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 

After months of data collection, scientists agree: The delta variant is the most contagious version of the coronavirus worldwide. It spreads about 225% faster than the original version of the virus, and it's currently dominating the outbreak in the United States. A new study, published online Wednesday, sheds light on why. It finds that the variant grows more rapidly inside people's respiratory tracts and to much higher levels, researchers at the Guangdong Provincial Center for Disease Control and Prevention reported. On average, people infected with the delta variant had about 1,000 times more copies of the virus in their respiratory tracts than those infected with the original strain of the coronavirus, the study reported. In addition, after someone catches the delta variant, the person likely becomes infectious sooner. On average, it took about four days for the delta variant to reach detectable levels inside a person, compared with six days for the original coronavirus variant. 

In the study, scientists analyzed COVID-19 patients involved in the first outbreak of the delta variant in mainland China, which occurred between May 21 and June 18 in Guangzhou, the capital of Guangdong province. The researchers measured the levels of virus in 62 people involved in that outbreak and compared them with the levels in 63 patients infected in 2020 with an early version of the virus. Their findings suggest that people who have contracted the delta variant are likely spreading the virus earlier in the course of their infection. And the scientists underscore the importance of quarantining immediately for 14 days after coming into contact with someone diagnosed with COVID-19, as the U.S. Centers for Disease Control and Prevention recommends.  Or even better, getting fully vaccinated. Preliminary data shows that in some U.S. states, 99.5% of COVID-19 deaths in the past few months were among people who weren't vaccinated, the CDC's director, Dr. Rochelle Walensky, said Thursday at the White House.  "We know that the delta variant ... is currently surging in pockets of the country with low vaccination rates," Walensky said. "We also know that our authorized vaccines prevent severe disease, hospitalization and death from the delta variant."

Study cited available in Virological (July 7, 2021):

https://virological.org/t/viral-infection-and-transmission-in-a-large-well-traced-outbreak-caused-by-the-delta-sars-cov-2-variant/724