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Why were we unprepared for the Omicron variant?

Mario Petrov

The Omicron variant of coronavirus has gradually adapted to human immunity in several regions. Researchers push for better diagnostic surveillance in the Global South.

Berlin.  The Omicron variant of SARS-CoV-2 was first described in South Africa a year ago. In a very short time, it spread across the globe. To date, it is unclear exactly where and when this virus originated. Researchers from Charité – Universitätsmedizin Berlin and Partners for African Cooperation have already shown in a study that the precursors of Omicron existed on the African continent long before it was first discovered. The variant virus appeared gradually over several months in various African countries (Science (2022); online since 1 December).

Since the beginning of the pandemic, the coronavirus has been changing constantly, the University Medical Center Berlin said in a statement. The biggest leap in the evolution of SARS-CoV-2 occurred a year ago, when a variant was discovered that differs from the genetic material of the original virus by more than 50 mutations. First detected in a patient in South Africa in mid-November 2021, the variant, later known as Omicron BA.1, reached 87 countries around the world within weeks. By the end of December 2021, it had displaced the previously dominant delta virus worldwide.

Study disproves previous hypotheses

Since then, there has been speculation about the origin of this rapidly spreading variant. Primarily, two hypotheses are discussed: Either the coronavirus was transmitted from humans to animals and evolved there before re-infecting a human, like Omicron. Or the virus survived in a human with a suppressed immune system for a longer period of time and mutated there. A new analysis of COVID-19 samples collected in South Africa before Omicron was discovered now refutes both assumptions.

The analysis was carried out by an international research team led by Professor Jan Felix Drexler, a scientist at the Charité Institute for Virology and the German Center for Infection Research (DZIF).  Within the European and Pan-African network, the University of Stellenbosch in South Africa and the Benin Haemorrhagic Fever Reference Laboratory have participated significantly. Scientists first developed a specific PCR test to specifically detect the Omicron BA.1 variant, according to the report. They then applied it to analyze more than 13,000 samples from 22 African countries. The samples were collected between mid-2021 and early 2022. The research team detected viruses with Omicron-specific mutations in 25 people from six different countries who had already contracted COVID-19 in August and September 2021 – two months before the variant was first detected in South Africa.

The BA.1 variant has several precursors

To understand more about the origins of Omicron, the researchers also sequenced the viral genome of about 670 samples. Such sequencing enables the discovery of new mutations and also the detection of unknown viral lineages. The team found several viruses that have various similarities to Omicron but are not identical. “Our data show that Omicron had different precursors that mixed with each other and circulated in Africa at the same time for months,” Drexler explains in the University Medical Center report. “This indicates a gradual evolution of the BA.1 variant, during which the virus adapted better and better to people’s immunity.”

From the PCR data, the researchers also concluded that although Omicron did not originate only in South Africa, it was the first to dominate the infection process there and then spread from south to north across the African continent within a matter of weeks.

“The sudden emergence of Omicron is therefore not due to animal to human transmission, or emergence in an immunosuppressed person, even if this could have further contributed to the evolution of the virus,” Drexler stresses. “The fact that we were surprised by Omicron is instead due to the diagnostic blind spot in large parts of Africa, where probably only a small fraction of SARS-CoV-2 infections have been recorded at all. So the development of Omicron was simply overlooked.”

It is therefore important to significantly strengthen diagnostic surveillance systems on the African continent and in comparable regions of the Global South and to facilitate data sharing globally. Only good data can prevent potentially effective restrictive measures, such as travel restrictions, from being taken at inopportune times and thus causing more economic and social damage than good.

Source:

  • Ärzte Zeitung

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