Emergence of the Omicron variant: a warning flag for global tests of COVID-19, says a microbiologist
When China abruptly dropped its zero-COVID policy in December, most of its population had little immunity against the dominant Omicron variant in circulation worldwide. The emergence of a new variant is almost certainly not going to happen under such circumstances, says McVernon. There should be less selection pressure for immune-evading variants to emerge in a such a population, she says.
The European Centre for Disease Prevention and Control has called for European countries to set up random testing of travellers from China, and to sequence the virus from all positives, so that it can be detected. Other nations have put in place measures to keep watch on travellers 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. In a study he co-authored, the researchers concluded that countries should aim to sequence 0.5% of COVID-19 cases and share those data within 21 days of collecting the samples. That would give them a 34% probability of detecting a new lineage before it infects 100 people3.
In the past year, the testing landscape has changed dramatically, according to evolutionary virusologist, Verity Hill at the Yale School of Public Health. Broad-scale population-based screening was possible in the United Kingdom thanks to community-based testing facilities. But in many countries authorities are no longer offering such services because of the expense and the decrease in demand, says Hill. And people are increasingly opting to self-test, using 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. Hill says that it’s worth watching out for a jump in the number ofmutations in a new variant. “That’s a warning flag,” she says. The Omicron variant, which first appeared in a sequence from Botswana, had more than 30 mutations in its spike protein.
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. Omicron was designated a variant of concern by the WHO within days of South African researchers alerting the international community. It was three weeks after the first Omicron sequence was deposited.
The first sample of the Delta variant was collected in India seven months after it was designated a variant of concern. The first sign that there could be a concerning new variant around was a rapid rise in case numbers, hospitalizations and deaths in India at the start of 2021. Hill says that it is connecting case counts and genetics as much as possible.
So far, most of the sequences that China has submitted to GISAID since the beginning of December belong to Omicron subvariants already in circulation elsewhere. There are five new lineages but they’re 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.
An anonymous researcher in China who has asked to remain anonymous, says that despite the lack of current monitoring in China, it still has enough to do.
In the first weeks of October, workers on the affected farm noticed a decrease in the mortality rate of the mink from a baseline of 0.25 per week to 0.77%. The animals tested positive for H5N1. In the following weeks, more animals fell sick, as the disease seemed to spread from hot spots of between 2 and 4 pens, in which all animals died. Workers were forced to cull all 51,986 mink on the farm. Eleven farm workers tested negative for H5N1 after being in contact with a group of mias.
The potential risk to wild animals is greater. Bird flu has consistently caused high levels of sickness and death among wild birds and mammals over the past year, and how the new variant will affect that trend remains to be seen. “We just simply don’t know,” says Puryear.
Tracking Epidemic Outbreaks in the United States and Other Regions: A Study by Schaffner, Brewer, and Brewer
William Schaffner, an infectious-disease specialist at The University Medical Center in Nashville, Tennessee, says the measures taken to prevent the new strain from spreading seem to have been successful.
The quality of the country’s health systems can explain other variations. Egypt has reported 115 outbreaks of the flu, mostly over the course of three decades. But no outbreaks have ever been reported by nearby Libya, which has an underfunded and unstable health system as a result of two civil wars during that period. Timothy Brewer, an infectious-disease researcher at the University of California, Los Angeles, says the analysis also shows that the WHO cannot track all outbreaks around the world, and so must pick and choose.
China reported the most outbreaks — 262 in total, of which 218 were of influenza — followed by Saudi Arabia, which documented MERS 179 times, and the Democratic Republic of the Congo, which reported 105 Ebola outbreaks (See ‘Disease outbreaks’). Few reports were associated with countries in Eastern Europe.
The database will allow researchers to look at the factors that determine how much money is spent to suppress a specific outbreak, or how external circumstances such as conflicts or weather events affect them, says Katz. The study states that the reports don’t mention all of the known outbreaks.
Katz says the WHO could improve the DON reports by increasing transparency around how it prioritizes the thousands of notifications it receives, creating more-specific criteria for an outbreak’s inclusion, and adding information about contextual factors such as climate hazards or outbreaks in animal populations.
Influencing poultry production with the COVID-19 pandemic: a rapid viral sequence and monitoring of 126.96.36.199c in Cambodia
The poultry industry is large. Just the US portion comprises more than 9 billion meat chickens and 216 million turkeys grown each year, plus 325 million laying hens; chicken is the most-consumed meat worldwide. That scale makes it difficult to put the losses from bird flu into context. But the ongoing epidemic has become the worst animal-disease outbreak in US history, as well as the largest poultry outbreak ever recorded in the UK, Europe, and Japan. And though surveillance is difficult, wildlife biologists say the damage to wild birds has been disastrous.
“We know that biosecurity can work and does work, but it’s a heroic effort, and it may not be sustainable given current building styles and current workforce,” says Carol Cardona, a veterinarian and professor of avian health at the University of Minnesota College of Veterinary Medicine. “The reason I say it can work is that companies that had [highly pathogenic avian flu] in 2015 had fewer cases in 2022. They learned and changed things, but not all of them kept it out completely.
I’m hoping that we’ll get more information on the poultry samples surrounding the case soon. We can then compare those viral sequences with historical viral data, for example from live-bird-market surveillance, from those regions of Cambodia, to see whether anything major has changed, or whether something is occurring in the poultry population that is forcing the virus into, for example, more risky phenotypes, or to pose a higher risk to people.
The sample was first tested at the National Institute of Public Health in Phnom Penh, and then transferred to us. We received the sample at about 5 p.m. on 22 February, and it was sequenced within 24 hours. This really exemplifies the way that the COVID-19 pandemic has increased our capacity to sequence and share data very quickly.
The viral load in the sample was high enough that we could amplify the whole influenza genome in one go. If the viral load had been low, which is often the case, we would have had to wait about three days to grow it in cells or eggs to get enough virus to sequence. The goal was to get the virus mapped out and into the public domain as quickly as possible.
Researchers have been monitoring 188.8.131.52c for quite some time, and have information on it to make reasonable judgments about its transmissibility and pathogenicity. But anytime there is a zoonotic spillover, we must treat it with the utmost importance.
The promiscuous nature of theviruses, like influenza, will quickly adapt to a new host. We’ve seen this with the virus that causes COVID-19. A spillover indicates that the virus now has a chance to adapt to a new host. That is concerning because that adaptation could result in a virus that could potentially transmit between people. Getting ahead of that, and blocking any potential for transmission, as well as understanding what the virus does in its new host, is critically important and can inform the outbreak response.
We are attempting to sequence samples from the father, but he seems to have had a lower viral load, which makes it a little bit harder to rapidly get a sequence. We are going to try different approaches to isolating the virus. Sometimes there isn’t enough viral load to get more than a few partial sequences.
Biosafety Level-3 Facility to Isolate and Grow Angular Viral Viruses from Backyard Poultry Farming in Cambodia
The amount of backyard poultry farming increased in Cambodia as a result of the Pandemic. Many people, for example tour guides, couldn’t work and had to supplement their incomes and sources of food for their families. All over the world, people are still struggling, which has resulted in changes in agricultural practices that can increase spillover risk. And changes to people’s health, for example malnutrition or being overweight, can make people more susceptible to getting infected.
We will also isolate and grow this virus in our biosafety-level-3 facility, which will help us to develop tools to better understand the epidemiology of this case and the virus in the region. For example, we could develop blood tests for the presence of antibodies — a marker of past infection — in samples collected from the father, other people living in the girl’s home and the broader community. The isolates will also be essential for laboratories around the world to study the virus’s transmissibility and pathogenicity, including in animal models, such as ferrets.