BW.1 – New Omicron Subspecies Escapes Immunity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), continues to evolve through genomic mutation. Emerging SARS-CoV-2 variants are classified as variants of interest (VOI) and variants of concern based on their infectivity, pathogenicity, and ability to evade immune responses induced by both natural infection and vaccination. (VOC).

study: SARS-CoV-2 BW.1, a fast-growing Omicron subspecies in southeastern Mexico with an associated escape mutationImage credit: Ebrahim Lotfi /


The SARS-CoV-2 Omicron variant is now prevalent in most countries of the world. The constant genomic variation of Omicron variants has led to the emergence of several subvariants, highlighting the importance of regular genomic surveillance.

New research published in research plaza A preprint server* reports the presence of mutations that aid in immune escape in the BW.1 (BA. strain, a subvariant of Omicron, descended from the BA.5.6.2 lineage.

SARS-CoV-2 BW.1 contains mutations similar to BQ.1 variants that aid immune escape. BQ.1 is one of the most rapidly propagating lineages and contains several mutations such as S:K444T, S:L452R, S:N460K and S:F486V.

In the current study, the authors believe that BW.1 may have emerged in Mexico in early July. By October, BW.1 was the predominant circulating strain on the Yucatan Peninsula.

Mexico is an important Latin American country that has extensively sequenced the SARS-CoV-2 genome. Previous studies have reported that the Yucatán Peninsula is one of the major entry routes for SARS-CoV-2 variants in Mexico due to its very high rate of tourist influx and commercial activity.

About research

The genome sequences and associated metadata for BQ.1, BA.5.6.2 and BW.1 were obtained from GISAID. All relevant genome sequences were collected on 7 November 2022, including PANGO v.4.1.3 of the phylogenetic information base.

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Genomic alignment and phylogenetic rearrangement analysis of BW.1 and its parental variant BA.5.6.2 were performed using multiple sequence alignment (MSA) in Nextstrain’s default pipeline. Genomic alignments helped detect mutations in BW.1, and phylogenetic reconstruction allowed tracing back to its origin.

Main findings

Although Mexico is currently in a phase of low COVID-19 incidence after a wave of BA.2/BA.5, genomic analysis of samples collected from Yucatán Island over the past few weeks revealed a large number of BW.1 variants. prevalence was shown.

Interestingly, researchers observed a spike in COVID-19 cases on the Yucatan Peninsula in October. During this period, the BW.1 variant defeated other SARS-CoV-2 variants present in the region, including its parent variant.

Genome analysis suggests that BW.1 may originate in Mexico during the 5th epidemiological wave and may be derived from the BA.5.6.2 strain reported to be circulating in Yucatán during that period. strongly indicated. Interestingly, out of a total of 105 his BW.1 genome sequences collected from the GISAID database, 95 were collected in Mexico.

Two synonymous substitutions in BW.1 are traced to the Mexican sequence in the BA.5.6.2 genome. Only two of his mutations were detected that distinguish his BA.5.6.2 in Mexico from his Omicron strains found elsewhere in the world. A nucleotide transition, T7666C, present in 2,458 sequences worldwide and present in 82.48% of all BA.5.6.2 sequences, was absent in the Mexican BA.5.6.2 genome, including BW.1.

Analysis of the Mexican genome sequence revealed that the BA.5.6.2 and BW.1 sequences shared the synonymous substitution C14599T. It was present in only 4% of his BA.5.6.2 sequences worldwide.

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Most of the BW.1 genomic sequence differed from the parental BA.5.6.2 by two point mutations. The presence of nucleotide transition G2144A and transversion T22942G was observed in 98.09% and 92.38% of the BW.1 genome, respectively. Notably, the parental BA.5.6.2 group did not contain the T22942G mutation. It was first detected in his BW.1 strain sequenced in Mexico in early August.

The BW.1 variant is descended from the omicron lineage BA.5.6, but its genome shares a common evolutionary history with the BQ.x variant. This is because both BW.1 and BQ.x are derived from his BA.5 lineage.

Both of these subvariants inherit more than 54 mutations, including S:L452R, associated with increased infectivity, conferring spike stability, and promoting viral fusion. It also contains the S:F486V mutation associated with reduced efficacy of multiple monoclonal antibodies.

Both BQ.1 and BW.1 variants contain important additional BD mutations, such as S:K444T and S:N460K, which increase viral resistance to bebuterobimab, interfere with antibody recognition, and enables immune escape by The presence of the S:N460K mutation increases fusogenicity and resistance to neutralization.


The authors of the current study emphasized the importance of genomic surveillance and mutation tracking that could shed light on identifying SARS-CoV-2 strains that adversely affect the global population. The BW.1 strain is likely to increase COVID-19 cases worldwide.

*Important Notices

Research Square publishes non-peer-reviewed, preliminary scientific reports and should not be taken as conclusive, to guide clinical practice/health-related actions, or to be treated as established information. .

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