Influenza and other respiratory viruses · 2026
Advancing Genomic Surveillance of Human Parainfluenza Viruses in Côte d'Ivoire Using Twist Hybrid-Capture Sequencing.
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Koumba-Koumba Olivia Cariolh, Ouattara Yakoura Karidja, Kadjo Herve A, Kane Mouhamed, Kouao Maxime Diané, Kouassi Helene, Mbra Ange-Michele, Mouliom Alida, Ndiaye Ndeye Awa, Dia Ndongo, Coulibaly Daouda, Adjogoua Edgard, Agbessi Therese K, Diagne Moussa Moise
Аннотация
BACKGROUND: Human parainfluenza viruses (HPIV1-3) are major causes of acute respiratory infections, yet their genomic epidemiology remains poorly characterized in sub-Saharan Africa. We evaluated hybrid-capture sequencing for HPIV genomic surveillance in Côte d'Ivoire using respiratory samples collected through the national sentinel surveillance network from January 2022 to December 2024.
METHODS: Among 268 RT-qPCR-positive samples, 49 were selected for sequencing using the Twist Respiratory Virus Research hybrid-capture panel on the Illumina iSeq 100 platform. Genome assembly and phylogenetic analyses were performed using CZ-ID and IQ-TREE.
RESULTS: Hybrid-capture sequencing recovered 29 near-complete genomes: 9 HPIV1, 10 HPIV2, and 10 HPIV3. Genome recovery was strongly dependent on viral load, with a marked negative correlation between cycle threshold (Ct) value and genome coverage (r = -0.91) and optimal performance at Ct ≤ 30. Viral co-detections were identified in 25 sequenced samples; adenovirus type B was the most frequent co-detected pathogen, while HPIV3 showed the broadest co-detection profile. Phylogenetic analysis revealed limited diversity for HPIV1, greater diversity for HPIV2, and pronounced heterogeneity for HPIV3, including co-circulation of divergent lineages.
CONCLUSIONS: Hybrid-capture sequencing provides a practical approach for HPIV genomic surveillance in routine settings and offers detailed insight into HPIV circulation in West Africa, supporting lineage tracking and the design of future genomic surveillance strategies.
METHODS: Among 268 RT-qPCR-positive samples, 49 were selected for sequencing using the Twist Respiratory Virus Research hybrid-capture panel on the Illumina iSeq 100 platform. Genome assembly and phylogenetic analyses were performed using CZ-ID and IQ-TREE.
RESULTS: Hybrid-capture sequencing recovered 29 near-complete genomes: 9 HPIV1, 10 HPIV2, and 10 HPIV3. Genome recovery was strongly dependent on viral load, with a marked negative correlation between cycle threshold (Ct) value and genome coverage (r = -0.91) and optimal performance at Ct ≤ 30. Viral co-detections were identified in 25 sequenced samples; adenovirus type B was the most frequent co-detected pathogen, while HPIV3 showed the broadest co-detection profile. Phylogenetic analysis revealed limited diversity for HPIV1, greater diversity for HPIV2, and pronounced heterogeneity for HPIV3, including co-circulation of divergent lineages.
CONCLUSIONS: Hybrid-capture sequencing provides a practical approach for HPIV genomic surveillance in routine settings and offers detailed insight into HPIV circulation in West Africa, supporting lineage tracking and the design of future genomic surveillance strategies.