Coronavirus may have originated from horseshoe bat, says NIH-halted study as it calls for more samples from China
The new coronavirus likely originated in horseshoe bats and may have evolved in Yunnan Province, but an origin elsewhere in Southeast Asia outside China cannot be ruled out. These are the conclusions by an international team of scientists from US, China, Australia, and Singapore, which includes experts from EcoHealth Alliance, whose study on coronaviruses was stopped abruptly by the Trump administration.
The current study analyzed all known coronaviruses in Chinese bats and used genetic analysis to trace the likely origin of the novel coronavirus to horseshoe bats. "We find that SARS-CoV-2 (the virus that causes Covid-19) is likely derived from a clade of viruses originating in horseshoe bats (Rhinolophus spp.). The geographic location of this origin appears to be Yunnan province. However, it is important to note that: our study collected and analyzed samples solely from China; many sampling sites were close to the borders of Myanmar and Lao PDR (People’s Democratic Republic), and most of the bats sampled in Yunnan also occur in these countries," says the research team in the pre-print published in bioRxiv.
"For these reasons, we cannot rule out an origin for the clade of viruses that are progenitors of SARS-CoV-2 that is outside China, and within Myanmar, Lao PDR, Vietnam or another Southeast Asian country," they add. The results suggest that future sampling and viral discovery should target two hotspots of coronaviruses in southern and southwestern China in particular, as well as neighboring countries where similar bat species live. These regions are characterized by a subtropical to a tropical climate, dense, growing and rapidly urbanizing populations of people, a high degree of poultry and livestock production, and other factors that may promote cross-species transmission and disease emergence, say the team.
"Additionally, faster rates of evolution in the tropics have been described for other RNA viruses which could favor cross-species transmission of RNA viruses in these regions. Both SARS-CoV (severe acute respiratory syndrome-coronavirus) and SADS-CoV (swine acute diarrhea syndrome coronavirus) emerged in this region, and several bat SARSr-CoVs (SARS-related coronaviruses) with high zoonotic potential have recently been reported from there, although the dynamics of their circulation in wild bat populations remain poorly understood. Importantly, the closest known relative of SARS-CoV-2, a SARS-related virus, was found in a Rhinolophus spp. bat in this region," says the study.
According to researchers, the significant public health and food security implications of these outbreaks reinforce the need for enhanced, targeted sampling and discovery of novel coronaviruses. "The emergence of SARS-CoV-2 further underscores the importance of bat-origin coronaviruses to global health, and understanding their origin and cross-species transmission is a high priority for pandemic preparedness," says the team.
"Because intensive sampling has not, to our knowledge, been undertaken in countries bordering southern China, these surveys should be extended to include Myanmar, Lao PDR, and Vietnam, and perhaps across southeast Asia," they say. For many years, Dr Peter Daszak from the New-York based EcoHealth Alliance, along with other scientists from the organization, has been conducting a National Institutes of Health (NIH)-supported research on coronaviruses and other infectious agents, focusing on the transmission of these viruses from animal hosts to human beings. But the grant to EcoHealth Alliance was abruptly terminated by NIH on April 24 this year.
The move has been criticized by several scientists, including 77 US Nobel laureates as well as scientific societies. Stating it sets a "dangerous precedent" by interfering in the conduct of science and "jeopardizes public trust" in the process of awarding federal funds for research, the Nobel Laureates have also demanded that the decision be investigated and the grant reinstated.
In the latest study, the researchers examined partial genetic sequences of 781 coronaviruses found in bats in China, more than one-third of which have never been published. They compared these to sequence information already documented in computer databases on bat and pangolin coronaviruses. The analysis of bat and viral evolution strongly supports the suspected origin of the virus in horseshoe bats, but it is not definitive evidence, largely because a lot is currently not known about such viruses. They found a Rhinolophus coronavirus that was 96.2% identical in sequence to SARS-CoV-2, the closest relative yet found. The analysis also demonstrates that a significant amount of cross-species transmission has occurred among bat hosts over evolutionary time.
Recent coronavirus outbreaks in humans — SARS, Middle East respiratory syndrome, and SARS-CoV-2 — have been caused by a group known as beta-coronaviruses. But the new analysis suggests alpha-coronaviruses may actually be better at jumping species barriers, and could also lead to epidemics in humans or animals. “Future work discovering and characterizing the biological properties of bat alpha-coronaviruses may, therefore, be of potential value for public and livestock health,” they write.
While commenting on the research, Dr Daszak tweeted that the study adds more evidence that SARS-CoV-2 emerged naturally. "Work funded by NIH grant terminated 'for convenience' by NIH director, protested by 77 Nobel Laureates, 31 US scientific societies. Future plans were to sequence receptor binding domains to see if viruses (are) able to infect humans. That work cannot happen without NIH grant," he said. Dr Daszak added, "Key takeaway message (from the study) is: we need more sampling of bats in China (expect many more SARS-CoV-2-related viruses for example); bats across Southeast Asia; other mammals across the region; pangolins and others in wildlife trade."