Genomic epidemiology is the study of genetic sequences of pathogens to understand patterns of transmission and spread. Research has shown that the novel coronavirus SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, has an incubation period of approximately five days before the patient develops symptoms. The spread of an illness during the incubation period where a patient is unaware of the infection is called “cryptic transmission”, and recent analysis of the genetic sequence of the coronavirus has indicated that the infection may have spread further than we realised. 

The analysis was outlined in a series of tweets by Trevor Bedford, a researcher at the Fred Hutchinson Cancer Research Center, where he concludes that many more people are likely to be part of a chain of infections leading from the first infections in the US due to cryptic transmission. 

The research studied the genetic sequence of the virus from two confirmed patient samples in Seattle. Viruses are known to mutate often, with SARS-CoV-2 mutating on average twice per month. The genetic codes of the virus of the two unrelated cases were genetically similar, which Bedford claims indicates transmission while in the US.

In a supplementary blog post, Bedford states that they estimate the number of infections in Seattle to be approximately 600, which is the same stage Wuhan was at around the 1st of January. At that stage, Wuhan was just reporting clusters of patients with unexplained viral pneumonia, however, within three weeks Wuhan had thousands of infections and was put on a large-scale lockdown. Bedford claims we are now at a critical time to mitigate the spread of the infection and outlined the guidelines issued by health officials to reduce the spread. 

While the number of confirmed cases is still rising, the World Health Organisation has stated that there is still time to “push this virus back” and the plans should start with containment.