When developing a therapy or vaccine against an emerging virus, knowing how long it has been in existence can tell scientists how many forms may exist, how prevalent it is, and even whether it is hazardous enough to merit an intervention.
For SARS-CoV-2, its history of existence is not well known. When COVID-19 was recognized as an outbreak in late December of 2019, health authorities assumed that was approximately when it emerged in Wuhan, China. However, since that time, many theories—from the reasonable to the ridiculous—have surfaced on where the true “index case” arose. These range from the Huanan Seafood Wholesale Market, to bats on to pangolins and then humans, to a laboratory accident at the Wuhan Institute of Virology, all the way to bioweaponry and a conspiracy to create a new world order involving Microsoft founder Bill Gates, the Chinese Communist Party and 5G wireless networks.
In response to this uncertainty, scientists have issued calls for investigations to determine the true origins of COVID-19. In the United States, the White House has ordered an inquiry to be conducted with the U.S. Intelligence Community into the virus’ first appearance in China. “Knowing how COVID-19 emerged is critical for informing global strategies to mitigate the risk of future outbreaks,” one group of scientists wrote in Science magazine.
New Study Points to Different Emergence
Another group of scientists suggests an earlier date for when the virus first emerged. A new study, also published in Science and led by researchers at the University of Arizona, University of California, San Diego, and Illumina Corp., in San Diego, used “molecular clock” tools and epidemiology simulations to determine that, instead of December, the SARS-CoV-2 virus probably first entered human circulation as early as mid-October 2019, two months earlier than current assumptions. In addition, the study’s simulations create the scenario in which more than three-quarters of mutating SARS-Cov-2 viruses died out before causing any disease in humans.
The study also questions where the virus first arose. While the first incidences of COVID-19 cases were reported among people who had been at the Huanan Seafood Wholesale Market, the study determined that the market was not the site of the new virus’s emergence. In fact, Chinese researchers (in retrospect) reported COVID -19 diagnoses going back to November of that year, in people who had no connection to the market. The study also helps debunk some speculation that the virus was emerging in Europe at the same time.
By using “molecular clock” evolutionary analysis, which counts the mutation rates of genes to determine when a virus from which all SARS-CoV-2 variants emerged, the researchers found that this common progenitor arose probably as early as October, long before the “index case” of the disease appeared in humans. Using tools such as epidemic simulations, based on our current knowledge of the virus’ biology (which was not understood in 2019), the researchers also could determine how the virus was behaving when it was still unknown. These simulations showed that SARS-Cov-2 was able to sustain itself enough to create an epidemic just 29.7 percent of the time. In the other 70.3 percent of the time, the virus infected a few people before disappearing, with an average longevity of eight days.
“We saw that over two-thirds of the epidemics we attempted to simulate went extinct,” said Joel Wertheim, professor of medicine at UC San Diego. “This finding supports the notion that humans are constantly being bombarded with zoonotic pathogens.”
Looking Ahead: Determining What Makes a Dangerous Virus
The study raises the question about the dangers of “zoonoses,” diseases that begin because a pathogen, like SARS-CoV-2 or HIV, “spills over” from animal sources into humans, triggering a new disease. The original strain of SARS-CoV-2 was able to turn into an epidemic organism because it became widely dispersed in urban areas, which favored the persistence of pathogenic strains and eased its transmission.
The study also underscores the importance for public health officials and drug/vaccine developers to look more carefully at potential pathogens that don’t appear as deadly in their earliest emergence as they became further on. HIV, the authors wrote, was far more deadly (100% fatal when first observed in humans) than COVID-19 when it started visibly infecting humans in the Democratic Republic of the Congo, but took years to arise after its initial “jump” from chimpanzees to humans. While diseases like Ebola, SARS, and MERS had a shorter period of spillover, they caught official attention because of their high fatality and transmission rates.
“Pandemic surveillance wasn’t prepared for a virus like SARS-CoV-2,” Wertheim said. “We were looking for the next SARS or MERS, something that killed people at a high rate, but at hindsight, we see how a highly transmissible virus with a modest mortality rate can also lay the world low.”
The worldwide experience from COVID-19 underscores the need to strengthen surveillance efforts. As the World Health Organization wrote:
“One key lesson learned from this pandemic is that clear, caring, inclusive and regular communication from authorities contributes to public trust in the government’s response, which leads to improved understanding of individual responsibility and, subsequently, a greater willingness to adopt infection prevention practices as part of “the new normal.” Embedding these practices as part of our “new normal” can be a stepping stone to a “new future,” with benefits for other health issues, far beyond the response to COVID-19.”
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