SARS-CoV-2 variants in Dhaka city: Emergence of the Omicron

20 JAN 2022

Key Messages

• The Omicron variant was first detected in Bangladesh on 6 December 2021.
• In December 2021, the Omicron was detected in 5 out of 77 COVID-19 positive cases of Dhaka city tested in icddr,b lab. Others were Delta variant.
• During the first two weeks of January 2022, the Omicron was identified in 260 (69%) out of 379 samples positive for COVID-19 in icddr,b lab from samples received from Dhaka City.
• Complete sequencing analysis suggests that at least three different sub-types of the Omicron variant have been circulating in Dhaka.

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. 

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). 

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 Alpha variant was first identified in January 2021 and persisted till March 2021. 
• The Beta variant was first detected in March 2021 and replaced almost all other variants by May 2021. 
• The Delta variant was first identified in May 2021 and became the most dominant variant by replacing all other variants by June 2021. 
• Finally, Omicron arrived in Dhaka in December 2021 and has since emerged as the fastest growing variant since December 2021 and has become the most predominant variant in Dhaka city in a short period of time (figure below).

The emergence of the Omicron variant

• The Omicron variant in Bangladesh was first identified on 6 December 2021. The initial two Omicron cases were actually carried by two passengers who had returned from Africa.
• In December 2021, Omicron was detected in 5 out of 77 COVID-19 positive cases of Dhaka city tested by the TaqPath PCR in icddr,b lab. Others were Delta variant. (please see below Table)
• During the first two weeks of January 2022, Omicron was identified in 260 (69%) out of 379 of the samples positive for COVID-19.
• Median age of Omicron infected patients (33.5 years) was less than those infected by Delta (40 years).

We interviewed 29 Omicron infected patients over the phone and found the following information:

• Male 13, Female 16
• 27 patients had mild or no symptoms
• 24 of them had received 2 doses of vaccine, 3 had received only 1 dose.
• Only 1 was hospitalized for 1 day.
• None had travelled abroad, except one came from Saudi Arabia.

Phylogenetic analysis of Omicron variants in Bangladesh

• As of 20 January 2022, a total of 63 Omicron variants have been reported from Bangladesh to the GISAID database. 52 of those are from Dhaka city, 8 from Chattogram, and 3 from Jessore.
• Complete genomic analysis of Omicron variants reported from Bangladesh suggests that at least three introductions of Omicron variant happened in Bangladesh with African, Euro-American, and Asia Pacific origin.

 

What should be done to keep safe from COVID-19 

• Vaccination is key, get vaccinated.
• Keep wearing well-fitted facemask, maintain physical distancing, even though vaccinated or naturally infected.
• Wash hands with soap and water frequently.

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