A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

No abstract

Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak-between 14 February and 19 June 2021-near the epicentre of the previous epidemic 1,2 . Here we use next-generation sequencing to generate complete or near-complete genomes of Zaire ebolavirus from samples obtained from 12 different patients. These genomes form a well-supported phylogenetic cluster with genomes from the previous outbreak, which indicates that the new outbreak was not the result of a new spillover event from an animal reservoir. The 2021 lineage shows considerably lower divergence than would be expected during sustained human-to-human transmission, which suggests a persistent infection with reduced replication or a period of latency. The resurgence of Zaire ebolavirus from humans five years after the end of the previous outbreak of Ebola virus disease reinforces the need for long-term medical and social care for patients who survive the disease, to reduce the risk of re-emergence and to prevent further stigmatization.At least 30 outbreaks of Ebola virus disease (EVD) have been identified since the late 1970s, the most severe of which affected Guinea, Sierra Leone and Liberia from December 2013 to June 2016 1,2 . Guinea experienced a new outbreak of EVD in 2021, which started in Gouéké-a town about 200 km away from the epicentre of the 2013-2016 outbreak. The probable index case was a 51-year-old nurse, an assistant of the hospital midwife in Gouéké. On 21 January 2021, she was admitted to hospital in Gouéké suffering from headache, asthenia, nausea, anorexia, vertigo and abdominal pain. She was diagnosed with malaria and salmonellosis and was released two days later. Feeling ill again once at home, she attended a private clinic in Nzérékoré (40 km away) and visited a traditional healer, but died three days later. In the week after her death, her husband-as well as other family members who attended her funeral-fell ill, and four of them died. They were reported as the first suspect cases by the national epidemic alert system on 11 February. On 12 February, blood was taken from two suspect cases admitted to

Capabilities (TARMAC) initiative and the Defense Biological Product Assurance Office (DBPAO) through a task order award to the National Strategic Research Institute, FA4600-12-D-9000. All the outbreak control teams were made up of staff from the

In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay’s clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.