Did SARS-1.0 Come from Bats through Civets?
“If you tell a lie big enough and keep repeating it, people will eventually come to believe it.”
Although I cannot find the source of the above excellent quote (Was it a Nature editor exposed by Professor Graur?), it perfectly describes today’s topic.
After the previous two posts on SARS-Cov-2 virus (here and here), I was planning to extend the analysis to show its connection with bats and pangolins and explain the claims made in the scientific literature. In this context, I checked how SARS-1.0 mystery was solved so that we could utilize the same techniques.
What I came up with was rather unexpected. Despite sensational stories in the media, the origin of SARS-1.0 was never resolved. This is a serious problem, because those hypes and misleading claims created a foundation for sloppy science. Many researchers are now building on that foundation to connect SARS-Cov-2 with bats and pangolins.
2017-2018
Let us start with a letter published in Nature in 2018. It was titled “Don’t misrepresent link between bats and SARS”.
We find your report on bats and severe acute respiratory syndrome (SARS) sensationalist and misleading (Nature 552, 15–16, 2017). The important work it discusses does not claim to pinpoint conclusively the source of the SARS outbreak (B. Hu et al. PLoS Pathog. 13, e1006698; 2017), as implied by your “smoking gun” metaphor. The rapid rate of evolution of RNA viruses means that SARS could have arisen in one of many areas. Thus, your inference that the strain “could easily” have originated in this bat population is, in our view, unjustified.
Inflammatory statements about bats and disease have led to culling and roost destruction, compromising conservation efforts (K. J. Olival EcoHealth 13, 6–8; 2016). Accurate reporting of information on SARS, Middle East respiratory syndrome, Ebola and other emerging diseases is crucial for controlling outbreaks and for preventing unnecessary deaths of wild animals.
How did those authors miss the memo, when everyone and his grandma knew that SARS mystery was solved in 2005? Why did Nature publish such a letter in 2018, and that too from authors accusing Nature for being “sensationalist and misleading” ? That should alert you that truth was on the side of those authors.
To give you some context, the article being cricized was written by David Cyranoski in late 2017 - “Bat cave solves mystery of deadly SARS virus…Chinese scientists find all the genetic building blocks of SARS in a single population of horseshoe bats”. It was a “news story” based on a paper published in PLoS Pathogens. Note that despite “solving the mystery of deadly SARS virus” as claimed by Cyranoski, the original paper did not get a spot in highly coveted journals like Nature and Science. Does that puzzle you ?
2013
Not only the mystery of origin of SARS remain unsolved as late as 2017, the popular narrative of transmission from bats to civets to human was challenged by others before. Here is an interview from Jianfeng He, chief expert of the Guangdong provincial CDC and the director of Guangdong institute for infectious disease control and prevention. It was published in Journal of Thoracic Disease in an article titled “Ten years after SARS: where was the virus from?”. Please note that Guandong was the epicenter of SARS epidemic in 2003.
Research on the source of SARS virus is extremely challenging
Nanfang Daily: Recently, in a report titled “Masked palm civet has been wronged for a decade, bat was the real culprit of SARS virus”, CCTV cited the argument made by Prof Kwok-Yung Yuen, a renowned professor of communicable diseases from HKU Li Ka Shing Faculty of Medicine, that the natural host of SARS virus was Rhinolophus sinicus, or Chinese Rufous Horseshoe Bat. What do you think? Where was the SARS virus actually from?
Dr. He: This is not a new finding. In September 2005, Prof Kwok-Yung Yuen and his research team declared that wild bats were SARS virus’ natural host, and their findings were published in the Proceedings of the National Academy of Sciences on 27 September. Meanwhile, Prof. Zheng-Li Shi from Wuhan Institute of Virology, Chinese Academy of Sciences, Prof. Shu-Yi Zhang from the Institute of Zoology, and some researchers from Australia also tracked the source of SARS virus to bats, and their findings were published in Science in September 2005. However, these findings remain controversial. The SARS virus carried by bats is quite different from that found in human body, whereas the virus carried by civets has much higher homology. There is a possibility that the virus spread from bats to civets, in which it experienced some mutations before it was transmitted to human beings. However, there lacked sufficient evidences.
In my opinion, tracking the source of SARS virus must be based on objective evidences rather than assumptions. Many people believe that the virus might come from wild animal market, and its hosts might include civets, cats, snakes, wild boars, muntjac, rabbits, pheasants, and bats. However, no specific source has been identified. Today we still do not know where the SARS virus came from and how it disappeared.
If the chief expert of Guandong’s CDC was not convinced about bat to civet to human transmission, maybe you have been mislead by the media.
What Has Been Really Shown so Far?
Next, we will go over the published articles to discuss what has been shown so far regarding animal origin of SARS.
SARS showed up unexpectedly in China/Hong Kong in early 2003, and at that time nobody had any clue about where it came from. Rats were blamed first. Check - “Rats may have played role in Hong Kong SARS outbreak”.
The disease came back in early 2004, and at that time Chinese were prepared to catch the animal culprit. First they started hunting the rats.
This morning in Guangdong, the 32-year-old man who became mainland China’s first SARS case of the winter was released from the hospital. Earlier, he had told the Chinese media that he had never eaten civet, and that his only contact with wild game was with a mouse. He apparently threw a mouse out a window at some point before he became ill. One Guangdong newspaper quoted him as saying he had handled the mouse with chopsticks.
At the same time, DNA-based research found almost identical viruses in palm civets kept in cage in a restuarant, where many people got sick. So, civets became the next target. Guandong officials decided to confiscate and kill all civets. SARS never came back, and people were happy to accept civets being the culprit.
There was one big problem with the explanation of palm civets being the source. Civets in China were farmed, and a 2004 study published by Tu et al. (“Antibodies to SARS Coronavirus in Civets”) did not find SARS virus in farms far away from Guandong, the epicenter of SARS. That meant the civets of Guandong could have acquired the disease from humans just like tigers in New York zoo tested positive for SARS-CoV-2 in 2000. If civets ran the government, they could make a strong case of culling humans for spreading SARS to them.
At this time (2005), the attention shifted to bats. Why bat? It is just because bats were linked to many other “emerging” infectious diseases. Based on sequence comparison, Chinese researchers found a distant relative of SARS virus in bats and named it “SARS-CoV like” virus. That unfortunate naming permanently damaged the reputation of bats regarding SARS diseases despite no real link being established. In bioinformatics and sequence comparison, “like” is a nebulous concept entirely dependent on cutoff. Someone can choose different cutoffs to call rats, snakes, mosquitoes or yeasts “human-like” creatures, and you know how wrong that would be.
In a future post, We will go over the existing literature on SARS-bat connection and also align the actual viral sequences using MUSCLE so that you can see how dissimilar those viruses are. Also, this will give you some context about the now controversial “gain-of-function” research.
