While most people effectively clear SARS-CoV-2, there are several reports of prolonged infection in immunosuppressed individuals. Here we present a case of prolonged infection of greater than 6 months with the shedding of high titter SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. Through whole-genome sequencing at multiple time points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern. This provides support to the hypothesis of intra-host evolution as one mechanism for the emergence of SARS-CoV-2 variants with immune evasion properties.

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: Sexually transmitted infections (STIs), particularly genital ulcer diseases (GUD) are a neglected field in health care, partly due to the stigma associated with the diseases. Coinfection with HIV alters the clinical presentation, natural history and response to treatment. Moreover, STIs contribute significantly to increased risk of HIV transmission. Management of STIs at primary health care level is syndromic, driven by algorithms. In the absence of interest and expertise at secondary/tertiary care centres patients, who fail this management, suffer. Methods & Materials: We present a retrospective chart review of patients referred to our a specialist Infectious Diseases Unit with challenging or unusual STI/GUD, who did not respond to syndromic management. Results: We have closely documented 42 patients (23 male, 39 HIV positive) seen at King Edward VIII hospital for STI/GUD. The patients had an average of 2.6 different primary health care providers (range: 1-5) before coming to the tertiary site. Only 54.8% were formally referred. 15 patients had extensive chronic HSV ulcers (8 males, all HIV +). Of these, 7 responded to high doses of acyclovir (400 mg 8 hourly to 800 mg 5 times daily). Duration of treatment varied from 7 to 21 days. 6 chronic HSV ulcers (4 males) failed high dose acyclovir but responded to topical imiquimod treatment. Of 13 patients (9 males) with extensive condylomata acuminata (warts) 4 underwent curative circumcision and 9 required extensive ablation. 5 of the latter (3 males) had squamous cell carcinomas. All were managed syndromically as STIs for >18 months. 4 patients had chronic genital ulcers with no discernible cause and very low CD4 counts. These ulcers healed completely after commencement of anti-retroviral treatment. One male with penile abscesses and multiple urinary fistulas had trichomonas vaginalis repeatedly isolated and responded to a prolonged course of metronidazole. Other diagnoses included severe tinea cruris (4), lichen planus chronicus (2), papular pruritic eruptions (PPE) (1), penile pearly papules (PPP) (1), vitiligo (1). Conclusion: We need to develop expertise in the management of patients who do not respond to syndromic STI/GUS treatment and develop clear referral pathways to secondary and tertiary care centres with adequate facilities and investigative capacity for timeous diagnosis and intervention. This is particularly urgent in the context of HIV/AIDS.