Is the COVID pandemic waxing or waning?

That’s the question on the minds of healthcare providers and countless others as the number of people vaccinated increases, but so, too, does the number of new cases, at least in some regions.

So it’s helpful to understand that surges in cases are being driven by the appearance of new variants of COVID-19, which is the finding of a new study published at Scientific Reports.

For the study, researchers at the School of Veterinary Medicine at the University of California, Davis initially analyzed the genomes of 150 SARS-CoV-2 strains, mostly from outbreaks in Asia prior to March 1, 2020, while also examining epidemiology and transmission information for those outbreaks.

The team then combined all this information into a metric called GENI, or pathogen genome identity, and when they compared GENI scores with the phase of an epidemic, they found that an increase in genetic variation came immediately before a significant spike in cases.

"As variants emerge, you're going to get new outbreaks," said Bart Weimer, professor of population health and reproduction at the UC Davis School of Veterinary Medicine, noting that the merger of classical epidemiology with genomics provides a tool public health authorities could use to predict the course of pandemics, whether of coronavirus, influenza or some new pathogen. “In this way you can get a very early warning of when a new outbreak is coming. Here's a recipe for how to go about it.”

In South Korea in late February of 2020, for example, an increase in genetic variation immediately preceded exponential growth in cases. In Singapore, however, bursts of variation were associated with smaller outbreaks that public health authorities were able to quickly bring under control.

The team also looked at 20,000 sequences of SARS-CoV-2 viruses collected from February to April 2020 in the UK, and compared them with data on cases.

The results showed that the GENI variation score rose steadily with the number of cases. When the British government imposed a national lockdown in late March, the number of new cases stabilized but the GENI score continued to rise. 

According to the researchers, the study could also help explain superspreader events, where large numbers of people get infected in a single event when public health precautions are relaxed, and they expect that the study’s findings will encourage public health officials to measure virus variation and link it to the local transmission rate.

“Leveraging shared resources opens unexpected collaboration and avenues for applying relevant bioinformatic and disease modelling opportunities across the scientific community to solve global public health problems very quickly,” they concluded. “Based on this approach, we propose a systematic framework to merge epidemiology and genomics that was defined and validated in this work. The advantage of an evidence-based approach is the utility of whole-genome sequencing and surveillance that can be used to predict locations for new cases or used to quantitatively examine intervention effectiveness to control new cases.”