A report by scientists at Botswana Harvard Aids Institute Partnership (BHP) and their South African counterparts suggests that omicron coronavirus variant was already spreading before it was officially identified in the two countries.
The report a copy of which has been seen by Sunday Standard also states that Botswana had coronavirus under control but failed to contain the spread of the disease when omicron hit the country in November.
The scientists revealed that to determine when and where Omicron likely originated, they analyzed all 686 available Omicron genomes (including 248 from southern Africa and 438 from elsewhere in the world) retrieved from GISAID. GISAID is a global science initiative that provides open access to genome data of influenza viruses among others.
“Spatiotemporal phylogeographer analysis indicates that the BA.1/Omicron variant spread from Gauteng province of South Africa to seven of the eight other provinces and to two region of Botswana from late October to late November 2021, and shows evidence of more recent transmissions within and between South African provinces,” says the report.
The scientists were quick to point out that, “However, this does not imply that Omicron originated in Gauteng and these phylogeographer inferences could change as further genomic data accumulates from other locations.”
Botswana and South Africa had announced that they discovered Omicron mid-November 2021, a month before it was already spreading in October.
According to the report, at the end of November 2021, a big Delta-driven (another coronavirus variant) wave was coming to its end in Botswana and an Omicron wave was starting at the end of November 2021. The report shows that there was a sharp increase in positivity rate mid-November 2021 in Botswana.
By the first week of December 2021, the report says, Omicron was causing a rapid and sustained increase in cases in South Africa and Botswana
“Strong surveillance systems in South Africa and Botswana enabled the identification of Omicron within a week of observing a resurgence in cases in Gauteng Province. Omicron is now driving a fourth wave of the coronavirus epidemic in southern Africa and is spreading rapidly in several other countries,” the report says.
It says “genotypic and phenotypic suggest that Omicron has the capacity for substantial evasion of neutralizing antibody response and modelling suggests that immune evasion could be a major driver of the observed transmission dynamics.”
Vaccination therefore, the report says, remains critical to protect those at highest risk of severe disease and death. “The emergence of and rapid spread of Omicron poses a threat to the world and a particular threat in Africa where fewer than one in ten people are fully vaccinated,” the report warned.
The report says a rapid increase in COVID-19 cases was observed from mid-November 2021 in Gauteng province, the economic hub of South Africa containing the cities of Tshwane (Pretoria) and Johannesburg. Specifically, rising case numbers and test positivity rates were first noticed in Tshwane, initially associated with outbreaks in higher education settings.
On 19 November 2021, sequencing results from a batch of 8SGTF samples collected between November 2021 indicated that all were of a new and genetically-distinct lineage of SARS-COV-2 (COVID-1). Further rapid sequencing identified the same variant in 29 of 32 routine diagnostic samples from multiple locations in Gauteng Province, indicating widespread circulation of this new variant by the second week of November.
Crucially, the report says, this rise immediately preceded a sharp increase in reported case numbers. In the following four days, the presence of this lineage was confirmed by sequencing in another two provinces: Kwazzulu-Natal and the Western Cape.
Concurrently in Gaborone, the report says, Botswana (-360km from Tshwane), four genomes generated from samples collected on 11 November 2021 and sequenced on 17-18 November 2021 as part of weekly surveillance, displayed an unusual set of mutations.
“These were reported to the Botswana Ministry of Health and Wellness on 22 November 2021 as {unusual sequences” that were linked to a group of visitors (non-residents) on a diplomatic mission. The sequences were uploaded to GISAID on 23 November 2021, and it became apparent that they belonged to a new lineage,” the report says. It notes that a further 15 confirmed cases (not epidemiologically linked to the first four) were identified within the same week from various other locations in Botswana. All of these either had travel links from South Africa or were contacts of someone with travel links, the report says.
Noting that Omicron was wreaking havoc in the neighbouring countries in December last year, the report reveals that in Gauteng, weekly test positivity rates increased from +1% in the week beginning 31 October, to 16% in the week beginning 21 November 2021 and 35% in the week beginning November, concurrent with an exponential rise in Covid-19 incidence.
Nationally, daily case numbers exceeded 22 000(84%) of the peak of the previous wave of infections) by 9 December 2021. At the same time the proportion of PCR tests increased rapidly in all provinces of South Africa, reaching(0% nationally by the week beginning 21 November 2021, strongly indicating that the fourth wave was being driven by Omicron: an indication that has now been confirmed by virus genomes sequencing in all provinces.
“Similarly, Botswana experienced a sharp increase in cases, doubling every day 2-3 days late November to early December 2021, transitioning from a 7-day moving average of +10 case/10 000 to above 25 cases/100,000 in less than 10 days,” the report says.
