Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Background Human Pappilloma Virus (HPV) is the necessary cause of cervical cancer. A number of risk factors are believed to influence the role of HPV in the development of cervical cancer. This is so because majority of HPV infections are cleared and only a few are able to result into cancer. Chlamydia trachomatis (CT) is considered a potential cofactor in the development of cervical intraepithelial neoplasia (CIN), although different studies have produced contradicting information (Silins et al., 2005, Bellaminutti et al., 2014, and Bhatla et al., 2013). The objective of this cross-sectional study was to determine the prevalence and association of HPV-Chlamydial coinfection with cervical intraepithelial lesions and other risk factors for cervical intraepithelial lesions at a hospital in south western Uganda (MRRH). Methods The study included 93 participants, with an age range of 25 to 80 years, from whom cervical specimens were collected and enrolment forms were completed upon consent. Experienced midwives collected one cervical smear and two endocervical swabs from each participant. The swabs were used for HPV DNA and Chlamydia trachomatis antigen testing. Data was entered in Microsoft excel and analysed using STATA 12 software. With the help of spearman's correlation at the 0.05 level of significance, bivariate and multivariate analysis were done by logistic regression, to determine associations of risk factors to cervical lesions. Results The results showed the prevalence of HPV-Chlamydial coinfection to be 8.6% (8/93). Positive Pap smear results were found in 60.22% (56/93) participants, most of whom had low grade squamous intraepitherial lesion (LSIL) (54.84%). HPV-Chlamydial coinfection showed a significant correlation with a positive cytology result and only relatively significantly correlated with LSIL grade of cytological positivity. HPV was found to be the risk factors associated with cervical intraepithelial lesions at MRRH. Conclusion HPV, Chlamydia, and HPV-Chlamydial coinfection are prevalent infections and there is a likelihood of association between HPV-Chlamydial coinfection and with cervical intraepithelial lesions. This study recommends general sexually transimitted infections (STIS) screening for every woman that turns up for cervical cancer screening and a larger study, probably a multicentre study.

Background Globally, key subpopulations such as healthcare workers (HCW) may have a higher risk of contracting SARS-CoV-2. In Uganda, limited access to Personal Protective Equipment and lack of clarity on the extent/pattern of community spread may exacerbate this situation. The country established infection prevention/control measures such as lockdowns and proper hand hygiene. However, due to resource limitations and fatigue, compliance is low, posing continued onward transmission risk. This study aimed to describe extent of SARS-CoV-2 seroprevalence in selected populations within the Rakai region of Uganda. Methods From 30th November 2020 to 8th January 2021, we collected venous blood from 753 HCW at twenty-six health facilities in South-Central Uganda and from 227 population-cohort participants who reported specific COVID-19 like symptoms (fever, cough, loss of taste and appetite) in a prior phone-based survey conducted (between May and August 2020) during the first national lockdown. 636 plasma specimens collected from individuals considered high risk for SARS-CoV-2 infection, prior to the first confirmed COVID-19 case in Uganda were also retrieved. Specimens were tested for antibodies to SARS-CoV-2 using the CoronaChek™ rapid COVID-19 IgM/IgG lateral flow test assay. IgM only positive samples were confirmed using a chemiluminescent microparticle immunoassay (CMIA) (Architect AdviseDx SARS-CoV-2 IgM) which targets the spike protein. SARS-CoV-2 exposure was defined as either confirmed IgM, both IgM and IgG or sole IgG positivity. Overall seroprevalence in each participant group was estimated, adjusting for test performance. Results The seroprevalence of antibodies to SARS-CoV-2 in HCW was 26.7% [95%CI: 23.5, 29.8] with no difference by sex, age, or cadre. We observed no association between PPE use and seropositivity among exposed healthcare workers. Of the phone-based survey participants, 15.6% [95%CI: 10.9, 20.3] had antibodies to SARS-CoV-2, with no difference by HIV status, sex, age, or occupation. Among 636 plasma specimens collected prior to the first confirmed COVID-19 case, 2.3% [95%CI: 1.2, 3.5] were reactive. Conclusions Findings suggest high seroprevalence of antibodies to SARS-CoV-2 among HCW and substantial exposure in persons presenting with specific COVID-19 like symptoms in the general population of South-Central Uganda. Based on current limitations in serological test confirmation, it remains unclear whether seroprevalence among plasma specimens collected prior to confirmation of the first COVID-19 case implies prior SARS-CoV-2 exposure in Uganda.

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Xpert MTB/RIF (Xpert) and culture are the most reliable methods for tuberculosis diagnosis but are still poorly accessible in many low-resource countries. We aimed to assess the effects of OMNIgene Sputum (OM-S) and ethanol in preserving sputum for Xpert and OM-S for mycobacterial growth indicator tube (MGIT) testing over periods of 15 and 8 days, respectively. Sputum samples were collected from newly diagnosed smear-positive patients. For Xpert, pooled samples were split into 5 aliquots: 3 for Xpert on days 0, 7, and 15 without additive and 2 with either OM-S or ethanol at day 15. For MGIT, 2 aliquots were tested without preservative and 2 with OM-S at 0 and 8 days. Totals of 48 and 47 samples were included in the analysis for Xpert and culture. With Xpert, using day 0 as a reference, untreated samples stored for 7 and 15 days showed concordances of 45/46 (97.8%) and 46/48 (95.8%). For samples preserved with OM-S or ethanol for 15 days compared with untreated samples processed at day 0 or after 15 days, OM-S concordances were 46/48 (95.8%) and 47/48 (97.9%), while those of ethanol were 44/48 (91.7%) and 45/48 (93.8%). With MGIT, concordances between untreated and OM-S-treated samples were 21/41 (51.2%) at day 0 and 21/44 (47.7%) at day 8. In conclusion, Xpert equally detected tuberculosis in OM-S-treated and untreated samples up to 15 days but showed slightly lower detection in ethanol-treated samples. Among OM-S-treated samples, MGIT positivity was significantly lower than in untreated samples at both time points.