Gamuchirai Mary Kavhumbura

Background/Objectives: Influenza, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause overlapping respiratory illness, but Zimbabwean adult multipathogen data remain limited. We described influenza and RSV detection and co-detection with SARS-CoV-2 among adults enrolled in the ZIMCOVVAR study. Methods: This retrospective sub-study included nasopharyngeal specimens from adults with acute respiratory illness recruited in six Zimbabwean provinces during 2022-2023. Following exclusion of duplicate and unlinked records, 1,429 participants were analyzed. Influenza A, influenza B, and RSV were tested by multiplex real-time reverse-transcription polymerase chain reaction (PCR); recorded target cycle thresholds (Ct) ≤30 were provisionally classified as signals. Valid target-specific denominators remained unresolved. Proportions, confidence intervals, monthly patterns, and associations with SARS-CoV-2 status were examined. Results: The analytic cohort comprised 281 SARS-CoV-2-positive and 1,148 negative participants; median age was 35 years and 68.2% were female. Ct-defined influenza A, RSV, and influenza B signals occurred in 191/1,429 (13.4%), 53/1,429 (3.7%), and 2/1,429 (0.1%), respectively. Influenza A was recorded in 68/281 (24.2%) SARS-CoV-2-positive versus 123/1,148 (10.7%) negative participants. RSV was recorded in 3/281 (1.1%) versus 50/1,148 (4.4%), respectively. These are provisional signals per linked record, not valid-result positivity estimates; testing-group exclusion reversed the adjusted association. Conclusions: The selected adult cohort showed recorded influenza and RSV detections alongside SARS-CoV-2, supporting continued investigation of multiple respiratory pathogens in symptomatic adults. The findings require cautious interpretation because of nonrepresentative sampling and unresolved testing-group effects; quality-assured, multi-season surveillance is needed to inform local prevention planning.

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) depends on sequence quality and reliable specimen linkage. We characterised lineage distribution, genome quality and clinical-data linkage in 731 genomic records from Zimbabwe dated November 2022 to January 2024. Consensus sequences were analyzed using Nextclade, and genomic metadata were linked to clinical records by exact identifiers. Clinical data were available for 697 records; median age was 37 years (interquartile range, 27–48), and 71.4% were female. Fifty-nine Pango lineage assignments and 12 Nextclade clade labels were observed. XBB.1.5 descendants accounted for 443/731 records (60.6%); the most frequent exact assignments were XBB.1.5 (36.4%) and XBB.1.5.28 (17.4%). Quality-control categories were good for 24.9%, mediocre for 42.1% and bad for 33.0%. Identical aligned consensus sequences occurred in 186 pairs involving 372 records (50.9%). Five BA.2.86-group assignments had unresolved date–lineage conflicts. XBB.1.5 descendants were the most frequently assigned group in this historical dataset. Heterogeneous sequence quality, uneven sampling and unresolved record relationships constrain temporal interpretation and preclude national prevalence estimates. The findings highlight the importance of documented specimen linkage and reproducible analysis in retrospective genomic surveillance.