COVID-19 most probably did not exist in the East African region before the first official cases were reported in March 2020, a study by the EAC Secretariat in collaboration with the East African Health Research Commission (EAHRC) indicates.

The study aimed at verifying if COVID-19 infections had already occurred in the region in 2019 and therefore way before the first cases in Africa were reported by WHO in February 2020. It retested frozen swab samples taken from patients who presented with Severe Acute Respiratory Infections (SARI) between 1st November 2019 and 29th February 2020.

Some East African countries experienced higher than usual numbers of severe respiratory infections with persistent cough, fever and sometimes pneumonia during this period. The patients were not tested or diagnosed for COVID-19, as public attention to the new virus only started growing in January 2020. Test kits were also not yet available at the time. The symptoms might have been related to influenza, but it could not be disregarded that these SARI might have been caused by the COVID-19 causing virus, SARS-CoV-2.

The EAC Secretariat through the East African Research Commission (EAHRC) and Partner States’ National Public Health Reference Laboratories (NPHLS) implemented the study, to confirm whether these cases might have been caused by COVID-19. The study took samples from Kenya, Rwanda, South Sudan, and Uganda. The German Government provided technical and financial support through the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH and the Robert Koch-Institute in Berlin, Germany.

“1,153 frozen nasal and oropharyngeal swab samples taken from various influenza Sentinel Surveillance Sites in the four participating EAC Partner States were retested by RT-PCR in respective National Public Health Reference Laboratories in each country,“ says the report. Reverse Transcription Polymerase Chain Reaction (RT-PCR) is the standard method for detection of SARS-CoV-2, while swabs from the nose and throat are the most frequently used samples. RT-PCR is performed to detect genetic material from a specific organism, such as a virus.

All samples tested negative for RT-PCR, according to the study.

“None of the more than 1,000 samples tested positive for COVID 19. This is a strong indication that COVID 19 was not in the region before the first cases were reported in March 2020” says Dr Novat Twungubumwe, Acting EAHRC Executive Secretary, adding “However, the sample size and with it the study power is too small to proof the absence of COVID-=19 in the region with absolute certainty. Another limitation is the fact that samples were only available from the four of the six EAC Partner States.”

The study design had two phases. The first phase was the retesting in RT-PCR of swab samples from patients while the second would have been testing for antibodies in cases of positive test results. Because all the samples were negative in RT-PCR, the study did not progress to the second phase that would have involved testing the presence of antibodies to patients and their close family members.

The “two-step molecular and sero-epidemiological cross-sectional study in the East African Community Partner States on the Prevalence of SARS-CoV-2 in Patients with signs and symptoms of Severe Acute Respiratory Infection (SARI) between 1st November 2019 and 29th February 2020” is available on the EAC Website here. The study has been submitted for scientific publication.