The COVID-19 pandemic began in Wuhan, China, near the open wet market in the city. Although about a fourth of the early cases had no link to the market. It’s crucial that the world monitor these markets where live animals are sold to consumers. The interaction of large numbers of humans and animals in a crowded area increases the chances for disease transmission. Several major pandemics in the last 100 years resulted from the spillover of an animal virus into humans, including HIV, West Nile Virus, Ebola, and Avian Influenza. Governments typically monitor these markets by capturing birds and taking throat swabs or samples from the digestive tract. These are then analyzed for the presence of the virus. Collecting these samples can be labor-intensive. Did you ever try to capture a bird? They don’t typically want to be held.
Cronin et al. have investigated sampling the environment of the market – air, water, and surfaces – and perform a metagenomic analysis. The samples are sequenced and examined for the presence of important poultry pathogens, including avian influenza (H5N1). Their new method can detect 40 viruses that infect poultry, offering broad coverage and improved pathogen detection. Cornin compared environmental sampling to tradition methods and found their method at least as effective at detecting viral pathogens. Sample the air captured the most number of viruses and outperformed throat and digestive tract sampling. This method would make it easier to detect emrging pandemics and could allow for better mitigation efforts before a pandemic spread. I see no reason this could not also be expanded to include bacterial pathogens.