Advancing Genomic Surveillance of Human Parainfluenza Viruses in Côte d'Ivoire Using Twist Hybrid-Capture Sequencing

Abstract

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.