Nine more cases of the Omicron variant of the coronavirus have been detected in Bangladesh, taking the total confirmed tally to 64 till Thursday, according to GISAID, the global database for genomic data on the coronavirus.
The 9 latest cases were detected at the virology lab of the International Centre for Diarrhoeal Disease Research, Bangladesh, or ICDDR, B. The lab has already shared the report with GISAID.
Earlier, twenty-two more Omicron cases were revealed to have been identified in the country on January 17, that had taken the number of Omicron cases confirmed, through highly time-consuming and scarcely available genomic sequencing, to 55.
The country reported its first two cases of the Omicron variant last December 11, in two members of the Bangladesh women’s cricket team that had been forced to return early from the ICC Women’s World Cup qualifiers in Zimbabwe, deep in southern Africa where the most transmissible variant of SARS COV-2 till now is believed to have originated. Doctors in South Africa, the continent’s most developed country, were the first to alert the world of this new variant.
The number of cases being logged in Bangladesh of the variant could be of merely academic value, since the spread is suspected to have reached a far, far bigger number among the population by now. Genomic sequencing simply cannot keep up with the pace of the virus. In most countries, the R value of the variant – how many people an infected person goes on to infect on average- has been found to be twice or even thrice that of Delta. That presents an even greater challenge to identifying Omicron through genomic sequencing.
Most other countries are using or have stepped up use of a stroke of good fortune that actually allows for Omicron detection through the RT-PCR test itself with a very high degree of accuracy. Known as the ‘S’ Gene Target Failure or SGTF, it can save the authorities much time in identifying whether the wave Bangladesh is experiencing at the moment is driven by Delta or Omicron.
The standard RT-PCR test for Covid-19, since the start of the pandemic, has relied on detecting viral genes in nasopharyngeal samples. Some of the genes the test is optimised to seek out are the ‘S’ Gene (i.e. the Spike protein, that protruding bit on the virus surface that has become its most recognisable and targeted bit), ORF, the ‘N’ gene, Rdrp, and the ‘E’ gene. The first three are the most common.
Now due to the extensive number of mutations that have occurred on the Spike protein as it presents itself in the Omicron variant, the RT-PCR tests are failing to detect it. However the presence of ORF and N can still pretty much tell you that it is SAR COV-2 with a high confidence interval. Hence testing a sample where the others are present, in particular ORF and N, but Spike or S is missing, indicates that the test result is not only positive for COVID-19, but also that the patient has caught the Omicron variant.
Almost all countries in the world are making use of this technique for fast detection, and following up with genome sequencing to confirm. In Bangladesh, BSMMU Vice Chancellor Prof Md Sharfuddin Ahmed was probably the first to make any mention of a variation to the technique that BSMMU were starting to use, but it was mostly in passing and hardly got any attention.
The method has caught on very fast in India. Krishna Khairnar, one of the country’s key researchers in COVID-19 diagnostics, explained in an interview with the Press Trust of India recently: “The occurrence is called as ‘S’ Gene Target Failure (SGTF) positive cases. Such samples can be presumptively reported as Omicron positive and can be sent for fast-track genome sequencing for confirmation.”
The SGTF strategy will work as a kind of early detection at RT-PCR stage, and will help in screening COVID-19 positive samples of Omicron variant, he told the state-owned news agency.
The body that is tasked with advising the government on the technical side of policies that may be adopted to best tackle the pandemic is the National Technical Advisory Committee (NTAC) on Covid-19.
A look through its post-meeting bulletins sent out to media outlets over the past month reveals no mention of SGTF or anything like it.
