Researchers use combined approach to estimate the timing of first SARS-CoV-2 case

Reviewed by Emily Henderson, B.Sc.Mar 19 2021

Researchers who simulated early stages of the SARS-CoV-2 outbreak in Wuhan, China, conclude that the virus was likely circulating earlier than has been described, possibly even in mid-October 2019.

The findings do not reveal whether the virus that first emerged was less "fit" than the virus that spread throughout China, say the authors, but the estimates do further distance the first ("index") case from the outbreak at the Huanan Seafood Wholesale Market, which has received much attention.

A concerted effort has been made to determine when the SARS-CoV-2 virus first began transmitting among humans. Research suggests the first described cluster of COVID-19 - associated with the Huanan Seafood Wholesale Market in late-December 2019 - is unlikely to have marked the beginning of the pandemic, as COVID-19 cases from early December lacked connections to the market. What's more, newspaper reports by the Chinese government detail daily retrospective COVID-19 diagnoses going back through November.

To better estimate the timing of the first SARS-CoV-2 case, presumably in Hubei, China, Jonathan Pekar and colleagues used a combined approach. They first applied Bayesian molecular clock phylogenetics to estimate the timing of most recent common ancestor of sampled strains of the virus. Using an epidemiological model, the researchers then ran forward simulations.

Critically, their simulations considered the possibility that the variant of SARS-CoV-2 that first emerged was less fit than the variant that spread widely; the authors thus simulated two-phase epidemics wherein the first case was infected with a less fit variant that went extinct, but not before giving rise to a mutant strain that persisted.

In this approach, about two-third of SARS-CoV-2 events died off without igniting a pandemic. Based on their simulations, the authors predict SARS-CoV-2 was circulating in Hubei province at low levels in early-November 2019, and possibly as early as mid-October 2019. The inferred prevalence of this virus was too low to permit its discovery for weeks or months, they say.

By the time COVID-19 was first identified, the virus had established itself in Wuhan. The delay highlights the difficulty in surveillance for novel zoonotic pathogens with high transmissibility and moderate mortality rates.