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.