.4 (alias of XBB.1.9.1.4), and XBB.3 ( 2 ). After the emergence and rapid spread of JN.1 in different countries, WHO classified it as a Variant of Interest on 20 December 2023 ( 3 ).…”