Tracking the spread of virus variants in Malta needs to be strengthened, according to research on COVID-19 that has highlighted gaps in the country’s genomic surveillance system during the pandemic.
The study showed up extended instances of undetected virus transmission before erupting into larger outbreaks that are more readily identified. This underscored the importance of continuous monitoring.
The research into Malta’s COVID-19 situation, published in an American Society for Microbiology journal, showed that genomic surveillance – scientists’ tracking of the spread of variants and genetic changes to understand their impact on public health – was characterised by “periods of sequencing hiatus”.
“The longer the virus goes undetected, the more it can spread and cause bigger outbreaks,” said co-author Prof. Joseph Borg from the Department of Applied Biomedical Science at the University of Malta.
“Detecting and stopping the virus early is crucial to preventing these larger and more severe outbreaks.”
“The longer the virus goes undetected, the more it can spread and cause bigger outbreaks,” - co-author Prof. Joseph Borg from the Department of Applied Biomedical Science at the University of Malta
Although Malta’s first COVID-19 case was identified on March 7, 2020, the first sequenced case did not occur until more than five months later.
The system was eventually ramped up, but surveillance remained limited throughout the first two years of the pandemic and, according to the study, Malta has yet to fully employ sequencing information to manage its COVID-19 outbreaks.
“Initially, we faced challenges in carrying out enough sequencing, and it comes as no surprise really. We had limited equipment and trained personnel to perform the specific COVID-19 genomic sequencing,” Borg explained.
“The expectations were very high in such a short time frame. I think we were caught off guard, and I think the whole world was too....
“During the early phases when we did experience a high number of cases and deaths, this may also have made it difficult to prioritise DNA sequencing. But over time, experience was gained, and efforts increased to better understand the virus’s dynamics.”
Borg said it was important to continue investing in training of biomedical scientists, new equipment and resources.
The study was a collaboration between the US National Institutes of Health and biomedical lab scientists at Mater Dei Hospital’s Molecular Diagnostics for Infectious Diseases Laboratory, led by Dr Graziella Zahra, and experts from the COV-IRT team, including Borg.
It demonstrated “the critical role of genomic surveillance” in understanding the dynamics of the pandemic in such a small island – how the variants spread and their potential impact on transmission and disease severity.
Not many other countries could do that, Borg said.
“By strengthening genomic surveillance, we can improve the early detection of viral introductions and curtail their expansion, while also guiding public health interventions.”
‘Fascinating insights’
The research unveiled “fascinating insights” into Malta’s battle against COVID-19, as well as into its evolution in a highly connected and understudied country.
It showed that COVID-19 positivity rates in Malta remained low overall throughout the pandemic, with less than 10 per cent of those tested being infected.
The statistic was attributed to a “combination of effective public health interventions”, which allowed Malta to mitigate the pandemic’s impact.
Being an island may also have contributed due to its “advantage” in controlling access, making it harder for viruses to enter, Borg explained.
The study detected 173 independent virus introductions into Malta. Most of these came from Northern European countries (38.7 per cent) – a “significant” finding consistent with flight connectivity patterns.
By examining epidemiological data from Malta and cross-referencing it with genetic sequences of the virus, the team reconstructed the evolutionary journey and geographical dynamics of the disease.
“Our findings, like pieces of a puzzle coming together, tell a captivating story of resilience and scientific discovery,” Borg said.