Background: The World Health Organization (WHO) declared the Corona Virus Disease 2019 (COVID-19) outbreak a Public Health Emergency of International Concern on 30th January 2020, and a global pandemic on 11th March 2020. In the East African Region, the first COVID-19 case was detected and officially reported by the Republic of Kenya on 13th March 2020. However, an increase of patients presenting with Severe Acute Respiratory Infections (SARI) was noted between November 2019 and February 2020. This led to the question, if COVID-19 might already have been in the region before the 1st officially reported case. This study was conducted by the East African Health Research Commission (EAHRC) to answer this question. Five (5) of the six (6) East African Community (EAC) Partner States (Burundi, Kenya, Rwanda, South Sudan and Uganda) participated in the study that re-tested frozen oropharyngeal and nasopharyngeal swab samples taken and stored at the Influenza Sentinel Sites from patients who presented in this period of time with SARI like symptoms. All one thousand one hundred fifty-three (1,153) samples re-tested in RT-PCR were negative, which indicates that COVID-19 only started in the region when the first cases were reported.
Methods: This was a cross-sectional study which employed a retrospective molecular technique that was carried out on archived frozen nasal and oropharyngeal swab samples which was collected from the existing National Influenza Viruses Sentinel Surveillance Sites in each country. Five of the six EAC Partner States participated in the survey namely; Kenya, Rwanda, South Sudan, and Uganda. However, the Republic of Burundi did not have any archived nasal and oropharyngeal swab samples, while the United Republic of Tanzania chose not to participate in the study. The frozen nasal and oropharyngeal swab samples which were previously collected in the National Influenza Virus Infections Surveillance Sites within the Republic of South Sudan were transported to the Republic of Uganda through the WHO Country Office in Juba City, South Sudan and later analyzed at the Uganda Virus Research Institute (UVRI) in Entebbe Town of Uganda.
The study was planned to comprise two (2) different phases: The first phase was a retrospective laboratory study using archived frozen nasal and oropharyngeal swab samples. Should all test results be negative to SARS-CoV-2, then the study would be discontinued and not proceed to phase two. Should samples test positive, the respective patients would be contacted and their anti-body response would be tested to establish, if and for how long antibodies would be detectable after an infection.
The study used the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) diagnostic to test the RNA obtained from frozen samples of patients who presented with signs and symptoms of SARI at National Influenza Virus Infections Sentinel Surveillance Sites in the EAC Partner States between 1st November 2019 and 29th February 2020. All swab samples that were confirmed for influenza virus infections as well as those that did not bring positive results and were treated as suspect cases of SARS-CoV-2 infections were screened for COVID-19 with nucleic acid amplification tests (NAAT). Real-time RTPCR was used as the reference method for diagnosis of SARS-CoV-2 infections. The TIB-Molbiol test kits and related reagents were provided by the German Federal Robert Koch-Institute.
Results: Negative COVID-19 RT-PCR test results were obtained in a retrospective study of all the archived nasal and oropharyngeal swab samples from patients presenting with SARI-like signs and symptoms at various national influenza virus infections sentinel surveillance sites in four (4) EAC Partner States from 1st November 2019 to 29th February 2020 before the WHO declaration of the COVID-19 global pandemic. A total of 1,153 swab samples that were analyzed by molecular testing of archived frozen nasal and oropharyngeal swab samples from four (4) participating EAC Partner States were negative for COVID-19 in rdrp-gene and e-gene. All the swab samples which were tested picked Equine Arteritis Virus (EAV) which is an internal positive control used to ensure the quality of the viral RNA extraction step. Therefore, the second phase of the study which would have entailed testing for COVID-19 serum antibodies in patients whose frozen nasal and oropharyngeal swab samples turned out to be COVID-19 positive by RT-PCR did not continue in any of the four participating EAC Partner States..
Conclusion: The results strongly indicate that there were no infections with SARS-CoV-2 among patients with SARI-like symptoms in the EAC region before March 2020, when the first case was officially reported. The existing country-wide infrastructure for the National Influenza Virus Infections Sentinel Surveillance Systems in the EAC Partner States proved to be pivotal in retrieving archived frozen nasal and oropharyngeal swab samples. In this regard, these national sentinel surveillance sites should be strengthened and expanded to cover other biological pathogens of global public health importance such as Influenza Viruses, SARS, Crimean Congo Fever, Dengue Fever, Yellow Fever, Rift Valley Fever, Ebola Virus Diseases and other Viral Hemorrhagic Fevers (VHFs) and be expanded to cover more parts of each Partner State.
EAC's: East African Countries