An ancestor of the SARS-CoV-2 virus discovered in bat coronaviruses: a phenomenological comparison
Scientists compared the fragments of the coronavirus’s genomes at the 7th World One Health Congress in Singapore. The results suggest that some sections of bat coronaviruses and SARS-CoV-2 shared a common ancestor as recently as 2016 — just three years before the virus emerged in people in late 2019. The work has not been peer reviewed.
He says it’s a clever approach. “It gives you the purest signal of evolutionary time.” He points out, however, that some fragments were quite short, which makes those estimates less reliable because there are only a limited number of RNA nucleotides to compare.
What do fish vessels tell us about the world? A new prediction from the United Nations, and consequences for human development and humanitarian crises based on China
Fishing vessels give a lot of information when they hide their locations. Gaps in tracking data can suggest illegal activity, finds a modelling study (H. Welch et al. Sci. Adv. 8, ec2109; 2022.
The team found that on ships from Spain, the US, Taiwan and the Chinese mainland, almost all of the time lost to disabling was. However, most vessels that use AIS come from middle- and upper-income countries.
According to models from the United Nations (UN), the world’s population reached 8 billion on 15 November — a mere 12 years since it passed 7 billion, and less than a century after the planet supported just 2 billion people (see ‘People of the world’).
This could be the most reliable estimate that the UN has come up with. The organization now analyses data at annual intervals instead of five-yearly. And there has been a steady improvement in recent decades in the ability and capacity of many countries to collect statistics.
The most significant factor behind the UN’s updated forecast is that data from China have been more reliable since the end of the country’s one-child policy in 2015. The UN predictions suggest that China’s population has already peaked, and will now shrink year-on-year until at least the end of the century.
There are still significant blind spots when it comes to humanitarian crises and conflicts, such as Syria and Yemen.
Emergence of a new COVID-19 variant is unlikely in the Chinan population, says evolutionary virologist Jodie McVernon
Most of the population in China had little immunity against the dominant Omicron variant, when China dropped its zero-COVID policy in December. Jodie McVernon at the Doherty Institute says that it is unlikely that a new variant will emerge. She says selection pressure for immune-evading variant should be less in such a population.
The European Centre for Disease Prevention and Control has called on European countries to set up random testing for travellers from China and sequence the virus from all positive samples, so that emerging variant can be detected. Other nations, including the United States, Japan and Australia, have also put surveillance measures in place for travellers from China.
The study, which also looked at sequencing efforts in 189 countries up to the end of February 2022, found that during the first two years of the pandemic, 78% of high-income countries sequenced more than 0.5% of their COVID-19 cases, with some, including Denmark, Japan and the United Kingdom, consistently sequencing more than 5% of cases each week. The earlier such data are gathered and shared, the faster scientists can run laboratory tests to look at the new variant’s immune evasion, resistance to antiviral drugs and ability to infect cells, says Sintchenko.
But the testing landscape has changed drastically over the past year, says evolutionary virologist Verity Hill at the Yale School of Public Health in New Haven, Connecticut. Broad-scale population-based screening was feasible in countries such as the United Kingdom because researchers could tap into samples collected at community-based PCR testing facilities. Hill says that authorities in many countries are no longer offering these services because of expense and decrease in demand. And people are increasingly opting to self-test, using rapid antigen tests, or not test at all.
The main targets of the body’s immune responses are the host cell and spike protein of the SARS-CoV-2 virus. There is a chance that a jump in the number of mutations is something to watch out for. She says that it is a warning flag. The Omicron variant has more than 30 changes in the spike protein, which was first found in a sequence from Botswana.
The World Health Organization (WHO) only designates a new ‘variant of concern’ if a variant is better at evading existing immune system protections, causes more severe disease or is much more transmissible than currently circulating variants.
Omicron not only contained many mutations, but also rapidly became a dominant variant in the population, suggesting it was spreading faster than, and out-competing, other variants in the community. Within days of South African researchers alerting the international community to the variant’s rapid spread, the WHO designated it a variant of concern. That happened nearly three weeks after the first sequence was deposited.
The Delta variant was designated a variant of concern in May 2021, seven months after the first known sample was collected in India. There was a rapid rise in case numbers in India at the beginning of 2020 and this is a sign that there was a new variant around. Hill says that case counts and genetics are connected as much as possible.
Since the beginning of December, China has submitted a majority of the sequences that it has received to the GISAID. There are five new lineages — descendants of those subvariants — but these are unlikely to gain a foothold outside China, because of pre-existing immunity.
But the decreased population-wide surveillance outside China makes it more likely that a variant that emerges in China might initially go undetected, says Hill.
China is not sharing enough of the sequence according to Sintchenko. At the 3 January meeting of the WHO’s Technical Advisory Group on Virus Evolution, the scientists from the Chinese Center for Disease Control and Prevention presented their data on the over 2,000 genomes collected and sequenced since December 1. Only one-quarter of the sequence has been uploaded to the database.
Molnupiravir was developed by the pharmaceutical giant Merck, based in Rahway, New Jersey, and was authorized by regulators in the United States and United Kingdom in late 2021, and in Australia in early 2022. A company-sponsored clinical trial found that the drug — a pill taken for five days — reduced hospitalizations and deaths in people at risk of severe COVID-19.
The evidence that molnupiravir is linked to the big sequence is not conclusive. “The authors assume these mutations were associated with molnupiravir treatment without evidence the viral sequences were isolated from treated patients.”
The researchers’ analysis of global sequences showed that the prevalence of the suspect lineages rose substantially in 2022, the first year molnupiravir was widely used. The lineages were also much more likely to show up in sequencing data from countries where the drug was used — the United States, the United Kingdom and Australia — than in data from countries that hadn’t approved it, such as France and Canada.
Some of the lineages showing molnupiravir’s influence were represented with multiple sequences, which signaled that they were capable of spreading. Theo Sanderson is a Computational Biologist at the Francis Crick Institute in London and said that the work closes down the possibility that the virus can never be transmitted.
Rustem Ismagilov, a quantitative bioscientist at the California Institute of Technology in Pasadena, says the study underscores the need to quickly measure any risk that molnupiravir poses to sparking new variants and weigh them against the drug’s benefits. If we are playing Russian roulette we should know our odds.