{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T03:47:33Z","timestamp":1772250453548,"version":"3.50.1"},"reference-count":31,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["JP223fa627005"],"award-info":[{"award-number":["JP223fa627005"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Health, Labour and Welfare Sciences Research","award":["19HA1001"],"award-info":[{"award-number":["19HA1001"]}]},{"name":"Health, Labour and Welfare Sciences Research","award":["25HA2001"],"award-info":[{"award-number":["25HA2001"]}]},{"name":"Health, Labour and Welfare Sciences Research","award":["25HB1001"],"award-info":[{"award-number":["25HB1001"]}]},{"name":"Grant-in-Aid for Scientific Research","award":["10110713"],"award-info":[{"award-number":["10110713"]}]},{"name":"Grant-in-Aid for Scientific Research","award":["10110802"],"award-info":[{"award-number":["10110802"]}]},{"name":"Daido Welfare Foundation","award":["2019-18"],"award-info":[{"award-number":["2019-18"]}]},{"name":"Daido Welfare Foundation","award":["2023-9"],"award-info":[{"award-number":["2023-9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Human adenovirus type 3 (HAdV-3) in the species Mastadenovirus blackbeardi 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 (n = 110), resulting in near whole-genome sequences (~99% length) for 105 samples with high read coverage (~262.6 \u00b1 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\u20132022) 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 Mastadenovirus caesari (n = 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.<\/jats:p>","DOI":"10.3390\/v18010074","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T15:28:57Z","timestamp":1767626937000},"page":"74","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Tiled-Amplicon Whole-Genome Sequencing Method Reveals Endemic Circulation of Human Adenovirus Type 3 in Japan"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2180-2120","authenticated-orcid":false,"given":"Gabriel","family":"Gonzalez","sequence":"first","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naganori","family":"Nao","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0227-2515","authenticated-orcid":false,"given":"Koshiro","family":"Tabata","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3463-1834","authenticated-orcid":false,"given":"Yukari","family":"Itakura","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shinji","family":"Saito","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenichiro","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Japan Institute for Health Security, National Institute for Infectious Diseases, Tokyo 162-8640, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masaaki","family":"Kobayashi","sequence":"additional","affiliation":[{"name":"Kobayashi Pediatric Clinic, Shizuoka 426-0067, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nobuyoshi","family":"Kitaichi","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Health Sciences University of Hokkaido Hospital, Sapporo 002-8072, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nobuhisa","family":"Ishiguro","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Sophia Kita-Maruyama Clinic, Sapporo 060-0004, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4861-4349","authenticated-orcid":false,"given":"Tsuguto","family":"Fujimoto","sequence":"additional","affiliation":[{"name":"Japan Institute for Health Security, National Institute for Infectious Diseases, Tokyo 162-8640, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6499-9579","authenticated-orcid":false,"given":"Adriana E.","family":"Kajon","sequence":"additional","affiliation":[{"name":"Lovelace Biomedical Research Institute, Albuquerque, NM 87108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hirofumi","family":"Sawa","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Japan"},{"name":"One Health Research Center, Hokkaido University, Sapporo 060-0818, Japan"},{"name":"International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan"},{"name":"Global Virus Network, Baltimore, MD 21201, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1039-6278","authenticated-orcid":false,"given":"Nozomu","family":"Hanaoka","sequence":"additional","affiliation":[{"name":"Japan Institute for Health Security, National Institute for Infectious Diseases, Tokyo 162-8640, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"ref_1","unstructured":"ICTV (2025, July 02). Genus: Mastadenovirus. Available online: https:\/\/ictv.global\/report\/chapter\/adenoviridae\/adenoviridae\/mastadenovirus."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e0083622","DOI":"10.1128\/jcm.00836-22","article-title":"Adenovirus infections: New insights for the clinical laboratory","volume":"62","author":"Kajon","year":"2024","journal-title":"J. Clin. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1016\/j.jiac.2024.07.017","article-title":"Epidemiological impact of human adenovirus as causative agent of respiratory infections: An Italian multicentre retrospective study, 2022\u20132023","volume":"30","author":"Giardina","year":"2024","journal-title":"J. Infect. Chemother."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Kremer, E.J.J. (2021). What is the risk of a deadly adenovirus pandemic?. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009814"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1177\/1120672119891408","article-title":"Disinfectant potential in inactivation of epidemic keratoconjunctivitis-related adenoviruses by potassium peroxymonosulfate","volume":"31","author":"Hashizume","year":"2021","journal-title":"Eur. J. Ophthalmol."},{"key":"ref_6","unstructured":"NIID (2025, February 10). National Institute of Infectious Diseases\u2014Infectious Agent Surveillance Report, Available online: https:\/\/www.niid.go.jp\/niid\/en\/iasr.html."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.coviro.2011.12.008","article-title":"Structure of human adenovirus","volume":"2","author":"Nemerow","year":"2012","journal-title":"Curr. Opin. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1861","DOI":"10.1002\/1873-3468.13848","article-title":"The Adenovirus Death Protein\u2014A small membrane protein controls cell lysis and disease","volume":"594","author":"Georgi","year":"2020","journal-title":"Febs. Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3496","DOI":"10.1002\/1873-3468.13682","article-title":"Immune evasion by adenoviruses: A window into host-virus adaptation","volume":"593","author":"Oliveira","year":"2019","journal-title":"Febs. Lett."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.gene.2014.04.018","article-title":"Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D","volume":"547","author":"Gonzalez","year":"2014","journal-title":"Gene"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1002\/jmv.24749","article-title":"First isolation of a new type of human adenovirus (genotype 79), species Human mastadenovirus B (B2) from sewage water in Japan","volume":"89","author":"Yoshitomi","year":"2017","journal-title":"J. Med. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1099\/jmm.0.000625","article-title":"Genomic diversity of human adenovirus type 3 isolated in Fukui, Japan over a 24-year period","volume":"66","author":"Adhikary","year":"2017","journal-title":"J. Med. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Alm, E., Broberg, E.K., Connor, T., Hodcroft, E.B., Komissarov, A.B., Maurer-Stroh, S., Melidou, A., Neher, R.A., O\u2019Toole, A., and Pereyaslov, D. (2020). Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance, 25.","DOI":"10.2807\/1560-7917.ES.2020.25.32.2001410"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Takahashi, K., Gonzalez, G., Kobayashi, M., Hanaoka, N., Carr, M.J., Konagaya, M., Nojiri, N., Ogi, M., and Fujimoto, T. (2019). Pediatric Infections by Types 2, 89, and a Recombinant Type Detected in Japan between 2011 and 2018. Viruses, 11.","DOI":"10.3390\/v11121131"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00705-006-0842-8","article-title":"Detection and sequence-based typing of human adenoviruses using sensitive universal primer sets for the hexon gene","volume":"152","author":"Okada","year":"2007","journal-title":"Arch. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"bpaa014","DOI":"10.1093\/biomethods\/bpaa014","article-title":"Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding","volume":"5","author":"Freed","year":"2020","journal-title":"Biol. Methods Protoc."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2300505","DOI":"10.2807\/1560-7917.ES.2024.29.16.2300505","article-title":"Multiple introductions of monkeypox virus to Ireland during the international mpox outbreak, May 2022 to October 2023","volume":"29","author":"Gonzalez","year":"2024","journal-title":"Eurosurveillance"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief Bioinform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Lemey, P., Rambaut, A., Drummond, A.J., and Suchard, M.A. (2009). Bayesian phylogeography finds its roots. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000520"},{"key":"ref_24","unstructured":"National Institute of Infectious Diseases (2025, February 10). Infectious Disease Surveillance System in Japan, Available online: https:\/\/id-info.jihs.go.jp\/surveillance\/idss\/nesid-program-summary\/nesid_en.pdf."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nrg2323","article-title":"Rates of evolutionary change in viruses: Patterns and determinants","volume":"9","author":"Duffy","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Rice, A., Gonzalez, G., Carr, M., Dean, J., O\u2019Byrne, E., Aarts, L., Vennema, H., Banka, W., Bennett, C., and Cleary, S. (2025). Human respiratory syncytial virus genetic diversity and lineage replacement in Ireland pre- and post-COVID-19 pandemic. Microb. Genom., 11.","DOI":"10.1099\/mgen.0.001379"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"751","DOI":"10.3201\/eid2904.221878","article-title":"Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland","volume":"29","author":"Martin","year":"2023","journal-title":"Emerg. Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41541-023-00754-3","article-title":"A recombinant virus-like particle vaccine against adenovirus-7 induces a potent humoral response","volume":"8","author":"Mazboudi","year":"2023","journal-title":"npj Vaccines"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Wang, S.L., Chi, C.Y., Kuo, P.H., Tsai, H.P., Wang, S.M., Liu, C.C., Su, I.J., and Wang, J.R. (2013). High-incidence of human adenoviral co-infections in Taiwan. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0075208"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"6209","DOI":"10.1128\/JVI.00515-15","article-title":"Interregional Coevolution Analysis Revealing Functional and Structural Interrelatedness between Different Genomic Regions in Human Mastadenovirus D","volume":"89","author":"Gonzalez","year":"2015","journal-title":"J. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e0060523","DOI":"10.1128\/aem.00605-23","article-title":"The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling","volume":"89","author":"Zhang","year":"2023","journal-title":"Appl. Environ. Microbiol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/1\/74\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T05:22:00Z","timestamp":1767763320000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/1\/74"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":31,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["v18010074"],"URL":"https:\/\/doi.org\/10.3390\/v18010074","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,5]]}}}