SARS-CoV-2 genome analysis could boost disease surveillance

Continued monitoring of the evolution of the virus that causes COVID-19 as the pandemic progresses could strengthen disease surveillance systems and aid preparedness for new variants, a study suggests.

Last year, the World Health Organization (WHO) indicated that identifying the genetic makeup of the virus that causes COVID-19 called SARS-CoV-2 could play a vital role in controlling the COVID-19 pandemic.

According to the study published in Nature Communications this month (6 May), researchers assessed the genetic diversity of the variants of SARS-CoV-2 that were linked to infections in Ghana from March 2020 to September 2021.

We observed the importation of different variants, including variants of concern (Alpha, Beta, Eta, and Kappa) in January and March 2021, and later detection of Delta in June 2021."

Collins Morang'a, coauthor of the study and bioinformatician at the Ghana-based West African Centre for Cell Biology of Infectious Pathogens of the University of Ghana

"Travellers from neighbouring countries such as Burkina Faso, Côte d'Ivoire and Nigeria had some of these variants although they had not been reported in these countries at the time."

According to the study, a total of 1,123 genomes made up of samples from 121 travellers and 1,002 community members were analysed, resulting in the observation that different variants were responsible for COVID-19 disease waves in the country.

"Genetic diversity of SARS-CoV-2 infections represents the intrinsic differences between the SARS-CoV-2 variants … that could increase the ability of the virus to bind easily to the human cells, reduce the ability of the human immune system to kill the virus, reduce the ability to detect the virus during testing, and/or increase the ability of the virus to multiply in the body," the study said.

Morang'a, explained that the study gives a valuable understanding of the variants that circulated or are circulating and how they might limit the effectiveness of vaccines.

Morang'a said that all genomic data storage and bioinformatics analysis were performed on the University of Ghana high performance computing cluster and subsequently deposited in a database of GISAID, a global initiative for sharing influenza data, which is openly accessible.

"Unexpectedly, a variant that was under monitoring in countries such as Mauritius had been detected in travellers from Gabon and Nigeria and suddenly dominated infections from April to June 2021," he said, adding that after the detection of the Delta variant in travellers which was the most dominant variant (32 per cent), it quickly spread across the country, becoming the most dominant lineage in July 2021 and remaining so until September 2021 across Ghana.

The study aimed to provide a framework for continued monitoring of the evolution of SARS-CoV-2 in Ghana and Africa at large, Morang'a explained, adding that it represents a significant milestone in local capacity building for genome sequencing and analysis in Sub-Saharan Africa.

Segun Fatumo, group leader of African Computational Genomics and associate professor of noncommunicable disease epidemiology at the London School of Hygiene & Tropical Medicine in England, said the study represented the most extensive genomic analysis of COVID-19 viruses in Ghana.

"Using SARS-CoV-2 genomic sequence of more than a thousand individuals, the authors were able to track the molecular evolution and their variants in Ghana, showing the transmission of SARS-CoV-2 variants into Ghana from other countries," Fatumo said.

He added that the study provided an opportunity for African policymakers to strengthen disease surveillance systems and create policies that would help with preparedness for the next pandemic.

Morang'a said that the COVID-19 pandemic is not likely to end, and Africa should remain alert to fight it because new variants may emerge around the globe, adding that vaccinations and therapeutic options should be prioritized.