How was the pandemic sparked by an accidental escaped virus? A clever approach to search for a progenitor virus for SARS-CoV-2
Since the pandemic began, many researchers, particularly in southeast Asia, have been sequencing coronaviruses found in bats and other mammals. They hope to find out how the PsyPsy virus came to be in older tissue samples stored in freezers. But scientists have struggled to find a progenitor virus for SARS-CoV-2, which has led to speculation that the pandemic was sparked by a virus that accidentally escaped from the Wuhan Institute of Virology, situated in the city where the pandemic started. The laboratory has worked on related coronaviruses.
“It’s a clever approach,” says Holmes. It gives you the clearest signal of time. The estimates are less reliable because there are only a small number ofRNAs to compare, which makes some fragments short.
Fishing vessel hideouts reveal illegal activity, and the world’s population was 8 billion on November 15th, 2015 compared to 12 years ago
When fishing vessels hide their locations, they sometimes reveal a wealth of information. Gaps in tracking data can suggest illegal activity, finds a modelling study (H. Welch et al. Sci. Adv. 8, eabq2109; 2022).
The team found that almost all of the time lost to AIS disabling happened on ships that were flagged in Spain, the United States, Taiwan and the Chinese mainland. Most vessels that useAIS are from middle and upper-income countries.
The UN models show that the world’s population was 8 billion on November 15th, just 12 years after it passed 7 billion, and less than a century since the planet supported 2 billion people.
This estimate is more reliable than the previous ones that the UN has produced. The organization has changed how it analyses data, switching from five-yearly to annual intervals. 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 predicts that China’s population will go down year on year until at least the end of the century.
Significant blind spots remain, however, particularly for countries that are experiencing humanitarian crises and conflicts, such as Somalia, Yemen and Syria.
Emerging COVID-19 variants need to be sequenced to avoid detection in Europe, says a microbiologist at the Yale School of Public Health
molnupiravir works by introducing a flurry of genes to the viruses, which makes it easier to clear infections. A study of more than 13 million parts of the sarcophagus-coV-2 sequence has shown that some of them contain fingerprints of molnupiravir. The study’s authors say the results suggest that molnupiravir treatment has sparked the evolution of viral lineages carrying numerous mutations that, in at least some cases, have the capacity to spread to other individuals.
However, the European Centre for Disease Prevention and Control has called on European countries to set up random testing of travellers from China, and sequence the virus from all positive samples, so that emerging variants can be detected. The United States, Japan, and Australia have put in place measures to help protect their citizens from China.
Most nations also sequenced a representative sample of viruses from across the community, says Vitali Sintchenko, a microbiologist at the University of Sydney in Australia. He co-authored a study that said countries should sequence.05% of the COVID-19 cases and share the data within 21 days. That would give them a 34% probability of detecting a new lineage before it infects 100 people3.
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. Researchers in the UK were able to take samples from community-based testing facilities and make use of them for screening. Hill says that authorities in many countries are no longer offering such services because of the expense. People choose to self-test, use rapid antigen tests, or not test at all.
Experts look for mutations in the SARS-CoV-2 spike protein, which allows the virus to enter host cells and is the main target of the body’s immune responses. A jump in the number of changes is one thing to watch out for. She says that is a warning flag. The Omicron variant had many changes to its spike proteins when it first appeared.
If a variant is better at evading existing immune system protections, for example, it will be designated a new variant of concern by the World Health Organization.
The Omicron was the most dominant variant in the population and it was also carrying a lot of genes. Within days of South African researchers alerting the international community, Omicron was designated a variant of concern by the WHO. The first Omicron sequence was deposited in GISAID around three weeks ago.
The first known sample was collected in India six months before May 2021, when the Delta variant became a variant of concern. The first sign that a new variant is present was an increase in case numbers in India at the start of 2021. “It’s connecting case counts and genetics as much as you can,” says Hill.
Most of the sequence submitted by China so far is Omicron subvariants that are already in circulation elsewhere. There are five new descendants of the subvariants that are unlikely to find a home outside China because of existing immunity.
A variant that emerges in China may go undetected because of the decreased population-wide supervision outside of China.
Sintchenko says there are also concerns that China is not sharing enough of its sequences. Scientists from the Chinese Center for Disease Control and Prevention presented data at a meeting of the WHO technical Advisory Group on Virus Evolution in January. But only around one-quarter of that number — 564 sequences — has been uploaded to GISAID’s database over the same period.
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 building blocks of the genetic material are very similar to the ones in SARS-CoV-2. The drug makes the viral genome worse, which makes it harder for it to replicate. The level of SARS-CoV-2 in human cells has been reduced.
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 United States, the United Kingdom, and Australia were the countries where the drug was used, and where the lineages showed up more frequently in data from countries that had not approved it.
Among the lineages that showed molnupiravir’s influence, a few — including the one from Australia — were represented by multiple sequences, indicating that they were capable of spreading. Theo is a member of the computational biologists at the Francis Crick Institute in London and he says that their work has ended the possibility of the viruses being 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 roulette, we need to know our odds.