Virus World

Repeated emergence of SARS-CoV-2 variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.

Published in Science (May 24, 2022):

https://doi.org/10.1126/science.abm1208 

Preliminary findings suggest that B.1.1.7, a SARS-CoV-2 variant first identified in the United Kingdom, might be more transmissible because it spends more time inside its host than earlier variants do. Previous studies have estimated that B.1.1.7, which is now spreading rapidly in a number of countries, is roughly 50% more contagious than earlier coronavirus variants are. Yonatan Grad at the Harvard T.H. Chan School of Public Health in Boston, Massachusetts, and his colleagues examined the results of daily SARS-CoV-2 tests on 65 people infected with SARS-CoV-2, including 7 infected with B.1.1.7 (S. M. Kissler et al. Preprint at https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37366884; 2021).

The team looked at how long the virus persisted, and the amount of virus present at each time point. In people infected with B.1.1.7, infections lasted an average of 13.3 days, compared with 8.2 days in people with other variants. There was little difference in the peak concentrations of the virus between the two groups. These findings hint that B.1.1.7 is more easily transmitted than other variants are because people who catch it are infected for a relatively long time, and can therefore infect a larger number of contacts. This suggests that longer quarantine periods might be warranted for individuals infected with this variant. The findings have not yet been peer reviewed.

Preprint available at:

https://dash.harvard.edu/handle/1/37366884 

Nearly three-quarters of virus genomes sequenced last month were of new variant, say South African health officials.  The Omicron variant has fuelled a “worrying” surge in coronavirus cases in South Africa and is rapidly becoming the dominant strain, local health officials have said, as more countries including the US detected their first cases. The United Arab Emirates and South Korea – which is already battling a worsening outbreak and record daily infections – also confirmed cases of the Omicron variant.  Dr Michelle Groome of South Africa’s National Institute for Communicable Diseases (NICD) said there had been an “exponential increase” in infections over the past two weeks, from a weekly average of around 300 new cases per day to 1,000 last week, and most recently 3,500. On Wednesday, South Africa recorded 8,561 cases. A week earlier, the daily tally was 1,275. “The degree of increase is worrying,” Groome said.  The NICD said 74% of all the virus genomes it had sequenced last month had been of the new variant, which was first found in a sample taken on 8 November in Gauteng, South Africa’s most populous province. While key questions remain about how transmissible the Omicron variant is, which has been detected in at least two dozen countries around the world, experts are rushing to determine the level of protection afforded by vaccines. World Health Organization (WHO) epidemiologist Maria van Kerkhove told a briefing that data on how contagious Omicron was should be available “within days”. The NICD said early epidemiological data showed Omicron was able to evade some immunity, but exisiting vaccines should still protect against severe disease and death. BioNTech’s chief executive, Uğur Şahin, said the vaccine it makes in a partnership with Pfizer was likely to offer strong protection against severe disease from Omicron.

As governments wait for a fuller picture to emerge, many continued to tighten border restrictions in the hope of stopping the virus spread. South Korea imposed more travel curbs as it detected its first five Omicron cases and fears grew about how the new variant could affect its ongoing Covid surge. Authorities halted quarantine exemptions for fully vaccinated inbound travellers for two weeks, who now require a 10-day quarantine. Daily infections in South Korea hit a record on Thursday of more than 5,200, with concern growing over the sharp rise in patients with severe symptoms. Earlier this month restrictions were eased in the country – which has fully vaccinated nearly 92% of adults – however infections have surged since and the presence of Omicron has fuelled fresh worries about pressure on the already strained hospital system. In Europe, the president of the European Union’s executive body said there was a “race against time” to stave off the new variant while scientists established how dangerous it is. The EU brought forward the start of its vaccine rollout for five-to-11-year-olds by a week, to 13 December. “Prepare for the worst, hope for the best,” Ursula von der Leyen, president of the European Commission, told a news conference. Britain and the United States have both expanded their booster programs in response to the new variant, while Australia is reviewing its schedule. Top American infectious diseases specialist Anthony Fauci stressed that fully vaccinated adults should seek a booster when eligible to give themselves the best possible protection. Still, the WHO has noted many times that the coronavirus will keep producing new variants for as long as it is allowed to circulate freely in large unvaccinated populations. “Globally, we have a toxic mix of low vaccine coverage, and very low testing – a recipe for breeding and amplifying variants,” said WHO chief Tedros Adhanom Ghebreyesus, reminding the world that the Delta variant “accounts for almost all cases”. We need to use the tools we already have to prevent transmission and save lives from Delta. And if we do that, we will also prevent transmission and save lives from Omicron,” he said.