{"id":142622,"date":"2021-12-02T19:32:57","date_gmt":"2021-12-02T23:32:57","guid":{"rendered":"https:\/\/antiguanewsroom.com\/?p=142622"},"modified":"2021-12-02T19:32:57","modified_gmt":"2021-12-02T23:32:57","slug":"the-mystery-of-where-omicron-came-from-and-why-it-matters","status":"publish","type":"post","link":"https:\/\/antiguanewsroom.com\/the-mystery-of-where-omicron-came-from-and-why-it-matters\/","title":{"rendered":"The mystery of where omicron came from \u2014 and why it matters"},"content":{"rendered":"
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NPR:<\/strong>\u00a0The discovery of the omicron variant of the coronavirus \u2014 which has a high number of concerning mutations \u2014 has kicked off a frenzy of research. Scientists are racing to figure out how transmissible this variant is and how resistant to vaccines it is.<\/p>

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They\u2019re also grappling with a mystery: How did omicron get created?<\/p>\n

NPR spoke with two scientists in the thick of this research. Trevor Bedford is a computational virologist and professor at the Fred Hutchinson Cancer Research Center in Seattle. Richard Lessells is an infectious disease specialist at the University of KwaZulu-Natal in Durban, South Africa, and part of the team that identified omicron in South Africa and alerted the world. Here\u2019s what they have to say.<\/p>

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Omicron\u2019s genetic family tree contains a big surprise<\/h2>\n

One of the key tools that scientists use to puzzle out the origin of a particular coronavirus variant is to look at its genetic code. Just as people who want to find out their ancestry \u2014 were their forebears Nordic? Mongol? \u2014 can find traces of that lineage in their genes, the virus\u2019s genome contains clues.<\/p>

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\u201cIt\u2019s been very common to use an evolutionary tree \u2014 or a family tree \u2014 of these SARS-CoV-2 viruses to catch introductions in places like Australia and Taiwan that have not had a lot of local spread,\u201d says Bedford. \u201cYou can figure out where the importations are coming from by looking at the viral genome and checking, \u2018Is it close in its sequence characteristics to [strains] that are circulating elsewhere that have been sequenced and shared with the database?\u2019 \u201d<\/p>\n

Scientists can then see, as they continue to take samples in the new region over time, how each particular strain starts to pick up additional \u2014 often benign \u2014 mutations step by step until it morphs into a significantly different strain.<\/p>

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But Bedford says that when you look at the family tree for this omicron variant, there\u2019s something surprising: \u201cWith omicron, your closest sequences are back from mid-2020 \u2014 so over a year ago. That is very rare to see.\u201d<\/p>\n

In other words, while scientists can tell that this variant evolved from a strain that was circulating in mid-2020, in the intervening months there has been no trace of all the intermediate versions that scientists would have expected to find as it morphed into its current form.<\/p>

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\u201cIt doesn\u2019t tie into anything that was circulating more recently,\u201d says Bedford.\u201d Yet its mutations put it a long way from that 2020 strain.<\/p>

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How to explain this?<\/h2>\n

Hypothesis No. 1: The animal source<\/h2>\n

It\u2019s possible, says Bedford, that the mid-2020 strain infected some unknown animal population, evolved as it spread among that population and has just recently spilled back over into humans.<\/p>\n

But Bedford thinks that this hypothesis is unlikely to prove true. \u201cThis is getting technical,\u201d he says. But the gist is that you\u2019d expect to see signs of the animal\u2019s genetic material in the genome, and instead there\u2019s an insertion of human RNA \u201cthat suggests that along [omicron\u2019s evolutionary] branch, it was evolving in a human.\u201d<\/p>\n

Hypothesis No. 2: \u201cCryptic spread\u201d in an unmonitored region<\/h2>\n

Another possibility, says Bedford, is that the mid-2020 strain started circulating in a location where there hasn\u2019t been a lot of monitoring \u2014 \u201cperhaps somewhere in southern Africa.\u201d That would have enabled the virus to evolve under the radar all this time. \u201cAnd eventually, by the time you get to 2021, it\u2019s picked up enough mutations that it has become [much more] transmissible and then kind of explodes onto the scene at that point,\u201d says Bedford.<\/p>\n

But he also finds this scenario \u2014 which scientists sometimes refer to as \u201ccryptic spread\u201d \u2014 hard to believe. \u201cBecause it would seem that as [this strain of the virus] was on its path to becoming omicron and becoming a quite transmissible virus, [the earlier versions] would have started to spread more widely before just now.\u201d And at that point, those earlier strains would have been noticed in countries that do have robust surveillance systems.<\/p>\n

Lessells agrees. On the one hand, he notes, there certainly are countries in Africa where there has not been much ongoing sampling of the coronavirus. Indeed, he says, earlier in the coronavirus pandemic, South Africa\u2019s labs picked up a variant that hadn\u2019t been seen before through testing a traveler from Tanzania, one of several sub-Saharan African countries \u201cwhere they weren\u2019t measuring the epidemic very well.\u201d<\/p>\n

\u201cNow,\u201d he adds, \u201cthat variant, to our knowledge, never really took off in any area. And we still don\u2019t know to what extent that was circulating in Tanzania and what the significance of it was.\u201d But he says the episode \u2014 and others like it \u2014 illustrate that once a variant reaches South Africa, at least, it is least likely to get identified. \u201cWe have seven [genomic] sequencing hubs that are each connected to the public and private diagnostic labs across the country,\u201d he says.<\/p>\n

Also, omicron in particular triggers a notable signature in the PCR tests that are being conducted on a routine basis to confirm infections. This warning flag, in fact, is what spurred a private lab to send samples to Lessells and his colleagues, who, upon sequencing them, discovered the omicron variant. \u201cIf you\u2019ve got representative sequencing and frequent sequencing, and if you can be nimble enough to respond to what you\u2019re observing in the cases in the diagnostic lab, then you can pick up these variants that are at a relatively early stage,\u201d he says. \u201cSo you\u2019d have to have a pretty big blind spot to be missing something that\u2019s really evolving over a period of months.\u201d<\/p>\n

Hypothesis No. 3: Incubation in an immunocompromised person<\/h2>\n

There is, however, one place the virus could have been hiding while it evolved into omicron that probably would have been in health officials\u2019 blind spot: inside the body of a single person. Specifically, a person whose immune system was suppressed \u2014 for example, as a result of an untreated HIV infection. In such instances, explains Bedford, the person\u2019s immune system is still strong enough to prevent the coronavirus from killing the person. But it\u2019s not strong enough to completely clear the virus. So the virus lingers inside the person for month after month, continually reproducing. With each replication, there\u2019s a chance it will acquire a mutation that makes it better at evading the person\u2019s antibody-producing immune cells.<\/p>\n

\u201cIt creates this kind of cat-and-mouse game where the immune response is chasing and the virus is running,\u201d says Bedford. \u201cAnd so over the course of the year, if you look in these individuals, you see, at the end of that time, generally a quite evolved virus.\u201d<\/p>\n

Lessells is one of several researchers to have demonstrated this phenomenon by retroactively analyzing a series of coronavirus samples that had been taken over a period of about six months from a woman who had HIV. Through an unfortunate series of unintended mishaps in her medical care, it later transpired that she was not being properly treated for her HIV infection during that time \u2014 even as she was enrolled in a larger study for which samples were being taken of the coronavirus that she harbored.<\/p>\n

\u201cBecause we had samples from a few different time points over that six-month period,\u201d says Lessells, \u201cwe could show how the virus evolved and variants with some of the same mutations as the variants of concern appeared over time in the samples.\u201d<\/p>\n

If this is how omicron was created, then presumably it wasn\u2019t until fairly recently that the virus finally spread into others from the person who was incubating it.<\/p>\n

Why wouldn\u2019t this spread have happened at earlier points during omicron\u2019s evolution in the immunocompromised individual\u2019s body?<\/p>\n

\u201cThat\u2019s a good question and a legitimate one,\u201d says Bedford. \u201cI don\u2019t have an obvious answer besides chance.\u201d Still, like Lessells, he currently considers this scenario the most plausible explanation for omicron\u2019s emergence.<\/p>\n

Why knowing omicron\u2019s source matters<\/h2>\n

Both scientists stressed that the scientific investigation of omicron is happening in real time, with new information coming out so fast that their views on its origins could change.<\/p>\n

Still, in the short run, says Bedford, making educated guesses as to omicron\u2019s source can help scientists assess the potential threat from the variant. For instance, he says, if omicron had been evolving out of sight in a large population of humans over a period of months, this suggests it\u2019s actually not that transmissible. After all, he says, \u201cwe\u2019ve still only seen a handful of these travel cases [arriving in various countries]. So that would suggest that it hasn\u2019t been spreading really rapidly \u2014 that it\u2019s taken a little while to ramp up to this level.\u201d<\/p>\n

But, he says, if omicron evolved in one person\u2019s body and only recently spread to a wider population, this means the level of circulation that is now being detected \u2014 or as Bedford puts it, \u201cthe time frame for getting to where we are now, where we\u2019re starting to pick up cases in travelers\u201d \u2014 was reached over a much shorter period. And this would suggest that the variant is much more transmissible.<\/p>\n

The larger takeaway: Ramp up HIV treatment<\/h2>\n

Regardless of the origins of omicron, Bedford and Lessells say its emergence is one more reminder that dangerous future variants could be created by the mutation of the virus in an immunocompromised person. This is especially urgent when it comes to the millions of people in southern Africa who have HIV and are not on medication. The point is not to blame or stigmatize people in this situation, they say, but rather to recognize that helping them is a key to ending the coronavirus pandemic. As Lessells puts it: \u201cThe intervention here is clear. We just need to strengthen our HIV response and get as many people as we possibly can onto effective treatment regimens.\u201d<\/p>\n

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NPR:\u00a0The discovery of the omicron variant of the coronavirus \u2014 which has a high number of concerning mutations \u2014 has kicked off a frenzy of research. Scientists are racing to figure out how transmissible this variant is and how resistant to vaccines it is. They\u2019re also grappling with a mystery: How did omicron get created? […]<\/p>\n","protected":false},"author":3,"featured_media":142623,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[],"class_list":["post-142622","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-regional"],"yoast_head":"\nThe mystery of where omicron came from \u2014 and why it matters - Antigua News Room<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/antiguanewsroom.com\/the-mystery-of-where-omicron-came-from-and-why-it-matters\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The mystery of where omicron came from \u2014 and why it matters\" \/>\n<meta property=\"og:description\" content=\"NPR:\u00a0The discovery of the omicron variant of the coronavirus \u2014 which has a high number of concerning mutations \u2014 has kicked off a frenzy of research. 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Scientists are racing to figure out how transmissible this variant is and how resistant to vaccines it is. They\u2019re also grappling with a mystery: How did omicron get created? 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