A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia

Abstract

Emerging diseases caused by coronaviruses of likely bat origin (e.g., SARS, MERS, SADS, COVID-19) have disrupted global health and economies for two decades. Evidence suggests that some bat SARS-related coronaviruses (SARSr-CoVs) could infect people directly, and that their spillover is more frequent than previously recognized. Each zoonotic spillover of a novel virus represents an opportunity for evolutionary adaptation and further spread; therefore, quantifying the extent of this spillover may help target prevention programs. We derive current range distributions for known bat SARSr-CoV hosts and quantify their overlap with human populations. We then use probabilistic risk assessment and data on human-bat contact, human viral seroprevalence, and antibody duration to estimate that a median of 66,280 people (95% CI: 65,351–67,131) are infected with SARSr-CoVs annually in Southeast Asia. These data on the geography and scale of spillover can be used to target surveillance and prevention programs for potential future bat-CoV emergence.

Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots

“…Using a macroscale approach, we assessed the distribution of locations with a greater risk of experiencing Sarbecovirus spillover events using landscape conditions and exposure of potential hosts (wildlife, domestic, human). Landscape conditions coupled with predictions of the distribution of known hosts and proxies for potential hosts and processes linked to human exposure to novel viruses can be a powerful tool for spatial sample prioritization when limited viral spillover information is available, such as for sarbecoviruses (16).…”

“…We use South, East and Southeast Asia (including West Papua) as our study region, where most Sarbecovirus hosts are concentrated (15,16) and where many unknown sarbecoviruses are estimated to exist (29). We define our study region as the terrestrial area of the following countries: Bangladesh, Bhutan, Brunei, Cambodia, China, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Philippines, Singapore, Sri Lanka, Thailand, Timor-Leste, and Vietnam.…”

“…Bat hosts of sarbecoviruses are broadly distributed but the highest diversity is in Southeast Asia (15). Human infection with Sarbecovirus from bats may be more frequent than reported from traditional surveillance (16) and potentially secondary hosts (17,18). Viral infection prevalence contributes to the risk of spillover (4), and can be influenced by biological factors such as birthing cycles (19,20) and external stimuli such as human changes to land use (7) (but see (21,22)).…”

International Collaboration is the Only Way to Protect Ourselves from the Next Pandemic

“…In a paper (Sanchez et al 2022) just published in Nature Communications, we show for the first time how hard defeating pandemics will be. We analyzed all known reports of viruses related to SARS and SARS-CoV-2 and mapped out the distribution of each species of bats in which they have been reported.…”

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

“…Despite the difficulties of inferring reliable phylogenies of SARS-CoV-2 (Morel et al , 2020; Pipes et al , 2021), as well as the controversy surrounding the first days and location of the pandemic (Koopmans et al , 2021; Worobey, 2021), the most parsimonious explanation for the origin of SARS-CoV-2 seems to lie in a zoonotic event (Holmes et al , 2021; Balloux et al , 2022). Direct bat-to-human spillover events may occur more often than reported, although most remain unknown (Sánchez et al , 2022). Bats are known as the natural reservoirs of SARS-like CoVs, and early evidence exists for the recombinant origin of bat (SARS)-like coronaviruses (Hon et al , 2008).…”