COVID-19: Global virus radar drops as genomic surveillance fails

Complacency abounds on COVID-19. With governments, employers and many ordinary citizens pretending the pandemic is over, complacency threatens to bite hard unless there is a reality check. One of the most concerning consequences of this complacency, or wishful thinking, is the slackening of genomic surveillance by scientists. Genomic surveillance is the early warning system for tracking new infectious diseases. Its role with the SARS-CoV-2 virus, which causes COVID-19, has been to track the spread of variants, monitoring changes to the genetic code of these strains and sub-strains. This is done by a laboratory method called genomic sequencing. As everyone should already know, the virus evolves as it spreads and new mutations can emerge that help the virus to defeat our immune system and infect human cells with greater efficiency. According to the World Health Organisation, the number of SARS-CoV-2 sequences submitted to GISAID, an international repository of viral genetic information, has dropped by 90 per cent since the start of 2022 and the number of countries submitting data has fallen by one-third. “Gaps in surveillance, testing and sequencing mean we do not understand well enough how the virus is changing,” WHO director-general Dr Tedros Adhanom Ghebreyesus said. The very first sequence of SARS-CoV-2 was shared with the world three years ago. “We urge all countries now experiencing intense transmission to increase sequencing and share those sequences,” he said. Dr Maria Van Kerkhove, an epidemiologist who is the technical lead on COVID-19 at the organisation, says the drop-off is a symptom of complacency about the disease. So it was vital to be vigilant and maintain rigorous surveillance. “As sequencing becomes less and less available at a global level, it’s difficult for us to track each of the subvariants of (the prevailing variant) Omicron,” Dr Van Kerkhove said. Another worry at this stage of the pandemic is the possibility of recombinant viruses. These happen when someone is infected with two variants simultaneously. This allows the pair to swap genetic material, resulting in offspring that carry mutations from both. That permits particularly troublesome combinations. The subvariant that is presently surging in the US, XBB.1.5 - known as the Kraken - is an example of a recombinant. It evolved from a fusion of two lineages. The original XBB lineage was good at dodging antibodies but poor at latching on to human cells (which determines infectivity). XBB.1.5 is good at both. The biggest concern held by Dr Kerkhove and others is the emergence of a new variant that has these two capabilities, plus another — the propensity to cause more severe disease. This third prong in COVID-19’s trident has thankfully been absent in the Omicron strain or any of its sublineages since Omicron displaced the Delta strain in late 2021. Omicron is unlikely to be the last variant of SARS-CoV-2. The next one could appear from any part of the globe where it is spreading. And the more spread the higher the likelihood, which is why the WHO has pleaded with Chinese authorities for as much information as it can provide, including results of genomic sequencing, in light of the explosion of cases in China after Beijing suddenly dropped its tough preventive controls. An estimated 900 million Chinese had been infected with COVID-19 up until January 11, representing 64 per cent of the population. To date results obtained show no nasty surprises and indicate the strains circulating in China are the same ones that have been seen elsewhere. “While the Chinese Centre for Disease Control and Prevention has earlier reported that Omicron sublineages BA.5.2 and BF.7 are currently circulating, WHO continues to ask that further sequences be shared with open access databases such as GISAID . . . and for continued collaboration with technical groups working on virus evolution, clinical care, and beyond,” a WHO spokesperson said on January 14. China’s official tally of 503,000 cases, isn’t plausible, according to Professor Michael Toole, associate principal research fellow at Burnet Institute in Melbourne. “Even if China has not yet reached 900 million cases, lessons from other countries with similarly abandoned public health measures say it soon will,” Professor Tool wrote in The Conversation. “The world may not see the full impact of the surge in China for another month or so. “During the Lunar New Year period, an expected two billion trips will be made within China. This will transmit the virus to remote rural villages where there is minimal health care and no genomic sequencing facilities. So, the virus could infect an immunocompromised individual who may harbour the virus for months. This could result in a mutation that emerges as a more transmissible variant. “Many countries, including Australia, insist on travellers having a negative COVID test within 48 hours of departure. Others like South Korea, Taiwan, Japan and Italy also require tests on arrival. South Korea has reported 23 per cent of travellers from China tested COVID-positive “So, the Australian policy of pre-departure testing makes sense but should also include the routine testing of wastewater from planes arriving from China. “That said, a new variant originating in China may not arrive directly but via countries, such as Indonesia, that do not require pre-departure testing. Random testing of wastewater on all arriving international flights would be helpful.” Regardless of any Chinese contribution, though, experts say periodic COVID waves are here to stay. That is because none of the Covid-19 vaccines so far available is good at preventing infections for more than a short period after administration. Dealing with SARS-CoV-2 variants is therefore less a matter of stopping transmission than of constant monitoring and adjusting COVID tests, treatments and vaccines as needed. And it is this monitoring which is getting harder. The WHO’s COVID-surveillance system relies on genomic-sequence data submitted from laboratories around the world to organisations such as GISAID, to show which variants are becoming dominant in various parts of the planet, whether those variants are more virulent, and how successful drugs and vaccines are against them. No sequences means no information on these points. Similarly, the WHO also tracks the proportion of cases caused by new variants that require admission to hospital, and, once there, transfer from normal wards to intensive care. That helps gauge changes in severity. But the means to collect these data, too, are disappearing, according to Dr Van Kerkhove. There is a deeper problem, as well. Dismantling the testing, sequencing and surveillance capacity built up in the past three years risks leaving the world unprepared for the next pandemic. Professor Toole said Australians similarly need to drop their complacency. “We need to improve our vaccination booster rate, make a serious investment in clean indoor air, use high-quality masks in poorly ventilated settings and provide easy access to COVID testing,” he said. “Currently, because of our misplaced comfort with widespread transmission, these measures are flagging or absent. That’s at our peril.” The prestigious medical journal, The Lancet, also cautioned against complacency last weekend, when marking the third anniversary of COVID-19. “Despite many efforts to learn from the pandemic during the past three years, and discussions on international treaties of pandemic preparedness, the global response remains inadequate and fragmented,” it editorialised. “In 2023, far from it being the end of the pandemic, there is a new, dangerous phase that requires urgent attention. “Rather than hoping for the end, letting our guard down, and thinking that the problem is somewhere else, everyone needs to remain alert; encourage maximum transparency in reporting cases, hospital admissions, and deaths; and accelerate collaborative surveillance of variant testing and vaccinations. The pandemic is far from over.” WITH THE ECONOMIST