{"doi":"10.1128/jcm.00999-09","title":"Rapid Semiautomated Subtyping of Influenza Virus Species during the 2009 Swine Origin Influenza A H1N1 Virus Epidemic in Milwaukee, Wisconsin","abstract":"<jats:title>ABSTRACT</jats:title>\n          <jats:p>In the spring of 2009, a novel influenza A (H1N1) virus (swine origin influenza virus [S-OIV]) emerged and began causing a large outbreak of illness in Milwaukee, WI. Our group at the Midwest Respiratory Virus Program laboratory developed a semiautomated real-time multiplex reverse transcription-PCR assay (Seasonal), employing the NucliSENS easyMAG system (bioMérieux, Durham, NC) and a Raider thermocycler (HandyLab Inc., Ann Arbor, MI), that typed influenza A virus, influenza B virus, and respiratory syncytial virus (RSV) and subtyped influenza A virus into the currently circulating H1 and H3 subtypes, as well as a similar assay that identified H1 of S-OIV. The Seasonal and H1 S-OIV assays demonstrated analytical limits of detection of &lt;50 50% tissue culture infective doses/ml and 3 to 30 input copies, respectively. Testing of the analytical specificities revealed no cross-reactivity with 41 and 26 different common organisms and demonstrated outstanding reproducibility of results. Clinical testing showed 95% sensitivity for influenza A virus and influenza B virus and 95 and 97% specificity compared to tissue culture. Comparisons of results from other molecular tests showed levels of positive agreement with the Seasonal and H1 S-OIV assay results of 99 and 100% and levels of negative agreement of 98 and 100%. This study has demonstrated the use of a semiautomated system for sensitive, specific, and rapid detection of influenza A virus, influenza B virus, and RSV and subtyping of influenza A virus into human H1 and H3 and S-OIV strains. This assay/system performed well in clinical testing of regular seasonal influenza virus subtypes and was outstanding during the 2009 Milwaukee S-OIV infection outbreak. This recent outbreak of infection with a novel influenza A (H1N1) virus also demonstrates the importance of quickly distributing information on new agents and of having rapid influenza virus subtyping assays widely available for clinical and public health decisions.</jats:p>","journal":"Journal of Clinical Microbiology","year":2009,"id":19065,"datarank":2.9791845271642603,"base_score":3.6888794541139363,"endowment":3.6888794541139363,"self_citation_contribution":0.5533319181170905,"citation_network_contribution":2.42585260904717,"self_endowment_contribution":0.5533319181170905,"citer_contribution":2.42585260904717,"corpus_percentile":null,"corpus_rank":null,"citation_count":39,"citer_count":28,"citers_with_citation_signal":24,"citers_with_endowment":24,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":130335,"name":"Eric T. 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Henrickson","orcid":null,"position":12,"is_corresponding":false},{"id":130334,"name":"Michael E. Bose","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.6888794541139363,"endowment":3.6888794541139363,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19641066","pmcid":"PMC2738075","openalex_id":"https://openalex.org/W2162191803","authors":[],"funders":[{"funder_name":"NIAID NIH HHS","grant_id":"U01-AI070428","title":null},{"funder_name":"PHS HHS","grant_id":"200-2008-25466","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"U01 AI066584","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"U01 AI070428","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"U01 AI077988","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"UO1-AI77988","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"U01-AI066584","title":null}],"total_grants":7,"fwci":5.909,"citation_percentile":0.96693434,"influential_citations":0,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":1},{"year":2014,"count":1},{"year":2015,"count":1},{"year":2020,"count":3},{"year":2021,"count":1},{"year":2022,"count":1}],"oa_status":"closed","license":"https://journals.asm.org/non-commercial-tdm-license","oa_locations":[{"url":"https://europepmc.org/articles/pmc2738075?pdf=render","host_type":"GREEN"},{"url":"https://journals.asm.org/doi/pdf/10.1128/JCM.00999-09","host_type":"publisher"},{"url":"https://doi.org/10.1128/jcm.00999-09","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19641066","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2738075","host_type":"repository"}],"fields_of_study":["Influenza Virus Research Studies","Respiratory viral infections research","Animal Disease Management and Epidemiology","Biology","Medicine","Environmental Science","Automation","DNA Primers","Disease Outbreaks","Genotype","Humans","Influenza A Virus, H1N1 Subtype","Influenza A virus","Influenza B virus","Influenza, Human","Reproducibility of Results","Respiratory Syncytial Viruses","Sensitivity and Specificity","Virology","Wisconsin"],"mesh_terms":["Automation","Disease Outbreaks","Genotype","Humans","Influenza, Human","Influenza A virus","Influenza B virus","Respiratory Syncytial Viruses","Sensitivity and Specificity","Virology","Wisconsin","Reproducibility of Results","DNA Primers","Influenza A Virus, H1N1 Subtype"],"keywords":["Subtyping","Virus","Virology","Influenza A virus","Biology","Multiplex","Orthomyxoviridae","Influenzavirus B","Outbreak","Microbiology","Genetics"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-04T01:37:03.227670Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}