The new Covid variants are a peril to us all

The writer, an epidemiologist at the London School of Hygiene and Tropical Medicine, is author of ‘The Rules of Contagion’

During every major epidemic I’ve worked on, there has been speculation about virus mutations. Mostly these mutations are innocuous, just random errors in a virus’s genetic code that don’t change how it infects or spreads. But every now and then, a collection of mutations crops up and dramatically changes the threat we face. In recent weeks, researchers have noticed three troubling new Sars-Cov-2 variants scattered among the various virus lineages circulating globally. Such variants could well change the pandemic’s shape in 2021. 

The first new variant was detected in south-east England in autumn 2020. It sparked concern after spreading easily, despite the control measures in place during November, outpacing existing variants to become dominant in much of the UK by the end of December. Early analysis of contact tracing data and local epidemic growth suggested this variant could be 40 to 70 per cent more transmissible than earlier viruses. It has since been detected in other countries, with initial patterns in Denmark and Ireland consistent with its accelerated growth in the UK. 

One of the challenges with a new variant is what to call it. Public Health England simply called it “Variant of Concern 202012/01”. The Covid-19 Genomics UK Consortium, who detected the variant, referred to it as “B.1.1.7” because it mutated from the existing “B.1.1” European lineage of Sars-Cov-2 viruses. The Nextstrain virus tracking platform dubbed it 501Y.V1, after one of the mutations it had picked up. 

Not long after 501Y.V1 came under scrutiny in the UK, another variant — now known as 501Y.V2 — became a concern in South Africa. As the name suggests, it shared some mutations with its UK-based relative, particularly a change in the “spike” protein that may help the virus latch on to cells more easily. There were also some differences. While 501Y.V1 seems to transmit more readily in the UK, early data suggests immunity from past infection or vaccination should protect against it. In contrast, 501Y.V2 has a mutation that makes it better at dodging immune responses in lab studies. It does this by changing the virus’s appearance, essentially giving a familiar trespasser a new disguise. 

As 501Y.V2 has become dominant in South Africa, cases and deaths have surged. This is despite evidence of considerable antibody levels following the 2020 epidemic wave, and the country’s coming summer months.

There’s been a similar puzzling resurgence of cases in Manaus, Brazil. Recent analysis of antibody levels among blood donors suggested the majority of the population was infected in 2020. Yet in early 2021, hospitalisations and deaths grew again. This coincided with detection of a third concerning variant, 501Y.V3, which shares similarities with the one in South Africa. By mid-December, almost half the Sars-Cov-2 viruses analysed in Manaus were 501Y.V3.

There have also been new outbreaks in areas of Colombia and Peru that have substantial antibody levels from earlier waves, leading to suspicions that new variants are circulating there too. Even if they don’t cause more severe disease for individuals, increased transmission could mean far more cases — and hence hospitalisations and deaths.

The emergence of three new variants with shared characteristics raises the possibility of “convergent evolution”, with viruses independently adapting to human populations around the world in similar ways. The many mutations in some of these variants — 23 for 501Y.V1 in the UK — suggests they may have emerged in an immunocompromised patient; chronic infections can give viruses more chances to adapt than in a patient who recovers quickly.

So where might this all lead? For viruses like HIV, there’s evidence that evolution can eventually result in less severe variants, as a virus that kills hosts quickly may not spread as easily as one that causes milder infection. Given that Sars-Cov-2 transmission tends to happen early in an infection, before someone becomes severely ill, it’s not clear that a less deadly Sars-Cov-2 virus would have an evolutionary advantage over existing variants. However, as epidemics and vaccination campaigns lead to growing immunity, there could be additional pressures on viruses to evolve. One recent study suggests seasonal coronaviruses evolve gradually to evade immunity generated in preceding years, leading to reinfections over time.

During every epidemic, there is debate about how to tackle the next disease threat. But these new variants — and the realisation there may be more out there undetected — suggests this debate is no longer hypothetical. The new strains should be treated as new threats, and countries urgently need to decide how to tackle them.

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