tag:theconversation.com,2011:/uk/topics/p1-98945/articlesP1 – The Conversation2021-08-27T09:44:34Ztag:theconversation.com,2011:article/1659812021-08-27T09:44:34Z2021-08-27T09:44:34ZCOVID: vaccine boosters are likely to increase protection against variants – new research<p>How well do vaccines protect against the new variants of the coronavirus? This is a question we – a group of scientists and doctors in Nottingham – <a href="https://stm.sciencemag.org/content/early/2021/08/10/scitranslmed.abj0847">set about answering</a> earlier this year, having collected blood samples from a number of nurses and doctors throughout the pandemic.</p>
<p>We started taking blood from healthcare workers back in April 2020, in the peak of the first wave, to see how many of them had been infected with the coronavirus and what their levels of antibodies were. We followed up with them in the summer and then again in the autumn, so we knew exactly who had had COVID-19 and when. </p>
<p>We then asked a group of them to give us blood samples after they had received their first and second vaccine doses. We measured their antibody levels after each dose, and also specifically their levels of neutralising antibodies, which are those that attack and nullify the virus (as distinct from binding antibodies, which flag the virus to other immune cells).</p>
<p>We also kept hold of these samples so that we could, in the future, test how well the antibodies created by vaccination neutralised <a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/">variants of the coronavirus</a> that the participants hadn’t seen. We subsequently measured the antibodies’ activity against the original form of the virus that was identified in Wuhan as well as the beta (B1351) and gamma (P1) variants.</p>
<h2>How to test for protection</h2>
<p>Neutralising antibodies attach to a virus in a way that prevents it from infecting cells. The higher the levels of neutralising antibodies against a variant of the coronavirus, the less likely that a person will become infected or get severe COVID-19 from that variant. </p>
<p>To measure neutralisation, we used a mouse virus called MLV, which had been modified so that it could infect but not replicate inside a cell. The virus also carried a gene that causes it to generate light once it gets inside a cell.</p>
<figure class="align-center ">
<img alt="Illustration of the SARS-CoV-2, showing the spike proteins on its surface" src="https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=602&fit=crop&dpr=1 600w, https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=602&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=602&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=757&fit=crop&dpr=1 754w, https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=757&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/348153/original/file-20200717-25-1v585an.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=757&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">SARS-CoV-2, with its spike proteins shown in red. Different variants of the virus have slight changes to these proteins.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/File:SARS-CoV-2_without_background.png">US Centers for Disease Control and Prevention/Wikimedia Commons</a></span>
</figcaption>
</figure>
<p>We then covered the surface of MLV with the spike proteins found on the outside of the coronavirus, which are what it uses to infect cells. Each variant has slight differences in its spike proteins, and this system, called pseudotyping, enabled us to “swap out” the proteins of the different variants we were interested in, so we could test the antibodies against them all. </p>
<p>In principle we could have used the variants of the coronavirus themselves, but since this requires <a href="https://www.merriam-webster.com/dictionary/biocontainment">biocontainment</a> we chose MLV instead. It is easier to handle in lab conditions and has been <a href="https://www.mdpi.com/1999-4915/12/9/1011">shown to perform</a> just like the coronavirus when pseudotyped.</p>
<p>In a lab, we then looked to see whether – in the presence of the healthworkers’ antibodies – MLV could get inside a cell when coated with the various different sets of spike proteins. If a healthcare worker had neutralising antibodies against a variant, these blocked the virus from entering the cell, meaning no light was emitted. If they didn’t have virus-neutralising antibodies, then the modified virus could enter the cell and we could measure the light emitted once inside. </p>
<p>When we cross-referenced this data with who had been infected earlier on in the pandemic, we found that volunteers who had previously caught the virus (which is similar to having an additional vaccine dose) had higher levels of antibodies after their first and second vaccine doses than uninfected volunteers. The effect was very noticeable for the variants. </p>
<p>In particular, past infection plus two doses of vaccine increased the chances of neutralising the beta and gamma variants. The level of neutralisation in this scenario was similar to that seen in fully vaccinated but uninfected people when confronted with the original, Wuhan form of the virus – a level that we know is protective against disease.</p>
<p>In our experiments we didn’t directly study the impact of an additional vaccine dose, but our results suggest that one is likely to increase levels of immunity to commonly circulating variants of concern. Each additional exposure to the virus in general – whether by vaccination or infection – seemingly expands the immune system’s ability to recognise it, making it more likely for someone to show a stronger antibody response to any form of the virus in future. </p>
<p>Even against forms of the virus that we didn’t look at, such as delta, we would expect protection to be higher after more instances of viral exposure. The effect of this could be to reduce levels of infection, transmission and, in some highly vulnerable people, disease.</p>
<h2>A boost for boosters?</h2>
<p>There’s <a href="https://www.theguardian.com/commentisfree/2021/aug/13/covid-boosters-dose-vaccine">considerable debate</a> currently about how best to use global vaccine supplies. Should additional doses be used to better protect the few who are already double vaccinated, or should there be more equitable distribution, to spread basic vaccine coverage more widely around the world? </p>
<p>On the one hand, a recent population study from <a href="https://www.gov.uk/government/news/vaccines-highly-effective-against-b-1-617-2-variant-after-2-doses">Public Health England</a> reported that receiving two doses of either the Pfizer of AstraZeneca vaccine provides high levels of protection against disease caused by the now dominant delta variant (B16172). This would suggest that booster doses aren’t needed – at least not initially.</p>
<p>There’s also <a href="https://webcache.googleusercontent.com/search?q=cache:e2sHTn7NdDMJ:https://www.medrxiv.org/content/10.1101/2021.08.24.21262415v1+&cd=1&hl=en&ct=clnk&gl=uk">emerging evidence</a> (still awaiting review by other scientists) that natural infection with delta may produce stronger protection than that created currently by vaccines. This would suggest that those who’ve already caught delta are currently well protected.</p>
<figure class="align-center ">
<img alt="A woman being vaccinated against COVID-19" src="https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=356&fit=crop&dpr=1 600w, https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=356&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=356&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=448&fit=crop&dpr=1 754w, https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=448&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/417804/original/file-20210825-25-7ablyt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=448&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Vaccine boosters are being considered in the UK to raise the protection levels of those most vulnerable to COVID-19.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/senior-woman-being-vaccinated-against-coronavirus-1877488087">David Pereiras/Shutterstock</a></span>
</figcaption>
</figure>
<p>On the other hand, we know that some variants – such as <a href="https://theconversation.com/covid-19-vaccines-why-its-important-you-get-your-second-dose-161940">delta</a> and <a href="https://theconversation.com/covid-the-beta-variant-is-surging-in-mainland-europe-should-the-uk-be-worried-164815">beta</a> – are less well controlled by vaccines, and there’s also emerging evidence that the immunity generated by COVID-19 vaccines <a href="https://www.bbc.co.uk/news/health-58322882">wanes over time</a>. </p>
<p>In the face of these challenges, our data suggests that an additional vaccine dose would likely generate gains in levels of immunity, especially against variants of concern. Giving an extra dose might therefore be crucial for reducing infection and transmission in health and care settings and to protect particularly vulnerable people from severe disease.</p>
<p>As such, our work supports the <a href="https://www.gov.uk/government/publications/jcvi-interim-advice-on-a-potential-coronavirus-covid-19-booster-vaccine-programme-for-winter-2021-to-2022/jcvi-interim-advice-potential-covid-19-booster-vaccine-programme-winter-2021-to-2022">UK government’s plan</a> to provide a targeted booster vaccine dose <a href="https://www.bbc.co.uk/news/health-57667987">this autumn</a>. This may well prove to be an effective strategy in protecting people against variants from here on.</p><img src="https://counter.theconversation.com/content/165981/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ana Valdes receives funding from UK Research and Innovation COVID-19 Rapid Response (COV0331 MR/V027883/1) and from the UK National Institute for Health Research Nottingham Biomedical Research Centre. She is also consultant for Zoe Global Ltd.</span></em></p><p class="fine-print"><em><span>Jonathan Ball receives UK Research and Innovation funding to develop next-generation COVID-19 vaccines.</span></em></p><p class="fine-print"><em><span>Benjamin Ollivere does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>People who had previously caught the coronavirus, which is similar to having an additional vaccine dose, had more neutralising antibodies against COVID variants after being vaccinated.Ana Valdes, Professor of Molecular and Genetic Epidemiology, University of NottinghamBenjamin Ollivere, Professor of Orthopaedic Trauma, University of NottinghamJonathan Ball, Professor of Molecular Virology and Director of the Wolfson Centre for Global Virus Research, University of NottinghamLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1590662021-04-23T13:06:46Z2021-04-23T13:06:46ZCOVID-19 in Brazil: how Jair Bolsonaro created a calamity<p>Brazil has had what is arguably the worst pandemic policy response in the world, driven by its far-right president, Jair Bolsonaro. The president’s choices in handling COVID-19 have triggered an unparalleled tragedy in the country, with potentially catastrophic implications worldwide. </p>
<p>Matters have deteriorated considerably since the emergence of a <a href="https://theconversation.com/brazil-coronavirus-variant-what-is-it-and-why-is-it-a-concern-an-expert-explains-156234">new and more contagious variant</a>
in the country, known as P1. The death toll in Brazil has been rising relentlessly, <a href="https://susanalitico.saude.gov.br/extensions/Covid-19_html/Covid-19_html.html%5D">reaching 4,250</a> on April 8 – the <a href="https://www.cbsnews.com/video/brazils-covid-crisis-reaches-catastrophe-as-daily-death-toll-is-highest-in-world/">highest number of daily fatalities</a> from the disease on Earth. </p>
<p>The health system has collapsed in numerous cities. There, oxygen supplies are rationed, ICU beds are fully occupied, and both staff and equipment are lacking. </p>
<p>There are reports of <a href="https://news.yahoo.com/brazil-covid-patients-tied-beds-113617869.html?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuZ29vZ2xlLmNvbS8&guce_referrer_sig=AQAAAKXXeLpKKv5vD92v0Lylj0ZQz9Co3aORdz7v2A3VcDXz_Eu6u4Kz0QM8ZyIUUTu_J6Lhyj6rp21rsqCjwWZupRr62EQlKf8EGvIiRnf5Gutrg8rrTGUFd6-8dAgkf_S_3cgQRqo6uv8kuli_VzIiW9G-lX8t_H61JRjPA6WRPx2L">patients being tied up</a> in order to be intubated, for want of anaesthetics. <a href="https://www.nexojornal.com.br/expresso/2021/03/24/O-cen%C3%A1rio-tr%C3%A1gico-nos-hospitais-do-Brasil-que-chega-a-300-mil-mortos">Hundreds have died</a> on trolleys, hospital floors or at home, even when their families could procure much-needed oxygen tubes in the parallel market.</p>
<p>Three factors have converged to create this living hell. </p>
<p>First, Brazil is one of the most unequal countries on Earth, and <a href="https://www.globalpolicyjournal.com/blog/21/12/2020/between-two-epidemics-coronavirus-and-inequality-brazil-conversation-ggf-2035">deep and overlapping inequalities</a> have created vulnerabilities among disadvantaged populations. These vulnerabilities have become <a href="https://www.brasil247.com/brasil/desigualdade-cresceu-em-todos-os-trimestres-apos-o-golpe-contra-dilma-nkkpcroh">more entrenched</a> since 2016, when president Dilma Rousseff was removed from office in an impeachment that amounted to a parliamentary coup d'état.</p>
<p>The pandemic provides further evidence of the country’s inequality: COVID-19 disproportionately affects <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878714/">black Brazilians</a>, <a href="https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00081-4/fulltext">the poor</a> and <a href="https://link.springer.com/article/10.1007/s41027-020-00252-3">the unemployed</a>.</p>
<p>Second, Brazil has always suffered from acute political and institutional limitations, which have gotten worse since Rousseff was ejected from office. The two governments since 2016 have sponsored neoliberal reforms that increased labour precarity, eroded social security, and left public services dramatically underfunded. These reforms were underpinned by a <a href="https://www.bbc.com/news/world-latin-america-38311053">constitutional amendment</a>, which froze non-financial expenditures of the federal government in real terms for 20 years.</p>
<p>The new fiscal regime has legitimised brutal funding cuts in the name of an arbitrary fiscal rule. Brazil’s universal health system, inspired by the British NHS, has been degraded in recent years under this programme of austerity.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Graph showing daily COVID cases in Brazil gradually increasing to around 70,000." src="https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=424&fit=crop&dpr=1 600w, https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=424&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=424&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=532&fit=crop&dpr=1 754w, https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=532&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/396565/original/file-20210422-21-19j5xth.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=532&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"></span>
<span class="attribution"><a class="source" href="https://ourworldindata.org/coronavirus/country/brazil">Our World In Data</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Finally, there is the role played by Bolsonaro himself. As COVID-19 spread, the president systematically downplayed the risks and <a href="https://www.newyorker.com/news/daily-comment/brazils-covid-19-crisis-and-jair-bolsonaros-presidential-chaos">blocked any centrally coordinated response</a>. He also undermined mayors and state governors when they tried to impose their own lockdowns, social distancing rules or mask mandates.</p>
<p>Administrative confusion inevitably created a patchwork of rules in the country, which Bolsonaro used as an argument against any and all restrictions. The president has also forced the country’s ministers of health – of which there have been <a href="https://www.bbc.com/news/world-latin-america-56410626">four over the past year</a> – to focus on unproven cures like <a href="https://theconversation.com/ivermectin-why-a-potential-covid-treatment-isnt-recommended-for-use-157904">ivermectin</a> and <a href="https://www.newyorker.com/news/daily-comment/brazils-covid-19-crisis-and-jair-bolsonaros-presidential-chaos">hydroxychloroquine</a>, all the while leaving the health system to implode.</p>
<h2>Declining social support</h2>
<p>The only significant measure to protect the poor was <a href="https://www.aljazeera.com/economy/2020/4/4/brazils-legislators-approve-coronavirus-war-budget">initiated by the left</a> in Congress: an emergency income support of 600 reais (US$108) a month during the pandemic, together with other expansionary measures including credit lines for small and medium enterprises. These measures were approved as part of a “war budget” bypassing the fiscal deficit limits. Bolsonaro then presented the income support as his own grant to the poor, which <a href="https://www.ipea.gov.br/portal/images/stories/PDFs/relatorio_institucional/200724_ri_o%20brasil_pos_covid_19.pdf">boosted his popularity</a> significantly. </p>
<p>However, with the start of the new fiscal year, in January, the income support programme ended just as the latest wave of COVID-19 infections was ramping up. It was replaced in April by a <a href="https://noticias.r7.com/prisma/r7-planalto/congresso-nacional-aprova-a-pec-que-recria-auxilio-emergencial-12032021">much smaller grant</a> of <a href="https://www.reuters.com/article/us-brazil-economy-emergencyaid-idUSKBN2AB2T8">250 reais</a> a month for up to three months, conditional on deeper reforms of the public administration and fiscal cuts elsewhere. </p>
<p>The lack of federal support has made it impossible for the states and municipalities to impose local lockdowns, virtually guaranteeing that the pandemic would get worse.</p>
<h2>Necropolitics in action</h2>
<p>The situation in Brazil is a prime example of “<a href="https://www.e-ir.info/2020/05/19/bolsonaros-brazil-in-times-of-covid-19-a-necropolitical-pharmakon/">necropolitics</a>” in action. Necropolitics is the use of political power to dictate whether people live or die. In this iteration, COVID-19 is taken to be a fact of nature that only affects the weak. </p>
<p>This is factually wrong, but this politics of resentment, conspiracy and misinformation is typical of the world’s current cohort of authoritarian leaders, who often spin falsehoods in order to create conflict, shift attention and block alternative policies. </p>
<p>Bolsonaro has declared that he is avoiding serious COVID measures in order to <a href="https://theconversation.com/just-like-trump-brazils-bolsonaro-puts-the-economy-ahead-of-his-people-during-coronavirus-136351">protect the economy</a>. However, this trade-off does not exist. International experience shows the economies that tackled coronavirus decisively had both lower death tolls and smaller contractions of economic activity (for example <a href="https://www.bbc.com/news/business-56768663">China</a>, <a href="https://www.bloomberg.com/news/articles/2021-04-20/asia-s-odd-couple-show-an-uncommon-resilience-to-global-crises">South Korea</a>, <a href="https://markets.businessinsider.com/news/stocks/coronavirus-economic-impact-germany-vietnam-v-shaped-recoveries-2020-7-1029372929">Vietnam</a>). Those that sought to avoid lockdowns suffered the highest death tolls and the worst economic shocks. Brazil’s economy is <a href="https://apnews.com/article/brazil-coronavirus-pandemic-covid-19-pandemic-jair-bolsonaro-economy-76f5067d05b032412f2de3278576881e">currently nosediving</a>. </p>
<p>Bolsonaro’s neglect of the pandemic has allowed the government to roll out, virtually unnoticed, a <a href="https://www.theguardian.com/commentisfree/2021/apr/05/the-guardian-view-on-jair-bolsonaro-a-danger-to-brazil-and-the-world">range of initiatives</a> that remove protections for labour and the environment, all the while opening up indigenous lands for agriculture and mining. It has also diverted attention from <a href="https://www.nytimes.com/2020/08/28/world/americas/brazil-bosonaro-corruption.html">corruption scandals</a> involving the president’s family. </p>
<p>Bolsonaro bears direct responsibility for the Brazilian tragedy in a manner that goes beyond the incompetence or mendacity of his response. The president has deliberately promoted the spread of COVID-19 to polarise the political atmosphere for his own gain, and to facilitate the roll out of a wholly destructive programme of government. </p>
<p>In the meantime, the population has been left exposed to coronavirus. The neoliberal reforms, the dismantling of the state and the destruction of the environment remain top of the government’s agenda. The outcome has been a skyrocketing death toll, the worst economic contraction in Brazilian history, and increasing <a href="https://brasil.elpais.com/brasil/2021-01-21/pesquisa-revela-que-bolsonaro-executou-uma-estrategia-institucional-de-propagacao-do-virus.html">social and political chaos</a>.</p><img src="https://counter.theconversation.com/content/159066/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>The Brazilian president has engineered the conditions for the virus to run rampant through the country while he pursues his own agenda.Alfredo Saad Filho, Professor of Political Economy and International Development, King's College LondonFernanda Feil, Assistant researcher, Universidade Federal Fluminense (UFF)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1535302021-01-21T21:48:37Z2021-01-21T21:48:37ZWhy new COVID-19 variants are on the rise and spreading around the world<figure><img src="https://images.theconversation.com/files/380025/original/file-20210121-17-1r712y0.jpg?ixlib=rb-1.1.0&rect=137%2C101%2C3730%2C2544&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Medical technician Amira Doudou prepares samples at the University Hospital Institute for Infectious Diseases in Marseille, France, Jan. 13, 2021, to study the highly contagious COVID-19 variant.</span> <span class="attribution"><span class="source">(AP Photo/Daniel Cole)</span></span></figcaption></figure><p>A new variant of coronavirus has swept across the United Kingdom and been detected in the United States, Canada and elsewhere. <a href="https://www.who.int/news/item/12-01-2021-global-scientists-double-down-on-sars-cov-2-variants-research-at-who-hosted-forum">Scientists are concerned</a> that these new strains may spread more easily. </p>
<p>As an evolutionary biologist, I study how mutation and selection combine to shape changes in populations over time. Never before have we had so much real-time data about evolution as we do with SARS-CoV-2: over <a href="https://www.gisaid.org">380,000 genomes</a> were sequenced last year.</p>
<p>SARS-CoV-2 has been mutating as it spreads, generating slight differences in its genome. These mutations allow scientists to trace who is related to whom across the <a href="https://nextstrain.org/ncov/global">family tree</a> of the virus.</p>
<p>Evolutionary biologists, including myself, have cautioned against over-interpreting the threat posed by mutations. Most mutations will not help the virus, just like randomly kicking a working machine is unlikely to make it better. </p>
<p>But every once in a while a mutation or suite of mutations gives the virus an advantage. The data are convincing that the mutations carried by the variant that first appeared in the U.K., known as B.1.1.7, make the virus more “fit.”</p>
<h2>Higher fitness or chance?</h2>
<p>When a new variant becomes common, scientists determine the reason behind its spread. A virus carrying a particular mutation can rise in frequency by chance if it is:</p>
<ul>
<li>carried by a superspreader;</li>
<li>moved to a new uninfected location;</li>
<li>introduced into a new segment of the population.</li>
</ul>
<p>The latter two examples are called “founder events”: a rapid rise in frequency can occur if a particular variant is introduced into a new group and starts a local epidemic. Chance events may explain the <a href="https://doi.org/10.1016/j.cub.2020.06.031">rise in frequency of several different SARS-CoV-2 variants</a>. </p>
<p>But B.1.1.7 is an exception. It shows a very strong signal of selection. For the past two months, B.1.1.7 has risen in frequency faster than non-B.1.1.7 in virtually every week and health region in England. <a href="https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201">This data, reported</a> on Dec. 21, 2020, helped convince U.K. <a href="https://www.cnn.com/videos/world/2021/01/04/boris-johnson-full-speech-coronavirus-variant-england-lockdown-vpx.cnn">Prime Minister Boris Johnson to place much of the country under lockdown</a> and led to widespread travel bans from the U.K. </p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1347691064430374912"}"></div></p>
<p>The rise of B.1.1.7 cannot be explained by a founder event in new regions, because COVID-19 was already circulating across the U.K. Founder events in a new segment of the population (e.g., following a conference) also aren’t plausible given the widespread restrictions against large gatherings at the time.</p>
<p>Our ability to track the evolution of SARS-CoV-2 is due to the massive effort by scientists to share and analyze data in real time. But the incredibly detailed knowledge we have about B.1.1.7 is also due to just plain dumb luck. One of its mutations altered a section of the genome used to test for COVID-19 in the U.K., allowing <a href="https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576">the picture of evolutionary spread to be drawn from more than 275,000 cases</a>. </p>
<h2>Evolution in action</h2>
<p>Epidemiologists have concluded that B.1.1.7 is more transmissible, but there are no signs that it is more deadly. Some researchers estimate that B.1.1.7 increases the number of new cases caused by an infected individual (called the reproductive number or Rt) by between <a href="https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576">40 and 80 per cent</a>; another preliminary study found that <a href="https://doi.org/10.1101/2020.12.24.20248822">Rt increased by 50-74 per cent</a>.</p>
<figure class="align-center ">
<img alt="A women pushing a cart through a nearly empty airport." src="https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/380037/original/file-20210121-15-1xmrigt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=528&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A woman pushes a luggage cart through Heathrow Airport in London, on Jan. 18, 2021.</span>
<span class="attribution"><span class="source">(AP Photo/Matt Dunham)</span></span>
</figcaption>
</figure>
<p>A 40-80 per cent advantage means that B.1.1.7 isn’t just a little more fit, it’s a lot more fit. Even when selection is this strong, evolution isn’t instantaneous. Our mathematical modelling, as well as that by <a href="https://covid19-sciencetable.ca/wp-content/uploads/2021/01/Update-on-COVID-19-Projections_January-12-2021_Final_English-2.pdf">others in Canada</a> and the <a href="https://www.nytimes.com/live/2021/01/16/world/covid-19-coronavirus#a-fast-spreading-variant-could-become-the-dominant-source-of-infection-in-the-us-by-march-cdc-says">U.S.</a>, shows that it takes B.1.1.7 a couple of months to reach its meteoric rise, because only a small fraction of cases initially carries the new variant. </p>
<p>For many countries, like the U.S. and Canada, where the number of COVID-19 cases has been precariously rising, a variant that increases transmission by 40-80 per cent threatens to push us over the top. It could lead to exponential growth in cases and overwhelm already threadbare medical care. Evolutionary change takes a while, buying us maybe a few weeks to prepare. </p>
<h2>More variants</h2>
<p>One surprise for researchers was that B.1.1.7 bears a remarkable number of new mutations. B.1.1.7 has accumulated 30-35 changes over the past year. B.1.1.7 doesn’t mutate at a higher rate, but it appears to have undergone a bout of rapid change in the recent past. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=489&fit=crop&dpr=1 600w, https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=489&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=489&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=614&fit=crop&dpr=1 754w, https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=614&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/379429/original/file-20210119-23-1p1uyv7.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=614&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Each dot represents a SARS-CoV-2 genome, with branches connecting related viruses to their ancestors. The centre representss the virus introduced into humans. The viruses furthest from the centre carry more mutations. Highlighted in gold are the three new variants.</span>
<span class="attribution"><a class="source" href="https://www.nextstrain.org">(NextStrain)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>The virus may have been <a href="https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201">carried by an immunocompromised individual</a>. People with weaker immune systems fight the virus constantly, with prolonged infections, recurrent rounds of viral replication and only a partial immune response to which <a href="https://doi.org/10.1056/NEJMc2031364">the virus is constantly evolving</a>.</p>
<p>Preliminary research reports that have yet to be verified have described two other variants of concern: one originally from <a href="https://www.doi.org/10.1101/2020.12.21.20248640">South Africa (B.1.351)</a> and one from <a href="https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586">Brazil (P1)</a>. Both variants show a recent history of excess mutations and rapid increases in frequency within local populations. Scientists are currently gathering the data needed to confirm that selection for higher transmission, not chance, is responsible.</p>
<h2>What changed to allow spread?</h2>
<p>Selection plays two roles in the evolution of these variants. First consider the role within those individuals in which the large number of mutants arose. <a href="https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563">B.1.1.7’s 23 mutations</a> and P1’s 21 mutations aren’t randomly arrayed across the genome but clustered in the gene encoding the <a href="https://theconversation.com/new-coronavirus-variant-what-is-the-spike-protein-and-why-are-mutations-on-it-important-152463">spike protein</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/new-coronavirus-variant-what-is-the-spike-protein-and-why-are-mutations-on-it-important-152463">New coronavirus variant: what is the spike protein and why are mutations on it important?</a>
</strong>
</em>
</p>
<hr>
<p>One change in the spike, called N501Y, arose independently in all three variants, as well as in immunocompromised patients studied in the <a href="https://doi.org/10.1056/NEJMc2031364">U.S.</a> and <a href="https://doi.org/10.1101/2020.12.05.20241927">U.K.</a> Other changes in the spike (e.g. E484K, del69-70) are seen in two of the three variants.</p>
<p>Beyond the spike, the three variants of concern share one additional mutation that deletes a small part of the drably named “non-structural protein 6” (NSP6). We don’t yet know what the deletion does, but <a href="https://doi.org/10.4161/auto.29309">in a related coronavirus NSP6 tricks a cellular defence system and may promote coronavirus infection</a>. NSP6 also hijacks this system to help <a href="https://doi.org/10.1080/15548627.2020.1817280">copy the viral genome</a>. Either way, the deletion might alter the ability of the virus to take hold and replicate within our cells.</p>
<h2>Easier transmission</h2>
<p>The parallel evolution of the same mutations in different countries and in different immunocompromised patients suggests that they convey a selective advantage to evade the immune systems of the individuals in which the mutations occurred. For N501Y, this has been backed up by experiments <a href="https://doi.org/10.1126/science.abc4730">in mice</a>. </p>
<p>But what accounts for the higher transmission rate from individual to individual? This is challenging to answer because the many mutations that arose at once are now bundled together in these variants, and it could be any one or a combination of them that leads to the transmission advantage.</p>
<p>That said, several of these variants have arisen before on their own and haven’t led to rapid spread. One study showed that <a href="https://doi.org/10.1101/2020.12.20.20248581">N501Y had only a weak transmission advantage on its own</a>, rising rapidly only when coupled with the suite of mutations observed in B.1.1.7. </p>
<p>While the evolutionary story of COVID is still being written, one important message is emerging now. The 40-80 per cent transmission advantage of B.1.1.7, and potentially the other variants B.1.351 and P1, <a href="https://www.nytimes.com/live/2021/01/16/world/covid-19-coronavirus#a-fast-spreading-variant-could-become-the-dominant-source-of-infection-in-the-us-by-march-cdc-says">will overwhelm many countries in the next few months</a>. </p>
<p>We’re in a race against viral evolution. We must roll out vaccines as quickly as possible, stem the flow of variants by restricting interactions and travel, and get in front of spread by ramping up surveillance and contact tracing.</p><img src="https://counter.theconversation.com/content/153530/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Sarah Otto volunteers on the BC COVID-19 Modelling Group, the Board of The Nature Trust of British Columbia, and on the Species at Risk Advisory Committee to Canada's Minister of the Environment. She receives research funding from the Natural Sciences and Engineering Research Council of Canada.</span></em></p>Multiple COVID-19 variants are circulating around the world and becoming more common. These mutations can alter the ability of the virus to take hold and replicate within our cells.Sarah Otto, Killam University Professor in Evolutionary Biology, University of British ColumbiaLicensed as Creative Commons – attribution, no derivatives.