Expert comment – Earlier origin of Omicron SARS-CoV-2 variant across Africa

Dr Matthew Chico, Associate Professor of Public Health at LSHTM, comments on new research revealing insights into the evolutionary origin of Omicron in patients across Africa
Matthew Chico quote card

Genetic ancestors of the Omicron (BA.1) variant of SARS-CoV-2 may have existed in several African countries several months before Omicron was first detected on the continent, according to a new paper published in Science.

Please note: this Science paper has since been retracted. Read the full retraction notice here.

These findings — revealed through the analysis of samples from over 13,000 patients with COVID-19 from 22 countries in Africa between mid-2021 and early 2022 — could improve our understanding of the gradual evolution of the variant and public health responses to future mutations.

Dr Matthew Chico and co-author of the study said:

“It was 24 November 2021, one year ago, when officials from South Africa first reported the presence of a new SARS-CoV-2 variant 'Omicron', which was declared ‘variant of concern’ by the World Health Organization two days later. In response, several governments prohibited international travel to and from South Africa, and seven other sub-Saharan countries, as Omicron cases spread exponentially around the world. 

“In the months that followed, scientists from over 40 institutions throughout Africa and with links to Africa worked together on a retrospective analysis of samples initially between mid-2021 to early 2022 from 22 African countries.  We used real-time polymerase chain reaction [PCR] methods on over 13,000 COVID-19 samples and found that genetically diverse Omicron ancestors already existed across Africa by August 2021, months before Omicron dominated transmission in the region. These results suggest that travel bans are unlikely to have a public health impact in the face of undetected and widespread infection.

“Our study does have limitations. We relied on convenience sampling driven by the availability of samples from COVID-19 patients in sub-Saharan Africa. Consequently, it is more difficult to make definitive statements about the frequency of the Omicron variant in the SARS-CoV-2 population at specific times and locations.  However, we can now be sure that Omicron ancestors were circulating across Africa by August 2021, well before public awareness and travel bans were introduced.

“Travel bans are blunt tools in pandemic response. Evidence to support them needs to come from ongoing surveillance and continuous sharing of genetic sequencing data so that variant-spread can be tracked in real-time.  It is the only way to know if the proverbial horse has already left the barn. Perhaps more importantly, travel bans imposed without a grounding in empirical evidence can have the unintended effect of curbing willingness to share data across borders. Reluctance to share data will leave all of us more vulnerable to future outbreaks.  However, we do have a historic opportunity.  The COVID-19 pandemic has enhanced laboratory capacities throughout the world, particularly in low- and middle-income countries.  We need to build on these investments and integrate new laboratory infrastructure into existing networks of regional disease surveillance.”

Update: A line about the retraction of this paper was added to this page on 21/12/2022.

Short courses

LSHTM's short and specifically designed courses provide the opportunity for intensive study in specialised topics.

These courses enable participants to refresh their skills and keep up to date with the latest research and knowledge in public and global health.