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Harvard-Affiliated Lab Is First to Discover Omicron Variant

Harvard's T.H. Chan School of Public Health partnered with Botswana's Ministry of Health and Wellness to found the Botswana-Harvard AIDS Institute Partnership in 1996.
Harvard's T.H. Chan School of Public Health partnered with Botswana's Ministry of Health and Wellness to found the Botswana-Harvard AIDS Institute Partnership in 1996. By Zing Gee
By Sophia C. Scott and Dekyi T. Tsotsong, Crimson Staff Writers

The Omicron variant — a new strain of Covid-19 — was first discovered by researchers at the Botswana-Harvard AIDS Institute Partnership on Nov. 19.

The Botswana-Harvard AIDS Institute Partnership was founded in 1996, and aims to promote collaborative research between the Harvard T.H. Chan School of Public Health and the Botswana’s Ministry of Health and Wellness, along with the training of health care professionals.

Sikhulile Moyo, the laboratory director for the lab in Gaborone, Botswana and the first scientist to discover the Omicron variant, said in a Dec. 3 press conference that the hypothesis around where the variant originated is “not very clear.”

“We are still trying to understand how so many mutations arose for Omicron in such a short period of time,” he said.

Roger L. Shapiro, a professor at the School of Public Health and chair of the board of directors of the Botswana-Harvard AIDS Institute Partnership, said during the press conference that the lab’s discovery of the Omicron variant was “not accidental.” He credited it to the lab’s partnership with the Botswana government and the country’s Covid-19 task force.

“Dr. Moyo has worked to continuously sequence the SARS-CoV-2 viruses that have been identified by our laboratory,” Shapiro said. “His team at [the Botswana-Harvard Partnership] has sequenced over 2,300 viruses, and is currently working to do many more.”

Four days after they uploaded a genomic sequence of the variant to the GISAID public database, other countries such as South Africa quickly identified the same mutations.

Moyo said though South Africa and Hong Kong also “detected” the mutated sequence, Botswana was the first to “deposit” it.

Simani Gaseitsiwe, the deputy laboratory director at the Botswana-Harvard Partnership, said in an interview that the lab aims to answer more questions about the “severity” of the virus and whether antibodies from patients with the Omicron variant are able to “neutralize the previous variant.”

“We’re trying to plan to start a cohort that would now follow up some of the patients who are infected with the variants,” he said. “There is a lot of interest to figure out exactly what is the impact of this highly mutated virus.”

Three days after the lab uploaded the sequence to the database, informing other countries about the discovery of a new variant, the United States instituted a travel ban to eight countries, including Botswana and South Africa.

Shahin Lockman, an associate professor at the School of Public Health and a clinical researcher at the Botswana-Harvard Partnership, said she worries that the travel bans imposed by Western countries are “counterproductive” and will disincentivize lower-income countries like Botswana from sequencing viral genomes to detect mutations in the virus.

“I trust that these scientists who were transparent this time would be transparent again next time, but that’s not always going to be true,” Lockman said. “There is only disincentive to share information if this is the consequence.”

Gaseitsiwe said the ban “seems a bit excessive.”

“Responses like these, they almost seem to make countries to be independent, isolated entities,” he said. “That decision will obviously have some negative impact.”

Lockman highlighted the importance of transparency in variant reporting and identification from scientists around the world.

“As a global community, it behooves us to support science and scientists in a sustainable and collaborative way in Africa and throughout the globe,” she said. “It’s kind of a win-win for everybody, and I’m very proud of our colleagues in Botswana.”

—Staff writer Dekyi T. Tsotsong can be reached at

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