Understanding the global Omicron threat

On Wednesday, the World Health Organization (WHO) said that preliminary evidence appears to indicate that vaccines may be less effective against infection and transmission linked to the Omicron variant of Sars-CoV-2, which also carries a “higher risk of re-infection”
A man wears a face mask as he walks past an image of Santa Claus at a Christmas market, in London(AP)
A man wears a face mask as he walks past an image of Santa Claus at a Christmas market, in London(AP)
Updated on Dec 17, 2021 06:46 AM IST
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By, Hindustan Times, New Delhi

On Wednesday, the World Health Organization (WHO) said that preliminary evidence appears to indicate that vaccines may be less effective against infection and transmission linked to the Omicron variant of Sars-CoV-2, which also carries a “higher risk of re-infection”. According to data compiled by GISAID, a global science initiative that provides open-access to genomic data of influenza viruses, a total of 60 countries have so far submitted to it sequencing data that shows the presence of this highly mutated variant on their shores.

With its ability to evade vaccines and higher transmissibility, the new variant has sparked concerns that it could drag the fight against the pandemic back several months.

The expanding global spread of Omicron

To be sure, the Delta variant still easily remains the world’s most dominant variant, accounting for 97.9% of the nearly 3.17 million genome sequences uploaded in the four weeks ending December 13 to GISAID.
To be sure, the Delta variant still easily remains the world’s most dominant variant, accounting for 97.9% of the nearly 3.17 million genome sequences uploaded in the four weeks ending December 13 to GISAID.

Of the 60 countries that have confirmed Omicron infections to GISAID, the United Kingdom has the largest share with 4,120 confirmed sequences of the variant till December 13, the latest date for which this information is available. It is followed by South Africa with 1,000 samples, the United States with 321 samples, Denmark with 216, and Switzerland with 125.

A better picture is provided by looking at the share of Omicron in all cases in these countries in this period. South Africa, unsurprisingly, with 90.1% of all infections being Omicron features among the top, closely behind Mozambique where the heavily mutated variant constituted 94.4% of all samples sequenced.

To be sure, the Delta variant still easily remains the world’s most dominant variant, accounting for 97.9% of the nearly 3.17 million genome sequences uploaded in the four weeks ending December 13 to GISAID. But the real cause of worry is that despite Omicron barely being flagged in even half GISAID’s 60-day sample period, it has already outstripped the combined proportion of the Alpha, Beta and Gamma variants. A total of 6,700 samples – about 2.1% – were Omicron and the other three variants of concern together numbered 22, less than 0.01% each in GISAID’s database.

A week ago, Delta’s share was 99.2% while Omicron’s share was 0.4% in the same database.

Regions where the new variant is taking hold are not faring well

A key characteristic of Omicron that has been observed is that it can lead to a massive spike in new cases. For instance, in South Africa, on average, there have been 22,852 new Covid-19 cases every day in the past week – far surpassing the previous peak of 19,766 cases a day in the first week of July this year.

South Africa, however, is far from being the only that has seen a record spike at the same time that Omicron infections have seen a spike.
South Africa, however, is far from being the only that has seen a record spike at the same time that Omicron infections have seen a spike.

South Africa, however, is far from being the only that has seen a record spike at the same time that Omicron infections have seen a spike. On Wednesday, the United Kingdom recorded 78,610 new Covid-19 cases — the highest in a single day since the start of the pandemic. This has pushed the seven-day average of daily infections to 57,417 – just below the peak of 59,508 touched on January 8.

Similar peaks can be seen even in smaller countries such as Norway and South Korea where the share of Omicron cases in the overall new infection tally has been rising in recent days. In each of these countries, the seven-day average of daily infections is currently at the highest ever , according to data gathered by Our World in Data. In Norway, there has been an average of 4,925 new cases a day in the past week, while in South Korea this number is 6,790.

The corresponding charts also show that the share of Omicron cases have been increasing at the same time in these countries.

Omicron appears to be single-handedly capable of pushing new waves

In London, the prevalence for Omicron cases (those with S-gene dropout) has been steadily rising. In the past week, 38.4% of all infections in the British capital have been Omicron cases.
In London, the prevalence for Omicron cases (those with S-gene dropout) has been steadily rising. In the past week, 38.4% of all infections in the British capital have been Omicron cases.

To truly understand the impact that Omicron can have on the outbreak in a region, it is crucial to look at how these infections are changing the outlook of the Covid wave. Very few countries (or even localised regions) consistently release data on the spread of particular variant. This exercise is generally done so by extrapolating genome sequencing data on the overall case turnout. This system is utilised by agencies such as the US’ Centers for Disease Control and Prevention to determine a prevalence of a variant — on Wednesday, it estimated that 2.9% of new Covid cases emerging in America were Omicron.

However, one advantage that Omicron’s heavily mutated nature offers is that in a widely used RT-PCR test, one of the three target genes is not detected (called S-gene dropout) and this can therefore be used as marker for this variant, while sequencing is awaited. Using this approach, some regions have been tracking this variant at near real-time, offering early clues on how prevalent it is.

In London, the prevalence for Omicron cases (those with S-gene dropout) has been steadily rising. In the past week, 38.4% of all infections in the British capital have been Omicron cases. But what is even more alarming is that on a daily level, this proportion is rising fast — on December 12 (latest date for which data is available) 1,669 of the city’s 2,779 Covid cases were Omicron (60.1%), according to data released by the UK Health Security Agency. Similarly, this proportion is also rising in Denmark (the only other major region which is currently publicly releasing S-gene dropout data). In just 10 days between December 1 and December 11, daily Omicron proportion has gone from 1.6% to 15.6%, data shows.

In both these regions, a worrying trend is that Omicron appears to be the cause of the spike in new infections as the new cases of the other variants appear to be stagnant.

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  • ABOUT THE AUTHOR

    Jamie Mullick works as a chief content producer at Hindustan Times. He uses data and graphics to tell his stories.

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