{"id":23859,"date":"2021-12-04T19:38:24","date_gmt":"2021-12-04T19:38:24","guid":{"rendered":"https:\/\/evaggelatos.com\/?p=23859"},"modified":"2021-12-04T19:40:28","modified_gmt":"2021-12-04T19:40:28","slug":"how-bad-is-omicron-what-scientists-know-so-far","status":"publish","type":"post","link":"https:\/\/evaggelatos.com\/?p=23859","title":{"rendered":"How bad is Omicron? What scientists know so far about the transmissibility, severity and deathrate of Omicron variant"},"content":{"rendered":"<div class=\"c-article-header__restrict\">\n<div class=\"u-clearfix\">\n<div class=\"c-article-teaser-text\"><span style=\"font-size: 24pt;\"><strong>COVID researchers are working at breakneck speed to learn about the variant\u2019s transmissibility, severity and ability to evade vaccines.<\/strong><\/span><\/div>\n<\/div>\n<\/div>\n<div class=\"c-article-author-list-container u-clearfix\">\n<ul class=\"c-article-author-list js-etal-collapsed js-no-scroll\" data-etal=\"25\" data-etal-small=\"3\" data-test=\"authors-list\" data-component-authors-activator=\"authors-list\">\n<li class=\"c-author-list__item\"><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03614-z#author-0\" data-test=\"author-name\" data-track=\"click\" data-track-label=\"view author info\" data-author-popup=\"author-0\">Ewen Callaway<\/a> &amp;<\/li>\n<li class=\"c-author-list__item\"><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03614-z#author-1\" data-test=\"author-name\" data-track=\"click\" data-track-label=\"view author info\" data-author-popup=\"author-1\">Heidi Ledford<\/a><\/li>\n<\/ul>\n<\/div>\n<div class=\"c-article-extras-additional-links\"><\/div>\n<div class=\"c-article-header\">\n<header>\n<div class=\"c-article-extras-additional-links\"><\/div>\n<\/header>\n<\/div>\n<div class=\"c-article-body u-clearfix\">\n<figure class=\"figure\">\n<div class=\"embed intensity--high\">\n<div class=\"embed intensity--high\"><img decoding=\"async\" class=\"figure__image\" src=\"https:\/\/media.nature.com\/lw800\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19923286.jpg\" alt=\"A nurse puts on her personal protective equipment\" data-src=\"\/\/media.nature.com\/lw800\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19923286.jpg\" \/><\/div>\n<\/div><figcaption>\n<p class=\"figure__caption u-sans-serif\"><span class=\"mr10\">South Africa is dealing with a large uptick in COVID cases, driven by a new, heavily mutated variant called Omicron.<\/span>Credit: Guillem Sartorio\/AFP\/Getty<\/p>\n<\/figcaption><\/figure>\n<p>Barely a week has elapsed since scientists in Botswana and South Africa alerted the world to a fast-spreading <a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03552-w\" data-track=\"click\" data-label=\"https:\/\/www.nature.com\/articles\/d41586-021-03552-w\" data-track-category=\"body text link\">SARS-CoV-2 variant now known as Omicron<\/a>. Researchers worldwide are racing to understand the threat that the variant \u2014 now confirmed in more than 20 countries \u2014 poses to the world. <strong>Yet it might take scientists weeks to paint a more complete picture of Omicron, and to gain an understanding of its transmissibility and severity, as well as its potential to evade vaccines and cause reinfections.<\/strong><\/p>\n<p>&nbsp;<\/p>\n<div class=\"recommended pull pull--left u-sans-serif\" data-label=\"Related\">\n<p><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03552-w\" data-track=\"click\" data-track-label=\"recommended article\"><img decoding=\"async\" class=\"recommended__image\" src=\"https:\/\/media.nature.com\/w400\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19914758.jpg\" alt=\"\" \/><\/a><\/p>\n<p class=\"recommended__title u-serif\">Heavily mutated Omicron variant puts scientists on alert<\/p>\n<\/div>\n<p>\u201cWherever I go, everyone says: tell us more about Omicron,\u201d says Senjuti Saha, a molecular microbiologist and director of the Child Health Research Foundation in Dhaka, Bangladesh. \u201cThere is so little understanding of what\u2019s going on, and that\u2019s true, even for scientists.\u201d<\/p>\n<p><i>Nature<\/i> rounds up what scientists know so far about the Omicron variant.<\/p>\n<h2>How fast is Omicron spreading?<\/h2>\n<p>Omicron\u2019s rapid rise in South Africa is what worries researchers most, because it suggests the variant could spark explosive increases in COVID-19 cases elsewhere. On 1 December, South Africa recorded 8,561 cases, up from the 3,402 reported on 26 November and several hundred per day in mid-November, with much of the growth occurring in Gauteng Province, home to Johannesburg.<\/p>\n<p>Epidemiologists measure an epidemic\u2019s growth using <i>R<\/i>, the average number of new cases spawned by each infection. In late November, South Africa\u2019s National Institute for Communicable Diseases (NICD) in Johannesburg determined that <i>R<\/i> was above 2 in Gauteng. That level of growth was last observed in the early days of the pandemic, Richard Lessels, an infectious-disease physician at KwaZulu-Natal University in Durban, South Africa, told a press briefing last week.<\/p>\n<p>Gauteng\u2019s <i>R<\/i> value was well below 1 in September \u2014 when Delta was the predominant variant and cases were falling \u2014 suggesting that Omicron has the potential to spread much faster and infect vastly more people than Delta, says Tom Wenseleers, an evolutionary biologist at the Catholic University of Leuven in Belgium. Based on the rise in COVID-19 cases and on sequencing data, <span style=\"font-size: 14pt;\"><strong>Wenseleers estimates that Omicron can infect three to six times as many people as Delta, over the same time period.<\/strong> <\/span>\u201cThat\u2019s a huge advantage for the virus \u2014 but not for us,\u201d he adds.<\/p>\n<p>Researchers will be watching how Omicron spreads in other parts of South Africa and globally to get a better read on its transmissibility, says Christian Althaus, a computational epidemiologist at the University of Bern, Switzerland. Heightened surveillance in South Africa could cause researchers to overestimate Omicron\u2019s fast growth. But if this pattern is repeated in other countries, it would be very strong evidence that Omicron has a transmission advantage, adds Althaus. \u201cIf it doesn\u2019t happen, for example, in European countries, it means things are a bit more complex and strongly depend on the immunological landscape. So we have to wait.\u201d<\/p>\n<p>Although genome sequencing is needed to confirm Omicron cases, some PCR tests can pick up a hallmark of the variant that distinguishes it from Delta. On the basis of this signal, there are preliminary indications that cases, although extremely low in number, are rising in the United Kingdom. \u201cThat\u2019s certainly not what we want to see right now and suggests that Omicron could indeed also have a transmission advantage in the UK,\u201d Althaus adds.<\/p>\n<h2>Can Omicron overcome immunity from vaccines or infection?<\/h2>\n<p>The variant\u2019s swift rise in South Africa hints that it has some capacity to evade immunity. Around one-quarter of South Africans are fully vaccinated, and it\u2019s likely that a large fraction of the population was infected with SARS-CoV-2 in earlier waves, says Wenseleers, based on heightened death rates since the start of the pandemic.<\/p>\n<p>In this context,<span style=\"font-size: 14pt;\"><strong> Omicron\u2019s success in southern Africa might be due largely to its capacity to infect people who recovered from COVID-19 caused by Delta and other variants, as well as those who\u2019ve been vaccinated.<\/strong> <\/span>A 2 December preprint<sup><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03614-z#ref-CR1\" data-track=\"click\" data-action=\"anchor-link\" data-track-label=\"go to reference\" data-track-category=\"references\">1<\/a><\/sup> from researchers at the NICD found that reinfections in South Africa have increased as Omicron has spread. \u201cUnfortunately, this is the perfect environment for immune-escape variants to develop,\u201d says Althaus.<\/p>\n<p>How well the variant spreads elsewhere might depend on factors such as vaccination and previous infection rates, says Aris Katzourakis, who researches viral evolution at the University of Oxford, UK. \u201cIf you throw it into the mix in a highly vaccinated population that has given up on other control measures, it might have the edge there.\u201d<\/p>\n<p>&nbsp;<\/p>\n<div class=\"recommended pull pull--left u-sans-serif\" data-label=\"Related\">\n<p><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03608-x\" data-track=\"click\" data-track-label=\"recommended article\"><img decoding=\"async\" class=\"recommended__image\" src=\"https:\/\/media.nature.com\/w400\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19922484.jpg\" alt=\"\" \/><\/a><\/p>\n<p class=\"recommended__title u-serif\">Omicron-variant border bans ignore the evidence, say scientists<\/p>\n<\/div>\n<p>Researchers want to measure Omicron\u2019s ability to evade immune responses and the protection they offer. For instance, a team led by Penny Moore, a virologist at the NICD and the University of the Witwatersrand in Johannesburg, is measuring the ability of neutralizing, or virus-blocking, antibodies triggered by previous infection and vaccination to stop Omicron from infecting cells. <span style=\"font-size: 14pt;\"><strong>To test this in the laboratory, her team is making \u2018pseudovirus\u2019 particles \u2014 an engineered version of HIV that uses SARS-CoV-2\u2019s spike protein to infect cells \u2014 that match Omicron, which harbours as many as 32 changes to spike.<\/strong><\/span><\/p>\n<p>Another South Africa-based team, led by virologist Alex Sigal at the Africa Health Research Institute in Durban, is conducting similar tests of virus-neutralizing antibodies using infectious SARS-CoV-2 particles. So is a team led by Pei-Yong Shi, a virologist at the University of Texas Medical Branch in Galveston, who is collaborating with the makers of the Pfizer\u2013BioNTech vaccine to determine how it holds up against Omicron. \u201cI was really very concerned when I saw the constellation of mutations in the spike,\u201d he says. \u201cWe just have to wait for the results.\u201d<\/p>\n<p>Previous studies of Omicron\u2019s spike mutations \u2014 particularly in the region that recognizes receptors on human cells \u2014 suggest that the variant will blunt the potency of neutralizing antibodies. For instance, in a September 2021 <i>Nature<\/i> paper<sup><a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03614-z#ref-CR2\" data-track=\"click\" data-action=\"anchor-link\" data-track-label=\"go to reference\" data-track-category=\"references\">2<\/a><\/sup>, a team co-led by Paul Bieniasz, a virologist at Rockefeller University in New York City, engineered a highly mutated version of spike \u2014 in a virus incapable of causing COVID-19 \u2014 that shares numerous mutations with Omicron. The \u2018polymutant spike\u2019 proved fully resistant to neutralizing antibodies from most of the people they tested, who had either received two doses of an mRNA vaccine or recovered from COVID-19. With Omicron, \u201cwe expect there to be a significant hit\u201d, says Bieniasz.<\/p>\n<figure class=\"figure\">\n<div class=\"embed intensity--high\">\n<div class=\"embed intensity--high\"><img decoding=\"async\" class=\"figure__image\" src=\"https:\/\/media.nature.com\/lw800\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19923292.jpg\" alt=\"People wait to be inoculated at a vaccination centre\" data-src=\"\/\/media.nature.com\/lw800\/magazine-assets\/d41586-021-03614-z\/d41586-021-03614-z_19923292.jpg\" \/><\/div>\n<\/div><figcaption>\n<p class=\"figure__caption u-sans-serif\"><span class=\"mr10\">Vaccines\u2019 potency against the Omicron variant could be blunted, early analyses suggest.<\/span>Credit: Horacio Villalobos\/Corbis\/Getty<\/p>\n<\/figcaption><\/figure>\n<h2>How will vaccines fare against Omicron?<\/h2>\n<p>If Omicron can dodge neutralizing antibodies, it does not mean that immune responses triggered by vaccination and prior infection will offer no protection against the variant. Immunity studies suggest that <span style=\"font-size: 14pt;\"><strong>modest levels of neutralizing antibodies may protect people from severe forms of COVID-19,<\/strong><\/span> says Miles Davenport, an immunologist at the University of New South Wales in Sydney, Australia.<\/p>\n<p><span style=\"font-size: 14pt;\"><strong>Other aspects of the immune system, particularly T cells, may be less affected by Omicron\u2019s mutations than are antibody responses.<\/strong> <\/span>Researchers in South Africa plan to measure the activity of T cells and another immune player called natural killer cells, which might be especially important for protection against severe COVID-19, says Shabir Madhi, a vaccinologist at the University of the Witwatersrand.<\/p>\n<p>Madhi, who has led COVID-19 vaccine trials in South Africa, is also part of efforts to conduct epidemiological studies of vaccines\u2019 effectiveness against Omicron. There are anecdotal reports of breakthrough infections involving all three vaccines that have been administered in South Africa \u2014 Johnson &amp; Johnson, Pfizer\u2013BioNTech and Oxford\u2013AstraZeneca. But Madhi says researchers will want to quantify the level of protection against Omicron provided by vaccines, as well as by previous infection.<\/p>\n<p>He suspects that the results will be reminiscent of how the AstraZeneca\u2013Oxford vaccine performed against the Beta variant, an immune-evading variant that was identified in South Africa in late 2020. A trial led by Madhi found that the vaccine offered little protection against mild and moderate disease, while a real-world analysis in Canada showed greater than 80% protection against hospitalization.<\/p>\n<p>If Omicron behaves similarly, Madhi says, \u201cwe\u2019re going to see a surge of cases. We\u2019re going to see lots of breakthrough infections, lots of reinfections. But there\u2019s going to be this unhinging of the case rate in the community compared to the hospitalization rate\u201d. <strong>Early reports suggest that most breakthrough infections with Omicron have been mild, says Madhi.<\/strong> \u201cFor me, that is a positive signal.\u201d<\/p>\n<h2>Will current boosters improve protection against Omicron?<\/h2>\n<p>The threat of Omicron has prompted some rich countries, such as the United Kingdom, to accelerate and broaden the roll-out of COVID vaccine booster doses. But it\u2019s not yet clear how effective these doses will be against this variant.<\/p>\n<p>Third doses supercharge neutralizing-antibody levels, and it\u2019s likely that this will provide a bulwark against Omicron\u2019s ability to evade these antibodies, says Bieniasz. <span style=\"font-size: 14pt;\"><strong>His team\u2019s work on the polymutant spike found that people who had recovered from COVID-19 months before receiving their jabs had antibodies capable of blocking the mutant spike. To Bieniasz, those results suggest that people with repeated exposure to SARS-CoV-2\u2019s spike protein, be it through infection or a booster dose, are \u201cquite likely to have neutralizing activity against Omicron\u201d.<\/strong><\/span><\/p>\n<h2>Does Omicron cause milder or more severe disease than previous variants?<\/h2>\n<p>Early reports linked Omicron with mild disease, raising hopes that the variant might be less severe than some of its predecessors. But these reports \u2014 which are often based on anecdotes or scant scraps of data \u2014 can be misleading, cautions M\u00fcge \u00c7evik, an infectious-disease specialist at the University of St Andrews, UK. \u201cEveryone is trying to find some data that could guide us,\u201d she says. \u201cBut it\u2019s very difficult at the moment.\u201d<\/p>\n<p>A major challenge when assessing a variant\u2019s severity is how to control for the many confounding variables that can influence the course of disease, particularly when outbreaks are geographically localized. For example, reports of mild disease from Omicron infection in South Africa could reflect the fact that the country has a relatively young population, many of whom have already been exposed to SARS-CoV-2.<\/p>\n<p>During the early days of t<strong>he Delta outbreak, there were reports that the variant was causing more serious illness in children than did other variants \u2014<\/strong> an association that dissolved once more data were collected, \u00c7evik says.<\/p>\n<p>Researchers will be looking for data on Omicron infections in other countries. This geographical spread, and a larger sample size as cases accrue, will give researchers a better idea of how generalizable the early reports of mild disease might be. Ultimately, researchers will want to conduct case-controlled studies, in which two groups of participants are matched in terms of important factors such as age, vaccination status and health conditions. Data from both groups will need to be collected at the same time, because the number of hospitalizations can be influenced by overall hospital capacity in a region.<\/p>\n<p>And, crucially, researchers will need to control for the level of economic deprivation. A rapidly spreading new variant may reach vulnerable groups more rapidly, \u00c7evik says, by nature of their work or living conditions. And such groups often experience more severe disease.<\/p>\n<p>All of this will take time. \u201cI think the severity question will be one of the last bits that we\u2019ll be able to untangle,\u201d she says. \u201cThat\u2019s how it happened with Delta.\u201d<\/p>\n<h2>Where has Omicron spread and how are scientists tracking it?<\/h2>\n<p>More countries are detecting the Omicron variant, but the capacity to rapidly sequence viruses from positive COVID-19 tests is concentrated in wealthy countries, meaning that early data on Omicron\u2019s spread will be skewed.<\/p>\n<p>Surveillance efforts in Brazil and some other countries are taking advantage of a distinctive result on a particular PCR test that could allow them to pinpoint potential Omicron cases for sequencing, says virologist Renato Santana at the Federal University of Minas Gerais in Brazil. The test looks for segments of three viral genes, one of which is the gene that encodes for the spike protein. Mutations in Omicron\u2019s spike gene prevent its detection in the test, meaning that samples containing the variant will test positive for only two of the genes.<\/p>\n<p>Even so, not everyone uses that test and it could take some time before Omicron\u2019s spread is fully mapped. Despite some guidelines urging countries to sequence 5% of their samples that test positive for SARS-CoV-2, few can afford to do so, says computational virologist Anderson Brito at the All for Health Institute in S\u00e3o Paulo, Brazil. And Brito worries that the <a href=\"https:\/\/www.nature.com\/articles\/d41586-021-03608-x\" data-track=\"click\" data-label=\"https:\/\/www.nature.com\/articles\/d41586-021-03608-x\" data-track-category=\"body text link\">travel bans <\/a>enacted by some countries against South Africa, and other southern African nations, in the wake of its Omicron discovery could discourage governments from sharing genomic surveillance data. \u201cWe are punishing those who did a good job,\u201d he says.<\/p>\n<p>In Bangladesh, which sequences about 0.2% of positive coronavirus samples, researchers would be eager to ramp up sequencing to keep tabs on Omicron and other emerging variants, says Saha. But resources are limited. Bangladesh is recovering from a large dengue outbreak, she adds. \u201cIn the global south, we are all worried about COVID, but let\u2019s not forget our endemic diseases,\u201d Saha says. \u201cWe can only do so many.\u201d<\/p>\n<\/div>\n<p><em>doi: <a href=\"https:\/\/doi.org\/10.1038\/d41586-021-03614-z\">https:\/\/doi.org\/10.1038\/d41586-021-03614-z<\/a> and https:\/\/www.nature.com\/articles\/d41586-021-03614-z<\/em><\/p>\n<div id=\"references\" class=\"c-article-references__container\">\n<section aria-labelledby=\"Bib1\">\n<div id=\"Bib1-section\" class=\"c-article-section\">\n<h2 id=\"Bib1\" class=\"c-article-section__title js-section-title\">References<\/h2>\n<div id=\"Bib1-content\" class=\"c-article-section__content\">\n<div data-container-section=\"references\">\n<ol class=\"c-article-references\">\n<li class=\"c-article-references__item js-c-reading-companion-references-item\"><span class=\"c-article-references__counter\">1.<\/span>\n<p id=\"ref-CR1\" class=\"c-article-references__text\">Pulliam, R. C. J. <i>et al.<\/i> Preprint at MedRxiv https:\/\/doi.org\/10.1101\/2021.11.11.21266068 (2021).<\/p>\n<\/li>\n<li class=\"c-article-references__item js-c-reading-companion-references-item\"><span class=\"c-article-references__counter\">2.<\/span>\n<p id=\"ref-CR2\" class=\"c-article-references__text\">Schmidt, F. <i>et al.<\/i> <i>Nature<\/i> https:\/\/doi.org\/10.1038\/s41586-021-04005-0 (2021).<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>COVID researchers are working at breakneck speed to learn about the variant\u2019s transmissibility, severity and ability to evade vaccines. Ewen Callaway &amp; Heidi Ledford South Africa is dealing with a large uptick in COVID cases, driven by a new, heavily mutated variant called Omicron.Credit: Guillem Sartorio\/AFP\/Getty Barely a week has elapsed since scientists in Botswana &hellip; <\/p>\n<p><a class=\"more-link btn\" href=\"https:\/\/evaggelatos.com\/?p=23859\">\u03a3\u03c5\u03bd\u03ad\u03c7\u03b5\u03b9\u03b1 \u03b1\u03bd\u03ac\u03b3\u03bd\u03c9\u03c3\u03b7\u03c2<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[85],"tags":[217,90],"class_list":["post-23859","post","type-post","status-publish","format-standard","hentry","category-85","tag-217","tag-90","item-wrap"],"_links":{"self":[{"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/posts\/23859","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=23859"}],"version-history":[{"count":3,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/posts\/23859\/revisions"}],"predecessor-version":[{"id":23862,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=\/wp\/v2\/posts\/23859\/revisions\/23862"}],"wp:attachment":[{"href":"https:\/\/evaggelatos.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23859"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23859"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/evaggelatos.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23859"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}