Quadram Institute researchers working with scientists in Zimbabwe have built up a detailed picture of how SARS-CoV-2 variants were introduced and transmitted in the southern African country during 2020.
Their findings, published in The Lancet Global Health, are based on the genomic sequencing of 156 positive samples taken across eight provinces (including metropolitan Bulawayo and Harare) in Zimbabwe between March and October 2020.
The epidemiological analysis identified two distinct phases of the SARS-CoV-2 pandemic in Zimbabwe. The first phase between March and June 2020 saw cases linked to international travel from Asia, Europe or the USA, and travel from neighbouring African countries.
Public health measures in this first phase, such as quarantine arrangements and suspension of tourism-related travel, appear to have been effective in delaying domestic spread.
After July 2020, a rapid increase in probable community transmission took place with cases centered around densely populated cities with proximity to land borders or international airports.
The genomic analysis of Zimbabwe’s samples showed there were at least 26 separate independent introductions of SARS-CoV-2 into the country that were associated with 12 global lineages. The same lineages that were observed during the initial period of introduction of SARS-CoV-2 into the country later spread through the community in the first epidemic wave.
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. 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 support and expertise to NMRL in Zimbabwe where necessary.
Professor Rob Kingsley, Group Leader at the Quadram Institute and Professor of Microbiology at the University of East Anglia, said: “The UK has been able to sequence COVID-19 at considerable scale but far less is known about the epidemiology of this disease in Africa. This research, undertaken with our colleagues in Zimbabwe, helped track the spread and evolution of the virus in order to help inform public health measures.”
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.
Reference: Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.
Tapfumanei Mashe, Faustinos Tatenda Takawira, Leonardo de Oliveira Martins, Muchaneta Gudza-Mugabe, Joconiah Chirenda, Manes Munyanyi, Blessmore V Chaibva, Andrew Tarupiwa, Hlanai Gumbo, Agnes Juru, Charles Nyagupe, Vurayai Ruhanya, Isaac Phiri, Portia Manangazira, Alexander Goredema, Sydney Danda, Israel Chabata, Janet Jonga, Rutendo Munharira, Kudzai Masunda, Innocent Mukeredzi, Douglas Mangwanya, Alex Trotter, Thanh Le Viet, Steven Rudder, Gemma Kay, David Baker, Gaetan Thilliez, Ana Victoria Gutierrez, Justin O’Grady, Maxwell Hove, Sekesai Mutapuri-Zinyowera, Andrew J Page, Robert A Kingsley, Gibson Mhlanga.
The Lancet Global Health https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00434-4/fulltext