Coronavirus (COVID-19) Collection
- The coronavirus disease 2019 (COVID-19) pandemic continues to spread worldwide (WHO 2020). Understanding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding, transmission dynamics, and re-infection with different SARS-CoV-2 clades in immunocompromised persons is an important clinical and public health challenge (Choi et al., 2020).
- As of June 30th, 2021, the ongoing SARS-CoV-2 pandemic has resulted in 180 million COVID-19 cases (with 3.9 million deaths) reported to the World Health Organisation (WHO). Of these, 5.4 million cases with 141,000 deaths have been reported from Africa (WHO Afro 2021). Currently, 150,000 COVID-19 cases have been recorded in Zambia, with 2,100 deaths (WHO COVID-19 dashboard – Zambia 2021).
- The SARS-CoV-2 pandemic has caused 171,292,827 confirmed COVID-19 cases with 3,687,589 deaths globally as of June 4th, 2021. Of these 3,530,845 cases occurred in sub-Saharan Africa (SSA) with 131,630 deaths (WHO Coronavirus dashboard, 2021; Africa CDC - Coronavirus Disease 2019 (COVID-19), 2021). Zambia reported its first COVID-19 case in March 2020 and has since recorded 96, 563 cases with 1,284 deaths as of June 4th, 202 (World Health Organisation, 2021). Eighteen months after the first COVID-19 cases were reported from Wuhan, China, several major knowledge gaps on COVID-19 pathology and pathogenesis remain, particularly in SSA.
- In patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, excessive inflammatory responses are considered to play a major role in the pathogenesis of severe coronavirus disease-2019 (COVID-19) disease, leading to acute respiratory distress syndrome and multiple-organ failure (Moore and June, 2020). Dysregulated inflammatory profile, defective immune responses and lymphopenia have also been identified as important features of severe disease (Del Valle et al., 2020; Bordoni et al., 2020).
- The WHO declared COVID-19, caused by SARS-CoV-2, a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 and later a pandemic on 11 March 2020 (WHO, 2020a). As of 28 September 2020, there were 32.7 million COVID-19 cases with 991,000 deaths worldwide reported to the WHO (2020b). All African countries have been affected and have reported a total of 1,172,342 COVID-19 cases, including 25,481 deaths (WHO, 2020b). As the global COVID-19 events unfolded, and Africa’s first COVID-19 case was reported from Egypt on 14 February 2020, many African countries prepared for the arrival of COVID-19 (Kapata et al., 2020).
- Genetic factors such as the HLA type of patients may play a role in regard to disease severity and clinical outcome of patients with COVID-19. Taking the data deposited in the GISAID database, we made predictions using the IEDB analysis resource (TepiTool) to gauge how variants in the SARS-CoV-2 genome may change peptide binding to the most frequent MHC-class I and -II alleles in Africa, Asia and Europe. We caracterized how a single mutation in the wildtype sequence of of SARS-CoV-2 could influence the peptide binding of SARS-CoV-2 variants to MHC class II, but not to MHC class I alleles.
- On December 31, 2019, aggregate cases of an apparently new respiratory syndrome were reported in the city of Wuhan, China by Chinese national health authorities to the World Health Organization (WHO) (Huang et al., 2020; Organization WH, 2020a). As of 13h February 2020, there have been 45 171 cases reported to the World Health Organization with 1104 deaths (Organization WH, 2020a). Outside China there have been 441 confirmed cases reported from 24 countries (Organization WH, 2020a; Organization WH, 2020b).