Researchers have scoured the viromes of more than 3000 rodents to pinpoint the risks and zones of disease emergence in Southeast Asia
Chapare haemorrhagic fever, which killed at least three people in Bolivia in late 2020, originated in rodents. These mammals, which carry numerous zoonotic diseases, are coming under increasing scrutiny from emerging disease specialists. An international research team recently made a major step forward in publishing the viromes - in other words the genetic material (DNA or RNA) of the viruses carried - of more than 30 Southeast Asian rodents and insectivores. This work echoed the IPBES report published on 29 October 2020, which stated that more than 800 000 viruses that are potentially dangerous to humans had yet to be discovered.
Compiling an inventory of rodent viruses
Over twelve years, from 2006 to 2018, the researchers collected lung tissue samples from 3284 rodents in Thailand, Laos and Cambodia. The Chinese Academy of Medical Sciences subsequently sequenced the DNA of the viruses found.
"We found some known viruses, particularly hantaviruses, mammarenaviruses and coronaviruses, and confirmed that certain species act as reservoirs" , says Serge Morand, health ecologist at CIRAD and co-author of the article. "But we also discovered new viruses that could be sources of new human infectious diseases."
In addition to the substantial progress this work on viruses represents, the samples were scrupulously sorted according to the habitats of the thirty species tested. Each rodent was thus ranked on a scale of "forest-farmland-urban" areas, according to its preferred habitat.
"Some rodents are specialists, in other words they only live in specific habitats: forests, rainfed farmland, urban areas, etc. Others are less specific, and can live in either urban or rural areas. For instance, Norway rats, and other species in the Rattus rattus complex, are an invasive species with many parasites", the ecologist explains. "Classifying animals according to habitat serves to identify the zones in which the viruses they carry may emerge."
Wild animal farms are in the spotlight
The emergence of SARS in China in 2002, when civet cats passed on the disease from bats to humans, occurred at a time when civet cats were increasingly being farmed in several parts of the country. Despite this precedent, which should have served as an example, wild animal farming has recently taken off in Southeast Asia. Serge Morand therefore considers that studying virus circulation within a given territory also means looking at the interactions between wildlife and human communities.
"Wild animals are increasingly being farmed in Southeast Asia, and this looks like being farm more dangerous than eating wild meat", Serge Morand says. "The theoretical data we compiled recently and shared with the rest of the scientific community are useless unless we can prevent such practices."
In many Southeast Asian countries, certain species of rats found in rice paddies are farmed as their meat is popular and sales boost farmers' incomes. However, on these farms, which are often small and family-run, sanitary and welfare standards are not respected and veterinary controls are insufficient. Farmed rodents are often stressed by this type of environment, which depresses their immune response, and they come into contact with both other animals and the humans handling them. There is a high risk of pathogen spillover and new infectious diseases.
Comparing virus ecology information and farming practices in a given territory allows researchers to pinpoint areas with a higher risk of disease emergence. The economic dynamics and interconnections between territories then show how viruses may be transmitted on a regional and global level. This is a particularly pressing issue in Southeast Asia in view of the new silk roads opened up by China, commercial routes aimed at linking Southeast Asia to central Asia, then the Caucasus, and finally Europe.
Wu, Z., Han, Y., Liu, B. et al. 2021. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. Microbiome 9, 18.