Pandemic Reads: OMG Omicron!

They wore fluorescent wigs and capes with gold tassels. They arrived in knee-high white platform boots, and with feathered wings affixed to their backs. Dressed like their favorite characters, or just wearing street clothes, they packed into Manhattan’s main convention hall — some 53,000 of them — over three days in November to celebrate their love of Japanese animation shows known as anime.

In the crowd was Peter McGinn, a 30-year-old health care analyst in town from Minneapolis. He attended discussion panels, chatted with strangers about his anime podcast and, at night, sang karaoke with friends. After flying home, he learned that one friend from the convention — an anime fan from North Carolina — had just tested positive for the coronavirus. In the days to come, many more of his friends from the convention would test positive, as well. Coughing and feeling tired, Mr. McGinn also took a test. He had the virus, too.

That was Nov. 23, a day before most scientists had even heard of the new variant that was tearing across southern Africa. The World Health Organization had not yet even given the variant a name — Omicron. But it was already present in the United States, undetected…

Some municipalities, like New York City, and states, like Massachusetts, built out large-scale contact tracing organizations. Most of the U.S. population — 60 percent — is vaccinated. Just a few weeks ago, before Omicron was identified, there was widespread hope that the pandemic, in this country at least, was easing. People felt safe as they flashed their proof of vaccination — at least one dose was required for entry, consistent with the city’s rules — and streamed into the Javits Center for the convention.

But amid tens of thousands of new Delta infections in the United States each day, Omicron’s landfall and spread are easily hidden. Many coronavirus infections are asymptomatic or have only minor symptoms, slipping under the radar.

Indeed, it remains unclear if the anime convention was a super spreader event. “We haven’t found evidence of widespread transmission at the convention,” Adam Shrier, a spokesman for New York City’s contact tracing program, Test and Trace Corps, wrote in an email…

When did you first have a sense of the existence of this new variant?

I am the principal investigator and leader of the Network for Genomic Surveillance in South Africa, which involves seven genomic facilities distributed across the country. There was an uptick of cases in Gauteng Province. It was only a small uptick—we had around two hundred cases in the whole country every day. But they started growing, and so we met with our network and said we needed to understand why they were growing in the province that had the largest previous wave of infections of Delta. That variant was extreme in Gauteng, with somewhere between sixty and eighty per cent of people having gotten infected by COVID, according to serology testing.

So on Friday, November 19th, we decided that we needed to increase genomic surveillance in Gauteng… When I noticed that mutated variant on Tuesday, I phoned the director general of health, and he told me he would set up a meeting with me and the minister of health in thirty-six hours. So we had thirty-six hours to confirm whether it was real. At the same time I wrote to the World Health Organization, because I am a part of the virus-evolution working group. The next morning, we got over a hundred samples from over thirty clinics in Gauteng, and we started genotyping, and we analyzed the mutation of the virus. We linked all the data with the P.C.R. dropout, the increase of cases in South Africa and of the positivity rate, and then we began to see it might be a very suddenly emerging variant. By Thursday morning we got all the genomes back, and they were all the same variant—around a hundred randomly selected samples, from all over Gauteng, in which the same test failed. By then I was confident enough to present the results to our minister of health, and minister of science and innovation, who took the results quite seriously and asked me to talk to the President, Cyril Ramaphosa, at half past 10 A.M., which I did….

Can you talk about the COVID situation in South Africa before this?

I would break it into two periods. The situation in the last month was of minimal infections, about two hundred infections per day with a test-positivity rate of less than one per cent, which means that we had more than enough testing. Some scientists thought we wouldn’t have a fourth wave because we had such a high level of population immunity. So during that moment in the last month, we thought that’s it. We won’t have any more problems with COVID. People were relaxed, thinking that we could go back to normal life. Even my lab was sequencing other pathogens and viruses because that is what we do.

So we were very surprised to see a variant emerge in a place with the highest population immunity in the country. I think that is one of the things that the world doesn’t realize. Some people tried to blame the variant on vaccine hesitancy. We have a problem with that, although potentially not as big a problem as the United States. But people really thought we got out of the woods. Unfortunately, the new variant emerged, and it seems clear that it can reinfect people, which is potentially the last nail in the coffin of herd immunity, which one of your Presidents famously talked about…

How has the vaccination campaign been going in South Africa, and do you connect the new variant to the slow speed at which many countries in Southern Africa began to get vaccinated?

The first thing to understand is that Johannesburg is what Atlanta is to the United States. It is our biggest travel hub. So we have no idea where this variant is from. It could be from South Africa, or it could be from anywhere else in the world or Africa. What we know is that it got amplified in South Africa.

I think it did not help at all South Africa or Africa to have such late access to the vaccines… We also had a massive supply problem until we gave up depending on COVAX from the W.H.O. and started procuring them independently. So they arrived far too late, followed by the third wave of infections. We have about twenty-five per cent of the population fully vaccinated, and that number has increased a lot. But, again, in countries like Botswana, they paid almost double the price for Moderna vaccines they have not yet received. So, in general, Africa got in the back of the queue of the vaccine.

So, I would be very reluctant to blame the problem on vaccine hesitancy, because that’s everywhere in the world…

The evolution of potentially dangerous variants like omicron has been ensured by the wealthy world’s decision not to protect vulnerable populations outside its borders. Put simply, strategies rich countries have implemented to limit the carnage from COVID-19 inside their borders have not been mirrored at a global scale. In European countries, Canada, Japan, and the United States, for example, great pains have been taken to prioritize treatment and vaccination for people with weakened immune systems. But globally, one of the world’s largest concentrations of immunocompromised people—the untreated HIV-positive people of southern Africa—has been all but ignored…

If humanity wanted to give a coronavirus a golden opportunity to circulate, adapt, and evolve inside the bodies of human beings, eventually taking on a form that threatens all—rich and poor alike—it couldn’t do better than to ignore the estimated 38.7 million people living with HIV, especially the roughly 10 million who remain untreated, most of them residing in sub-Saharan Africa. In 2020 it is estimated another 1.5 million people were newly infected with HIV, almost 700,000 of them in eastern and southern Africa. More than 600,000 people died of AIDS-related illnesses around the world in 2020, while international attention was focused on COVID-19.

The great HIV/AIDS pandemic is rarely mentioned these days. Now that very efficient, minimally toxic, and inexpensive treatments are available, along with prophylactic drugs that can block infection altogether, HIV has become the out-of-sight, out-of-mind virus. But it’s far from disappeared…

In the United States, meanwhile, access to testing and treatment for HIV is remarkably lower among African American and Latino men, accounting for their higher death rates due to HIV and possibly some of the racial disparity in COVID-19 mortality. From March to September 2020, in the early months of the COVID-19 pandemic and well before vaccines were available, the number of HIV tests at a single major lab plummeted by more than 600,000, and the number of viral load tests performed to monitor HIV-positive patients’ treatment fell by more than 60,000. Gay men of color were most effected by the downturn in access to HIV testing and treatment in America, according to an October study: “People with HIV in the USA, particularly those with pronounced immunodeficiency, seem to be at elevated risk of COVID-19 hospitalisation and mortality. The exacerbated COVID-19 outcomes in Black or African American and male people with HIV suggest profound health inequities faced during the COVID-19 pandemic.”

A Spanish study also found higher death rates in HIV-positive men in most of 2020. A study from February through June 2020 found that it’s possible HIV-positive Black men in Britain were also more likely in to suffer severe COVID-19 and to die of the disease if infected…

But there are still more than 10 million people in poor countries who carry HIV and either do not know it or refuse to seek care because of the tremendous stigma attached to being HIV-positive. Millions more suffer periodic treatment interruptions due to stock-outs of local drug supplies or their inability to get transport to a clinic or dispensary. Lockdowns and supply chain issues related to the COVID-19 pandemic have severely exacerbated these problems. It is estimated that 296,000 people in sub-Saharan Africa could die as a direct result of HIV treatment interruptions and exposure to COVID-19. “A chilling pattern of inequity shapes the burden of COVID-19 and HIV,” the British medical journal the Lancet said in November 2020…

The post Pandemic Reads: <em>OMG Omicron!</em> appeared first on Balloon Juice.