We will almost certainly never know the origins of COVID-19. But we can make an informed, by science, guess when it jumped to humans and the early chain of events that followed. A new paper in Science makes the case.
While the earliest cases of COVID-19 were reported from Wuhan’s “wet market,” retrospective consideration would term this a report of a cluster, not the index (initial) infection. Retrospective analysis based on hospitalization puts the index case back to the beginning of December. Chinese newspaper accounts suggest that the virus was already circulating in November.
By now, we are all familiar with the fact that COVID-19 mutates, and in a stable environment, mutation rates are relatively stable.  The stability of the rate of mutation and characterizing the viral genome can serve as a retrospective “clock” to determine when COVID-19 infected its first individual. The researchers coupled that information with a pandemics model spread based upon Wuhan's real data and reasonable assumptions about COVID’s spread. The result is a model of how this type of infection, airborne with easy transmissibility and “low” mortality, may develop. 
For a period of about a month, COVID-19 was not an “establish” infection. It spread from individual to individual but didn’t form long transmission chains – it went “extinct.” The researchers used the word coalesce, which is meant to capture the idea that COVID-19 reached a critical mass where its spread outpaced its extinction and those chains of transmission became longer, and the case rate began to rise. As you might expect, a faster transmission rate shortening the period to coalescence, a slower rate, increased the period. Population density in this early phase did not alter the time from index case to coalescence.
Many assumptions go into calculating that index case, so the results are not certain. But the best guess is that there was a 3-4 week window from the first case to the point of epidemic. The researchers also considered whether the virus had mutated during that interval, becoming more infectious, as we have seen subsequently. The model again suggests a 3 to 4-week window, even as they varied the virus's fitness.
In the computer simulations, 70% of epidemics went extinct, only 30% continue to spread as COVID-19 has done. Before coalescence, slower rates of transmission resulted in more extinctions, and population density had little impact. That changed with coalescence and the possibility of superspreader events. The researchers noted the empiric observation of “the outsize role of superspreading events.” Population density now became a driver of cases facilitating spread. From that point of view, the Wuhan wet market reports are perhaps the first superspreader event, but certainly not the inciting moment.
Based on this modeling, the researchers concluded that
- The “successful establishment” of COVID-19 was far from certain – more than two-thirds of the computer simulations went extinct.
- The prevalence of the virus, inferred by the model, was too low for weeks meaning that by the time it was detected, “the virus had firmly established itself in Wuhan.”
While much of our retrospective hand-wringing over the pandemic centers upon acting earlier, this study suggests that this may not be easily accomplished. Heightened surveillance may come with its own downsides, namely false alarms that cause mistrust, much as the boy who cried wolf found was the case.
 In the presence of vaccination or steadily rising immunity, this rate may accelerate, which is why some experts are concern about the effect of the variant on lengthening the pandemic.
 It is hard to find the correct adjective to describe COVID-19’s mortality. It is worse than seasonal flu and not as bad as Ebola – pick your own adjective.
Source: Timing the SARS-CoV-2 index case in Hubei province Science DOI: 10.1126/science.abf8003