When the Botswanan scientists saw the sequences, they were stunned.
Four international travelers had tested positive for COVID-19 on Nov. 11, four days after entering the country. But when the cases were genetically sequenced, where the genetic code of the virus is analyzed to look for worrying changes, the scientists discovered a variant they had never encountered before.
And soon, they alerted the world to what would become known as the omicron variant.
The team in Botswana was headed by Sikhulile Moyo, the laboratory director at the Botswana-Harvard AIDS Institute Partnership and a research associate with the Harvard T.H. Chan School of Public Health. Moyo is quick to give credit to his entire team, and to scientists working simultaneously on similarly alarming sequences in South Africa, for the discovery of omicron.
He spoke with NPR about the identification of the new variant, travel bans, what southern Africa needs from the rest of the world and what may come next. This interview has been edited for length and clarity.
When did you first suspect you might be dealing with a new variant? How long did it take for you to get concerned?
When we looked at it, we compared it with other sequences circulating in Botswana, and we realized this is an unusual pattern of mutations. The number of mutations that it had was just unbelievable.
We immediately alerted the Minister of Health on Monday, [Nov.] 22. We searched the databases as well, and we realized it was not [previously] seen in Africa. The closest that could be seen as a lineage was called B.1.1.207, which was a lineage common in United Arab Emirates. We got concerned because when we inquired to the Department of Health, we got notice that these individuals were traveling together.
Other groups [in South Africa] were also sequencing [samples] at the same time. On Tuesday, they saw that we had deposited some sequences [in a regional database] that looked similar to them. So, on the 23rd, we loaded our sequences to the public database.
On the 24th, South Africa went ahead and reported to the WHO, and on the 26th the WHO convened a meeting, and it was called a variant of concern.
Botswana and South Africa alerted the world to this variant, but it was found among travelers who reportedly flew in from Europe. And it was subsequently found that the variant was reported in the Netherlands a week before the announcement from Africa. How do you feel about the world reacting by banning travelers from southern Africa?
We were saddened. For me, personally, I felt that after two years into the epidemic, clearly as the global health community, we could be responding better and coordinating better.
How do you reward the countries that alert you of a potential dangerous pathogen with travel bans? My country was put on a red list, and I didn't feel good about that.
We know the repercussions. Flights were canceled, goods were not coming into the country, a lot of businesses lost millions. And our vaccine supply was being threatened because of delays on the way. Quite a trail of destruction.
So it was a roller coaster for us. On the one extreme, we felt [we were] contributing to the world in a small way. And on the other end, we felt, is that how you reward scientists or scientific progression?
What's the reaction been within Botswana?
A number of people are saying, "you scientists, you bigmouths, look what you've done. You've locked out Christmas."
Was the African ban outright racism?
I would call it an unfair treatment of African countries.
The alpha variant was raging in the U.K. [months ago], and none of the countries put the U.K. on the red list. Because we understand that it's a global village. Of course, we enhanced border screening, enhanced requirements for entering into the country, including maybe a quarantine and testing. But it was never shutting our door, because we understand that these viruses don't respect our natural borders.
What does Botswana want and need from the rest of the world? Is it vaccines? Is it better sequencing support? All of the above and more?
Other countries are going into boosters, and we are still struggling to reach all our population. We still have to vaccinate a large segment of our population. The government of Botswana has been very proactive in reaching out to other countries for procuring [vaccines]. But sometimes the delays are beyond whether you have the money to buy or not.
The health-care system [in Botswana during the pandemic] has been battered, and strengthening the health-care system, making sure that we have adequate resources in case we enter into a serious time, [will be important]. Right now, the infections have jumped. Every day, we have about two to three times more infections than we've seen the previous day. [Note: The average daily count is 298 new cases.]
But most important, we need to make sure that we more than multiply our sequencing capacity by 10 times.
How much sequencing are you able to do now?
The kind of resources we have are just a tiny drop in the ocean as compared to other countries in terms of sequencing capacity and sequencing strength. The U.K. generally can sequence more than 500 times the sequences we can generate in Botswana in a day.
As African scientists, we've come together and formed the Pathogen Genomics Initiative and the Africa CDC. We are using our little resources to make sure that countries are trained. The investment in HIV really helped us to be where we are. Because it was easy to come from HIV to do COVID sequencing.
We came up with a genomic surveillance plan which was very intentional. This is the reason why we were able to catch [the variant]. It's not luck. It's because we were able to implement some level of surveillance — very small surveillance, very few samples — but randomly selected and very representative of the entire country.
There are theories the omicron variant could have developed in an immune-suppressed patient over several months. Do you agree? And if there is any possibility that it could be true, what does that tell us about failure to diagnose and treat people with illnesses like HIV?
It's just a hypothesis. One study in South Africa recognized that an individual with uncontrolled HIV infection developed quite a number of [COVID] mutations. And that's what is supporting the hypothesis around immune-compromised [individuals].
One of the successes of Botswana is that they've been able to take care of the population in terms of HIV. You are trying to reach the last mile, maybe less than 5% of the people who are living with HIV but do not know their status.
If we prioritize in those areas, we vaccinate as many people as possible [against COVID], then we are making them less likely to die from either of the diseases.
What's your reaction to the unequal distribution of vaccines?
Just look at the statistics, you will be shocked. Look at Guinea, Guinea has 6.2%. Libya, 11%. Ghana, 2.7%. Kenya, less than 10%. You're talking about so many people not vaccinated.
How do we explain in a global village that it matters for an ordinary U.S. citizen that someone in Ethiopia or someone in Guinea is vaccinated? Why does it matter? The story of variants and the movement of variants is one story that tells us that it matters because we are a connected world.
So what's the story to tell?
We have a significant part of the world that is less than 20% vaccinated. If we increase vaccination in those countries, we are going to reduce the chances of this virus — giving it room to circulate in other parts of the world and generate more mutants.
I have one last question for you: Where do you think we will be one year from now?
If we really do our best and cover the world, I think we can win it together. But if we try and do our own corners and not take care of what's happening in other countries, I think we'll still have another two, three years of this pandemic.
Melody Schreiber (@m_scribe) is a journalist and the editor of What We Didn't Expect: Personal Stories About Premature Birth.