Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa

Morton, Ben; Barnes, Kayla G.; Anscombe, Catherine; Jere, Khuzwayo; Matambo, Prisca; Mandolo, Jonathan; Kamng’ona, Raphael; Brown, Comfort; Nyirenda, James; Phiri, Tamara; Banda, Ndaziona P.; Van Der Veer, Charlotte; Mndolo, Kwazizira S.; Mponda, Kelvin; Rylance, Jamie; Phiri, Chimota; Mallewa, Jane; Nyirenda, Mulinda; Katha, Grace; Kambiya, Paul; Jafali, James; Mwandumba, Henry C.; Gordon, Stephen B.; Cornick, Jennifer; Jambo, Kondwani C.

Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.