High abundance of butyrate-producing bacteria in the naso-oropharynx of SARS-CoV-2-infected persons in an African population: implications for low disease severity.

BACKGROUND: The association of the oral microbiome with SARS-CoV-2 infections and disease progression has been documented in European, Asian, and American populations but not in Africa. METHODS: We conducted a study in Ghana to evaluate and compare the naso-oropharyngeal microbiome in SARS-CoV-2-infected and uninfected persons before (pre-vaccine) and after vaccine availability (post-vaccine) in the country. 16S rRNA V3-V4 variable region was sequenced and analysed from DNA extracted from naso-oropharyngeal swabs. RESULTS: Considering only the infection status, infected and uninfected groups had no difference in their within-group diversity and was evident in the study population pre- and post-vaccine availability. The introduction of vaccines reduced the diversity of the naso-oropharyngeal microbiome particularly among SARS-CoV-2 positive persons and, vaccinated individuals (both infected and uninfected) had higher microbial diversity compared to their unvaccinated counterparts. SARS-CoV-2-positive and -negative individuals were largely compositionally similar varying by 4-7% but considering vaccination*infection statuses, the genetic distance increased to 12% (P = 0.003) and was mainly influenced by vaccination. Common among the pre- and post-vaccine samples, Atopobium and Finegoldia were abundant in infected and uninfected individuals, respectively. Bacteria belonging to major butyrate-producing phyla, Bacillota (particularly class Clostridia) and Bacteroidota showed increased abundance more strikingly in infected individuals before vaccines were available. They reduced significantly after vaccines were introduced into the country with Fusobacterium and Lachnoanaerobaculum being the only common bacteria between pre-vaccine infected persons and vaccinated individuals, suggesting that natural infection and vaccination correlate with high abundance of short-chain fatty acids. CONCLUSION: Our results show, in an African cohort, the abundance of bacteria taxa known for their protective pathophysiological processes, especially during infection, suggesting that this population is protected against severe COVID-19. The immune-related roles of the members of Bacillota and Bacteroidota that were found associated with infection and vaccination require further studies, and how these may be linked to ethnicity, diet and age. We also recommend expansion of microbiome-disease association studies across Africa to identify possible bacterial-mediated therapeutics for emerging infections.

Assessing the performance of regular surgical nose masks as a sampling method for SARS-CoV-2 detection in a cross-sectional study.

Nose masks are widely worn for protection against respiratory pathogens, including SARS-CoV-2. They have been reported as possible substrates for viral sampling and testing for COVID-19 but, evaluations have so far been purposive; involving individuals known to have the infection and using improved materials on the nose masks to trap the virus. We investigated the feasibility of using the regular 3-ply surgical masks and, voluntary coughing as a mode of particle expulsion for detecting SARS-CoV-2 infections in a cross-sectional study at Ghana's first COVID-19 testing reference laboratory, the Noguchi Memorial Institute for Medical Research, University of Ghana. Paired samples of naso-oropharyngeal swabs and nose masks already worn by 103 consenting adult participants (retro masks) were collected. Participants were also required to produce three strong coughs into a newly supplied sterile surgical nose mask. Pre-wetted swabs in Viral Transport Media (VTM) were used in swabbing the inner lining of each nose mask. The swabs used were then stored in VTM to maintain the integrity of the samples. PCR results of SARS-CoV-2 detection from the nose masks were compared to those from naso-oropharyngeal swabs ('gold-standard'). Out of the 103 participants tested with all three methods, 66 individuals sampled with naso-oropharyngeal swabs were detected as positive, and the retro and new masks matched 9 and 4, respectively. Only 3 individuals were positive across all three sampling methods accessed. The retro nose masks performed better in matching the gold-standard results than the new mask + coughing method, with 90% vs 80% sensitivity, positive predictive value of 13.6% vs 6%, and a weak but significant linear relationship (adj. R2 = 0.1; P = 0.0004). Importantly, we also show that the nose masks would work for sampling whether individuals are symptomatic or asymptomatic since gold-standard PCR cycling threshold (Ct) values for positive individuals did not differ between the two groups (P< 0.05). We recommend including features such as talking during participant engagement, use of a spontaneous cough inducer and increased coughing bouts > 3, to improve the performance of sterile nose masks for SARS-CoV-2 detection.