Mapping the spread of SARS-CoV-2 in Zimbabwe using genomic epidemiology

26th January 2021

Today’s announcement by Health Secretary Matt Hancock of UK support with genomics expertise to help other countries identify new COVID-19 variants comes as researchers at the Quadram Institute outline their work supporting scientists in Zimbabwe.

Today’s UK government announcement of the New Variant Assessment Platform will see other countries offered UK laboratory capacity and advice to analyse new strains of coronavirus.

In common with many other countries facing the start of the coronavirus pandemic, Zimbabwe recorded its first recorded case of the SARS-CoV-2 in March 2020. Extensive public health interventions were swiftly put in place to help control transmission and protect people.

Part of the public health measures taken by Zimbabwe included identifying the need to understand the detailed genetic epidemiology of SARS-CoV-2 and especially its behaviour in terms of transmission, capacity to mutate, and virulence.

Genomic surveillance of SARS-CoV-2 was key in order to help Zimbabwe understand and track the virus as it evolved, identify where the virus was coming from, how it was spreading, and inform public health control measures needed to limit its spread.

To complete the initiative, with this kind of detailed genetic detective work involved, the Ministry of Health and Child Care tasked its National Microbiology Reference Laboratory (NMRL) in Harare, with sequencing of the genetic material of positive samples from 100 coronavirus patients, between March and June 2020.

Key objectives for NMRL sought to help understand initial transmission of the disease, gain insight into domestic transmission of the virus, add context to the regional and global scientific data and to evaluate the role genomic sequencing could play in analysing infection outbreak.

The Quadram Institute on the Norwich Research Park, UK, as part of the COVID-19 Genomics UK (COG-UK) consortium was also undertaking genomic sequencing for the UK government.

Given the longstanding relationship and partnership between Zimbabwe and the UK in terms of academic and scientific research, the Quadram Institute was ideally placed to help provide the much-needed support and expertise to NMRL in Zimbabwe where necessary.

The Quadram Institute’s Professor Rob Kingsley said: “We were already working with scientists at NMRL to study typhoid fever in Zimbabwe and we used this close working relationship to rapidly pivot in response to the Covid-19 emergency. Our Zimbabwe colleagues continue to strive to apply the most recent technologies to address the ongoing epidemic.”

As a result, Zimbabwe’s NMRL has successfully sequenced genomes to help develop what could be called a “family tree,” or phylogenetic analysis, for the virus in Zimbabwe, based on the whole genome sequencing of positive samples taken from 100 people over 120 days.

The findings of the NMRL indicate that regional migration in southern Africa played a significant role in the transmission of the virus, certainly more so that intercontinental travel.

Whilst early cases of COVID-19 in Zimbabwe were introductions from travel from the USA, UK and Dubai, later cases centred around continental migration, largely from South Africa.

The genomic analysis of Zimbabwe’s 100 samples showed there were at least 25 separate independent introductions of SARS-CoV-2 into the country that were associated with eight global lineages. Ninety-five per cent featured the D614G genotype, a variant linked to increased transmissibility.

From May 2020 onwards, surveillance highlighted a rise in cases originating with Zimbabwean residents returning from neighbouring countries, especially South Africa.

With a two-week residential quarantine system in place, and most of the returnees were asymptomatic, testing was undertaken and on multiple occasions generated positive results for SARS-CoV-2. The genomic sequencing showed the cases were all from the same lineage implicating local transmission within the quarantine accommodation.

NMRL Research Scientist Tapfumanei Mashe, reiterated the importance of research towards the development of vaccines.

“Our experience of genomic sequencing of SARS-CoV-2 highlights the value of being able to build a very detailed picture of the virus and track its mutations for the potential to increase transmissibility, change virulence or influence the development of effective vaccines”, said Mashe.

A pre-print on the genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe is available on MedRxiv https://www.medrxiv.org/content/10.1101/2021.01.04.20232520v1?rss=1