The Omicron variant of COVID 19 has made landfall in Uganda.
The highly contagious variant was first discovered in southern Africa and has led to a reinstatement of multiple travel bans against some African countries.
Uganda currently has 127,655 cumulative COVID 19 infections with only 115 cases in hospitals countrywide
When was omicron first identified?
It was first detected on 23 November in South Africa using samples taken between 14 and 16 November. Joe Phaahla, South Africa’s health minister, said on 25 November that he believes the variant is behind an exponential daily rise in covid-19 cases across the country in recent days. The same day, the UK Health Security Agency (HSA) designated it a variant under investigation, triggering travel restrictions for people travelling to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. The World Health Organization had listed B.1.1.529 as a variant under monitoring, but its Technical Advisory Group on SARS-CoV-2 Virus Evolution decided on 26 November to class it as a variant of concern. The WHO has now named it omicron after the Greek letter.
What is happening in South Africa?
National daily cases have gone from 274 on 11 November to 1000 a fortnight later. While the rate of growth has been fast, absolute numbers are still relatively low compared with the UK, which saw 50,000 cases on 26 November. More than 80 per cent of South Africa’s cases are currently in the country’s Gauteng province. All of the 77 cases sequenced in the province between 12 and 20 November were identified as being caused by the variant. The estimated reproduction number, the average number of people that an individual is likely to infect, is almost 2 in Gauteng compared with nearly 1.5 nationally.
What do B.1.1.529’s mutations tell us?
What the mutations mean is currently theoretical and based on the experience of past mutations of SARS-CoV-2 rather than lab tests. Wendy Barclay at Imperial College London says “we don’t really know” if it will reduce the effectiveness of vaccines. Nonetheless, she adds that, in theory, the number of changes across the antigenic sites on the variant’s spike means the effectiveness of antibodies produced by covid-19 vaccines would be compromised.
Mutations on a part of the virus known as the furin cleavage site are similar to those seen in the alpha and delta variants, which could help the variant spread more easily. Barclay says “it’s very biologically plausible” that B.1.1.529 has greater transmissibility than delta.
The mutations also mean that the new variant is likely to be more resistant to antibody treatments such as those developed by Regeneron, which have been shown to save lives. “That is really a cause for concern,” says Barclay. One small bright spot is that, to date, there are no signs that the variant causes more severe disease.
How far has it spread?
Genomic sequencing has found the variant in South Africa, Botswana and Hong Kong. There are also reported cases in Israel, apparently originating from a traveller from Malawi, and in Belgium, from someone who had travelled from Egypt. UK health secretary Sajid Javid said it is “highly likely” that the variant has spread to other countries. As of 27 November, two cases had been detected in the UK, where about a fifth of positive cases are sent for genomic sequencing. Even in countries with low levels of sequencing, it may be possible to get early warning signs, because the variant is linked to a mutation called S-gene dropout, which is picked up by PCR tests, says Jeffrey Barrett at the Wellcome Sanger Institute in Hinxton, UK.