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20 JAN 2022
Key Messages
Variants of Concern (VOC)
SARS-CoV-2 changes over time, and when it can survive better than the original virus, it becomes VOC. Several VOCs have emerged and spread globally last year. The Omicron is the latest edition and has already spread to more than 100 countries, including Bangladesh. This variant is considered to have increased transmissibility and harbour new genetic changes, which may impact clinical manifestation and vaccine effectiveness. As part of the countrywide COVID-19 laboratory network, the Virology Laboratory of icddr,b has been testing COVID-19 since March 2020 and monitoring SARS-CoV-2 variants since December 2020.Â
How we track variants
Between 1 January 2021 and 14 January 2022, a total of 63,922 samples collected from COVID-19 suspected patients attending different collection booths across Dhaka city, were sent to the Virology Laboratory of icddr,b as part of the national COVID-19 testing system. The specimens were tested daily for the SARS-CoV-2 RNA using real-time PCR. Overall, 13,413 (21%) specimens were COVID-19 positive. A subset of positive samples having CT values <30 (n=1,259) were screened for variants until November 2021 by different techniques: (a) sequencing spike gene by the Sanger method; (b) complete sequencing by the Nanopore (MinION); and (c) complete sequencing by the Illumina (MiSeq).Â
However, from December 2021, due to the emergence of the Omicron variant, we tested all samples (n=456) using Real-time PCR targeting spike gene mutation by the Taqpath PCR.
Omicron variant screening by the Thermo Fisher’s TaqPath PCR
The TaqPath PCR targets three genes (ORF1a/b, Nucleoprotein, and Spike) of the SARS-CoV-2 genome, and all three targets need to be positive for most of the variants; however, the spike gene becomes negative for the Omicron variant. Therefore, theTaqPath PCR can be deployed for the identification of the Omicron variant. World Health Organisation (WHO) has endorsed this simple test as the best-positioned diagnostic for screening potential cases of Omicron.
We reconfirmed the TaqPath PCR-based potential Omicron samples by conducting complete genome sequencing of >10% randomly selected sub-samples (n=41) in our lab. All 41 were confirmed as Omicron with sequence based variant detection. We randomly selected 101 of the “Non-Omicron positive by TaqPath PCR” from the total 191 such positive samples and 99 of those were confirmed as Delta and 2 Omicron by sequencing. We concluded that the WHO-recommended TaqPath PCR method to identify the Omicron variant was 98.6% sensitive and 100% specific (estimates weighted for sampling). All 43 Omicron variant and 99 Delta variant cases confirmed by complete sequencing were submitted to GISAID.ORG.
Summary of variants of concern tracked in Bangladesh
The emergence of the Omicron variant
We interviewed 29 Omicron infected patients over the phone and found the following information:
Phylogenetic analysis of Omicron variants in Bangladesh
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What should be done to keep safe from COVID-19Â
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MMR