{"id":21485,"date":"2022-03-07T10:53:27","date_gmt":"2022-03-07T09:53:27","guid":{"rendered":"https:\/\/ppr-antibioresistance.inserm.fr\/?p=21485"},"modified":"2022-03-07T10:53:31","modified_gmt":"2022-03-07T09:53:31","slug":"how-tracking-coronavirus-variants-will-prepare-us-for-the-next-global-public-health-threat","status":"publish","type":"post","link":"https:\/\/ppr-antibioresistance.inserm.fr\/fr\/informations-et-communications\/actualites\/how-tracking-coronavirus-variants-will-prepare-us-for-the-next-global-public-health-threat\/","title":{"rendered":"How tracking coronavirus variants will prepare us for the next global public health threat"},"content":{"rendered":"\n

Published on MIT Technologie Review <\/a> on February 23, 2022<\/p>\n\n\n\n

Genomic surveillance of SARS-CoV-2 is helping us spot new variants and figure out how to respond. What else could it help us do? By\u00a0Linda NORDLING<\/p>\n\n\n\n

Tulio de Oliveira cuts a lonely figure as he paces across the parking lot of\u00a0Stellenbosch University<\/a>\u2019s new $100 million biomedical research building. It\u2019s early January, the height of summer in South Africa, and most students and staff are on holiday. But not de Oliveira. He\u2019s on a conference call with the country\u2019s president, Cyril Ramaphosa.<\/p>\n\n\n\n

It\u2019s the second time they\u2019ve spoken in just over a month. The first was right after his genomic sequencing lab had discovered a new covid variant. Today, they\u2019re talking about something else\u2014de Oliveira doesn\u2019t want to give specifics. The call has lasted for some time, and de Oliveira is pacing because he is, by his own admission, not a patient man. Still, his science is directly influencing policy\u2014something he relishes.<\/p>\n\n\n\n

\u201cThe pandemic has changed the way that science is done,\u201d he tells me once he\u2019s off his call. For one thing, science is happening faster. Six weeks earlier, his team had suddenly felt \u201ca little weirded out\u201d by a resurgence of covid cases in Gauteng, the country\u2019s most populous province. This uneasy feeling prompted a flurry of sequencing activity. It took them only a day to identify the highly transmissible new variant now called omicron. They briefed the health minister and the president, and spent another day checking their work. Then, on November 25, de Oliveira announced the discovery to the world.<\/p>\n\n\n\n

Omicron, which is better at evading the body\u2019s immune defenses than its cousins, has since spread everywhere, fueling unprecedented waves of the pandemic. In early January, it was causing\u00a0weekly infections to rise<\/a>\u00a0by\u00a065% in Europe, 78% in Southeast Asia, and 100% in the Americas<\/a>. Deaths were rising too, albeit more slowly.\u00a0<\/p>\n\n\n\n

Still, the team\u2019s detection and identification of the new variant in November provided a crucial early warning to the rest of the world. In the weeks after the discovery, scientists subjected omicron to a battery of tests. Massive efforts quickly got underway to understand its sensitivity to existing covid vaccines and figure out just how infectious and lethal it was. Policy-wise, the discovery sparked an uptick in booster vaccinations, renewed restrictions, and travel bans.\u00a0<\/p>\n\n\n\n

Before covid, de Oliveira was sequencing scourges like Zika, chikungunya, and tuberculosis from his base in Durban. The pandemic injected unprecedented resources into his field and generated immense political interest in his work. The lab at his new\u00a0Centre for Epidemic Response and Innovation<\/a>\u00a0is stocked with millions of dollars\u2019 worth of equipment\u2014much of it donated by wealthy labs, international health organizations, and manufacturers. Eventually, it\u2019s expected to be the most powerful sequencing lab in Africa.<\/p>\n\n\n\n

The spread of SARS-CoV-2 set off an avalanche of genomic sequencing all around the world. More than 7.5 million viral sequences have been uploaded to the global database\u00a0GISAID<\/a>, and scientists have sorted millions into\u00a0tree diagrams<\/a>\u00a0tracking the virus\u2019s evolution. That\u2019s the most sequences generated and shared for any germ by far. Sequencing has also grown more common in parts of the world that didn\u2019t have the technology before, which will be vital in spotting any new threats as they arise.\u00a0<\/p>\n\n\n\n

The glut of data on SARS-CoV-2 has allowed scientists to track, in close to real time, how the virus is evolving. And it\u2019s transformed the way we use genomic sequencing to inform health policy, says\u00a0Sharon Peacock<\/a>, a microbiologist at the University of Cambridge who leads the\u00a0UK\u2019s covid genomics consortium<\/a>. \u201cIf we look at previous threats, sequencing was used as a research tool, in a retrospective way,\u201d Peacock says. \u201cNow we have seen that sequencing can provide actionable information.\u201d<\/p>\n\n\n\n

With covid, scientists have tried to see if they can forecast how variations in a germ\u2019s genetic sequence might influence how it behaves in people and even help predict its next move. While there remain gaps in the global sequencing effort, which might allow variants to circulate undetected, capacity on continents like Africa has increased dramatically. And de Oliveira and his colleagues want to go further. <\/p>\n\n\n\n

While keeping an eye on covid, they want to use the momentum and funding they\u2019ve amassed for genomic sequencing to tackle other diseases, like tuberculosis, HIV, and viral hepatitis. And they want to see if the technology can give us an edge in the ongoing and deadly fight against antimicrobial resistance. <\/p>\n\n\n\n

Indeed, the full value of this work may not become clear until long after the pandemic recedes.<\/p>\n\n\n\n

\n\n\n\n

The science behind genomic tracking for viruses these days is relatively simple. To sequence a SARS-CoV-2 genome, scientists isolate the viral RNA from a patient sample such as a positive covid test swab. Then they process the RNA into a form that sequencing machines can read. <\/p>\n\n\n\n

Twenty years ago, it cost $100 million to sequence one human genome. Today, it costs less than $1,000. However, it\u2019s still not cost-effective to sequence every positive covid test to look for new mutations. So de Oliveira and his team prioritize samples from areas with unexpected upticks in infections reported by national laboratories or doctors in the field. <\/p>\n\n\n\n

Using this targeted approach, which he calls \u201cnonlinear sequencing,\u201d they were able to raise the alarm about not one but two variants of concern discovered in South Africa: omicron in November 2021, and beta a year earlier in the Eastern Cape province. <\/p>\n\n\n\n

While the rapid detection of new, more infectious versions of SARS-CoV-2 has certainly spurred governments and health systems to act, it has not stopped those variants from spreading. However, knowing about new variants does offer some time to prepare, Peacock says. Many countries rolled out booster vaccinations after scientists established that omicron was better at dodging our immune defenses. \u201cThere can\u2019t be any doubt in anyone\u2019s mind that real-time sequencing has had a real impact during the pandemic,\u201d she says.<\/p>\n\n\n\n

It\u2019s difficult to quantify the exact impact sequencing has had on hospitalizations or deaths. As one measure, using data from South Africa and elsewhere on how omicron behaved, scientists in the US estimated in early January that doubling the number of boosters given could prevent 41,000 deaths and more than 400,000 hospitalizations by the end of April.\u00a0<\/p>\n\n\n\n

Emma Griffiths, a genomic data expert based at\u00a0Simon Fraser University<\/a>\u00a0in Vancouver, Canada, says genomic surveillance has helped us understand why our diagnostics, vaccines, and therapeutics have become less effective over time, allowing us to update our arsenal of weapons. The pandemic has also built a backbone for sharing genome data across borders, she adds, which could be useful in future outbreaks. And just as important, the global SARS-CoV-2 sequencing boom helped establish sequencing technology in areas that did not have it, or had very little, before the pandemic.<\/p>\n\n\n\n

\n\n\n\n

In Peru, genomic sequencing was very \u201cniche\u201d before covid, says\u00a0Pablo Tsukayama<\/a>, a microbiologist at\u00a0Universidad Peruana Cayetano Heredia<\/a>\u00a0in Lima. But since April 2020 his lab has received increased funding from the government, which allowed it to discover a new variant of concern, lambda, by the middle of 2021.\u00a0<\/p>\n\n\n\n

While this discovery came too late to prevent the huge wave of illness that lambda caused in Peru, which racked up some of the world\u2019s highest excess mortality rates, he says Peru\u2019s new sequencing capacity will help it track new pathogens coming out of the Amazon rainforest, an area rich in biodiversity where diseases are at high risk of spilling over from animals to humans. <\/p>\n\n\n\n

\u201cWe need to be able to ring the alarm early,\u201d he says. \u201cThat\u2019s where my lab is going.\u201d<\/p>\n\n\n\n

Two thousand miles south of Lima, in Argentina\u2019s capital city, Buenos Aires,\u00a0Josefina Campos<\/a>\u00a0is also reaping the rewards of the pandemic\u2019s sequencing boom. Before covid, her genomics lab didn\u2019t actually do surveillance. Sequencing was a retrospective scientific pursuit rather than a tool to assist in public health. Now \u201ceveryone wants to sequence,\u201d she says.\u00a02022<\/p>\n","protected":false},"excerpt":{"rendered":"

Published on MIT Technologie Review on February 23, 2022 Genomic surveillance of SARS-CoV-2 is helping us spot new variants and figure out how to respond. What else could it help us do? By\u00a0Linda NORDLING Tulio de Oliveira cuts a lonely figure as he paces across the parking lot of\u00a0Stellenbosch University\u2019s new $100 million biomedical research […]<\/p>\n","protected":false},"author":139,"featured_media":21491,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[31],"tags":[],"acf":[],"yoast_head":"\nHow tracking coronavirus variants will prepare us for the next global public health threat - Interface nationale ANTIBIOR\u00c9SISTANCE<\/title>\n<meta name=\"description\" content=\"Informations, \u00e9v\u00e8nements et actualit\u00e9s autour de l'Antibior\u00e9sistance en France et \u00e0 l'international.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ppr-antibioresistance.inserm.fr\/fr\/informations-et-communications\/actualites\/how-tracking-coronavirus-variants-will-prepare-us-for-the-next-global-public-health-threat\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How tracking coronavirus variants will prepare us for the next global public health threat - 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