October 2, 2024—Public health officials are using testing and sequencing to speed up the detection of new variants of infectious diseases, according to a new study led by researchers at Harvard University's T.H. Chan School of Public Health. He says there is a need to increase the rate of decision-making.
The study was published September 5 in the journal PLOS Computational Biology. Jonathan Grad, professor of immunology and infectious diseases, was the corresponding author. Kirstin Oliveira Roster, a postdoctoral fellow in the Department of Immunology and Infectious Diseases, is the lead author.
To identify new strains of infectious diseases and protect the public from more contagious or virulent strains, public health agencies test populations and use those tests to perform genome sequencing, or genetic analysis of pathogens. It relies on implementing a process that determines the structure. However, it is unclear how various factors, including the amount of testing and sequencing, the timing of the outbreak, and the transmissibility of new variants, will affect the speed at which new variants are detected.
To expand the evidence base on best practices for variant detection, researchers are investigating how surveillance strategies, location of occurrence, and variant transmissibility affect the time it takes to detect new variants. Created a model to test. They incorporated new coronavirus disease (COVID-19) data from December 2020 to November 2021 in New York City into their model to determine whether new SARS-CoV-2 variants emerge depending on a combination of factors. We evaluated how quickly it could be detected. (The researchers noted that this model could be applied elsewhere and to respiratory infections.)
The study found that increasing the number of sequenced samples requires higher testing rates and speeds the detection of new variants. Specifically, increasing the sequencing rate by 1 percentage point reduced detection time by 44 days and reduced the number of infections by 502 cases per 100,000 people. Infectivity also had a major impact. A 0.1 percent increase in the transmissibility of the variant reduced detection time by 60 days, but added 133 infections per 100,000 people.
“In our simulations, the greatest improvement in detection speed was achieved by increasing the number of positive cases sampled for sequencing,” the researchers wrote. “However, factors beyond policymakers' control also influenced the time it took to detect new variants, meaning that even under ideal public health strategies, a wide range of detection results was possible. ” These findings will guide decision-making for future outbreaks. ”
Read the study: Surveillance strategies for the detection of new pathogen variants across epidemiological contexts
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