Where did the SARS-CoV-2 coronavirus originate?
The first cases of COVID-19, the disease caused by the SARS-CoV-2 virus, were reported in December, 2019 in the city of Wuhan, in the Hubei province of China. It is therefore reasonable to assume that the disease originated in or around Wuhan.
41 cases of COVID-19 were reported to local health authorities in Wuhan, during December 16, 2019 to January, 2020. The clinical features of these patients were reported in this study in the journal Lancet, in February, 2020:
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China
What is the connection between SARS-CoV2 and bats?
Scientists have been studying coronaviruses similar to SARS-CoV-2, in bats, for many years. For instance, a study in 2005 found that one species of bats is a natural reservoir for SARS-like coronaviruses, closely related to the SARS-CoV virus which caused the SARS outbreak in Southern China:
Bats Are Natural Reservoirs of SARS-Like Coronaviruses
Thus, it was known already in 2015 that there exists a “threat of cross-species transmission events leading to outbreaks in humans”, i.e. the coronavirus could undergo a suitable mutation and transfer from bats to humans:
A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence
This previous experience helped scientists to quickly identify in February, 2020 that the SARS-CoV-2 virus causing COVID-19 is closely related to a coronavirus found in bats:
A pneumonia outbreak associated with a new coronavirus of probable bat origin:
There is a 96% match between the genome of SARS-CoV-2 and that of a similar virus found in bats. Thus, it is highly likely that SARS-CoV-2 in humans originated when a similar virus mutated and was transmitted from bats to humans.
This transmission may have involved an intermediate mammalian host such as a pangolin. However, so far, the involvement of an intermediate host has neither been confirmed nor ruled out. Scientists also actively study bats in their natural habitats to find out which coronaviruses carried by them could be dangerous to humans, and how one could stay prepared for future pandemics.
The virus hunters who search bat caves to predict the next pandemic:
How did humans in Wuhan come into contact with these bats, and are such transmissions common?
The Huanan sea-food market has been officially pointed to as the place in Wuhan where the animal to human transmission of this virus took place. It is said that wildlife was unofficially being sold here for human consumption. In such markets, humans come into close contact with tissues from wild as well as farm bred animals, increasing the risk of viral transmission. Such transmissions happen more frequently than we realize. In the state of Karnataka, a disease carried by ticks has been infecting people for several years. The virus that causes this disease, called Kyasanur forest disease virus, was first identified in 1957. Monkeys that had died from tick bites transmitted it to humans who encountered them, in the Shimoga district. Even now, Kyasanur forest disease comes up seasonally. It is still limited in spread, and so has not received as much publicity as other viruses that have caused global infections (like SARS- CoV, SARS-CoV-2CoV2, the Ebola virus and so on). In general, as we increase chances of human- wildlife contact in various ways, the chance that an animal carried virus will be transmitted to humans increases.
Could the virus have been man-made, and deliberately released as a bio-weapon, after genetically engineering a naturally occurring corona-virus?
There is unanimity amongst scientists that the genetic structure of SARS-CoV-2 fits the pattern of natural mutation and transmission from animal to human. Early in March, 2020 LANCET carried the following statement:
Statement in support of the scientists, public health professionals, and medical professionals of China combating COVID-19
If humans had indeed engineered the virus, they would not have chosen the mutations that we in fact see in SARS-CoV-2. As explained below, computer simulations would not have picked these mutations because they do not make for a good bio-weapon on paper. In fact, models would predict that these are bad mutations to choose for high infectivity!
The proximal origin of SARS-CoV-2
Excerpt: “SARS-CoV-2 is very closely related to the virus that causes severe acute respiratory syndrome (SARS), which fanned across the globe nearly 20 years ago. Scientists have studied how SARS-CoV differs from SARS-CoV-2 — with several key letter changes in the genetic code. Yet in computer simulations, the mutations in SARS-CoV-2 don’t seem to work very well at helping the virus bind to human cells. If scientists had deliberately engineered this virus, they wouldn’t have chosen mutations that computer models suggest won’t work. But it turns out, nature is smarter than scientists, and the novel coronavirus found a way to mutate that was better — and completely different— from anything scientists could have created, the study found.”
Could SARS-CoV-2 have leaked accidentally from the Wuhan Virology Laboratory?
Answer: Extremely unlikely
As explained in this news article of April 29, 2020, such a scenario is highly implausible for various reasons:
Virologist Shi Zhengli has been studying bat corona-viruses at the Wuhan lab for many years. The first result announcing the genome sequence of SARS-CoV-2 also came from her lab in February, 2020. It was on her mind as to whether SARS-CoV-2 could have leaked from her lab. In the article: How China’s ‘Bat Woman’ Hunted Down Viruses from SARS to the New Coronavirus:
Shi is quoted as follows:
“Shi instructed her team to repeat the tests and, at the same time, sent the samples to another laboratory to sequence the full viral genomes. Meanwhile she frantically went through her own laboratory’s records from the past few years to check for any mishandling of experimental materials, especially during disposal. Shi breathed a sigh of relief when the results came back: none of the sequences matched those of the viruses her team had sampled from bat caves. “That really took a load off my mind,” she says. “I had not slept a wink for days.”
Thus it was concluded by Zhengli that the genome sequences studied in her lab were different from that of SARS-CoV-2. Further, the vox.com article cited above reports that it would take a minimum of 20 years of natural evolution for the closest genome sequence present in the lab to evolve to SARS-CoV-2. Also, as the same article reports, the bat-human interaction outside the lab is far more prevalent outside the lab than inside, making it much more likely that the zoonotic spill-over happened outside the lab. As with any scientific analysis, public data repositories are useful. Making the genome sequences from the coronaviruses present in the Wuhan lab at the time of the outbreak publicly available, would facilitate independent comparisons.
Nonetheless, biosafety is an important concern for pathogen labs all across the world. This is discussed for instance, in:
ADDITIONAL REMARKS and RESOURCES:
· Bats and zoonotic viruses: can we confidently link bats with emerging deadly viruses?
· Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
· Animal-to-Human SARS-associated Coronavirus Transmission?