COVID-19 cases in summer 2020 was not as low as previously thought, new genome-based model suggests

Many have attributed the low number of coronavirus disease 2019 (COVID-19) cases in the summer of 2020 to hot weather or increased outdoor activities. But a new study from researchers in Germany suggests this might not have been the case.

The results obtained from a genome-based computational pipeline called GInPipe use only time-stamped sequencing data, suggesting some European countries had a large number of undetected COVID-19 cases during this period.

Study: Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Image Credit: vchal / Shutterstock

Their findings suggest GInPipe could help with current genomic surveillance efforts — especially in countries where COVID-19 testing is limited. The researchers write:

In some of these regions pandemic control may be impossible or cause more harm than benefit and hence these regions may constitute reservoirs for the emergence of novel SARS-CoV-2 variants. Gaining insight in the pandemic dynamics in these regions through alternative methods, such as GInPipe, could yield valuable information that helps to direct global SARS-CoV-2 control efforts.”

The study “Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020” is available as a preprint on the medRxiv* server, while the article undergoes peer review.

How they did it

The researchers constructed the GInPipe method to reconstruct past incidences of COVID-19 cases using only time-stamped genetic sequences of SARS-CoV-2. They used the technique to reconstruct SARS-CoV-2 incidence history in several European countries such as Denmark, Scotland, Switzerland, as well as in Victoria, Australia.

Using the rebuilt incidence history data, the researchers predicted where SARS-CoV-2 would next hit and the probability of whether a person infected with COVID-19 would get tested.

Lastly, they looked at influences such as relaxation of testing policies and how they affected the number of reported COVID-19 cases.

GInPipe is effective in inferring pandemic trajectories

GInPipe worked well with simulated outbreaks and retained accuracy in reconstructing incidence data even when there was incomplete data or new viral variants. The accuracy of results did not falter when SARS-CoV-2 variants made up most of a country’s population — even when the variants’ mutations did not contribute to outbreaks.

The power of GInPipe lies in the swift reconstruction of incidence histories with a fine temporal resolution, without requiring phylodynamic inference, construction of a multiple sequence alignment, down-sampling, clustering by e.g. lineages, or masking of problematic sites in the virus genomes.”

The GInPipe also worked well with real-time sequencing with outputs delivered within minutes of receiving data sets. The researchers note the execution times were associated with the number of sequences, with the ability to analyze 1,500 per minute.

The reconstructed incidence history from GInPipe corresponded with daily reported infection rates in several European countries and the Victorian state of Australia. These results depended on the number of COVID-19 diagnostic tests performed. For this reason, the data matched the best with Denmark who conducted a large number of tests.

Higher number of COVID-19 cases than previously reported

In the first pandemic wave in Scotland and Victoria, Australia, the researchers found more cases than officially reported. This parallels the low number of COVID-19 testing performed during this time period, indicating a large number of infected individuals were not properly diagnosed.

There was also a rise in infections across all European countries during August 2020 — coinciding with the rise of B.1.177. The European summer of 2020 showed an underreporting of infections, which may have been due to a low number of available testing resources.

This suggests that it may be advisable to focus on testing symptomatic individuals when testing capacity is low. Nevertheless, the apparent under-reporting was overcome relatively quickly by either increasing testing capacities (Denmark, Scotland, Victoria) or re-focusing capacities or both (Switzerland).”

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Jocelyn Solis-Moreira

Jocelyn Solis-Moreira graduated with a Bachelor's in Integrative Neuroscience, where she then pursued graduate research looking at the long-term effects of adolescent binge drinking on the brain's neurochemistry in adulthood.