Coronavirus: Reasons behind community spread unlocked

New sequencing has revealed how coronavirus was able to spread in the community, identifying 76 infection clusters.

The Ruby Princess has been linked to clusters of coronavirus cases. Picture: AP

Health researchers in Victoria have used genomic sequencing to trace the origin of almost 1,000 cases of coronavirus in the state, with cruise ships, healthcare facilities and social venues the site of most transmission.

The genomic sequencing, conducted by the Doherty Institute using virus samples held by the Victorian health department from more than 900 COVID-19 patients, identified 76 clusters of infection.
The Doherty Institute’s director Benjamin Howden said the genomic sequencing helped identify unrecognised clusters of community transmission by resolving unknown cases and potentially linking separate clusters together.

“Sequencing allowed us to identify large clusters from social venues, healthcare facilities, and cruise ships, and importantly see how enforced social restrictions impacted transmission,” Professor Howden said.

Epidemiologists had tracked the source of many of Victoria’s 1573 COVID-19 cases, but epidemiologists have still been unable to establish how 165 of the cases were acquired, Community transmission is the biggest concern of health authorities.

Professor Howden said that because of the genomic sequencing, many of the cases of mystery transmission have now been ascertained.

“Sequencing can identify cases which were not originally allocated to a cluster but genomically do fall in a cluster and allows the department to further investigate how that exposure may have occurred and what the links may be,” Professor Howden said.

“Our sequencing showed that Victoria’s cases were representative of the global diversity of SARS-CoV-2. Consistent with epidemiological findings, we found that most of Victoria’s cases were imported with limited onward transmission.”

In total, 737 samples belonged to a genomic cluster, making up 81.6 per cent of the samples tested. Overall, of the 76 clusters of infection identified, 34 contained only cases with a history of overseas travel, while a further 34 clusters contained both travel associated and locally acquired cases.

A major cluster, comprising 94 per cent of the cases sampled, was linked to infections associated with social venues in Melbourne, indicative of strong community transmission. The chains of COVID-19 discovered in urban areas were largely connected to social activities, with 75 cases linked to high-density locations and 16 of those presenting no known source of infection.

Further analysis found traces of transmission associated with exposure to healthcare services, including one large cluster identified in a healthcare facility among patients and staff. Three cases from another two health services sampled found a total of 15 cases had attended the same social event.

Four clusters were linked with cruise ship passengers either returning to or disembarking in Melbourne. However, the data shows minimal onward transmission of the virus from cruise ship passengers, a result researchers say is dependent on the containment measures adopted to stamp out the disease within the high-risk group.

While genomic sequencing confirms hypotheses around clusters, Professor Howden said it also can link separate clusters together by identifying a common source of infection.

He said linking the epidemiological data from the health department with the genomic data from the Victoria’s pathology laboratories allowed researchers to track how the virus is moving and evolving, as well as the impact of the societal restrictions on the way the virus was spreading in Victoria.

“We would never use the genomic data completely in isolation, it always needs to be correlated with the epidemiological data. But those two together really can demonstrate when there’s been a large transmission or outbreak type of event, “ he said.

“So, it will really help understand those risk situations and where there might be a large number of cases coming from a small exposure event.”

Victoria’s Chief Health Officer, Professor Brett Sutton said public health responses to new cases of the virus need to be fast, focused and effective.

“Genomic sequencing is an incredibly powerful tool for our disease detectives to identify SARS-CoV-2 cases and clusters, which will be an ongoing challenge in Victoria and Australia,” he said.