Tiled-Amplicon Whole-Genome Sequencing Method Reveals Endemic Circulation of Human Adenovirus Type 3 in Japan

Human adenovirus type 3 (HAdV-3) in the species <i>Mastadenovirus blackbeardi</i> is a frequent cause of hundreds of respiratory infections in Japan, with outbreaks varying in clinical severity. Such a high frequency of cases could be due to regular migration of novel variants or persistent circulation of endemic strains. Either scenario would require different measures to ameliorate the burden on public health. We designed a new cost-effective whole-genome sequencing protocol based on tiled amplicons and nanopore sequencing to clarify the circumstances behind the frequent outbreaks. This protocol was used with clinical samples collected between 2011 and 2020 from Japanese patients with acute respiratory illness (<i>n</i> = 110), resulting in near whole-genome sequences (~99% length) for 105 samples with high read coverage (~262.6 ± 192 reads). Phylogenetic analysis indicated sustained circulation of endemic strains in Japan during the analyzed decade and their relation to other strains worldwide with publicly available genome sequences. However, a comparison with other Japanese HAdV-3 strains circulating since 2023 suggested the public health measures introduced during the COVID-19 pandemic (2020-2022) indirectly affected the prevalence of circulating HAdV-3 variants. Additionally, our approach enabled the detection and partial sequencing (~71% completion) of co-infecting strains from the species <i>Mastadenovirus caesari</i> (<i>n</i> = 4) in the examined samples. The detection of adenoviruses belonging to different species in the same sample highlights how our protocol enhances the distinction of circulating viruses. In conclusion, these results and the introduced protocol will enable timely characterization and clinical interventions to mitigate this virus.