Genomic Surveillance and Phylogenetic Characterization of Seasonal Human Coronaviruses in Kazakhstan

Seasonal human coronaviruses (HCoVs) remain underrepresented in genomic surveil-lance in Central Asia. We applied species-specific tiled amplicon sequencing on the Oxford Nanopore Technologies platform to residual HCoV-positive respiratory samples collected in Kazakhstan. Of 102 samples received, 17 were tested with tiled panels and seven were sequenced. Six consensus genomes were near-complete (97.27–100.00% unambiguous positions), whereas one additional HCoV-OC43 genome was partial (39.97%) and excluded from phylogenetic analysis. Maximum-likelihood trees were reconstructed from a quality-controlled panel derived from public GenBank accessions, and whole-genome, ORF1ab, and Spike topologies were compared. The HCoV-229E/187 genome was tentatively assigned to genotype 7b. HCoV-NL63/324 and HCoV-NL63/327 were tentatively assigned to genotype C2, and HCoV-NL63/487 was also tentatively assigned to C2, with lower confidence. HCoV-OC43/259 was G-associated in whole-genome and Spike analyses but showed a different, weakly resolved ORF1ab context. HCoV-HKU1/1042 was B-like but unresolved because Spike could not be evaluated. RDP4 screening identified study-associated candidate signals for HCoV-229E/187, HCoV-OC43/259, and HCoV-HKU1/1042, but not for the three Kazakhstan HCoV-NL63 genomes. Automated breakpoint and parental assignments were treated as provisional and did not confirm individual recombination events. These findings expand genome-level evidence for all four endemic HCoV species in Kazakhstan while illustrating the importance of coverage-aware, cross-locus interpretation of genotype assignments.