{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T18:08:56Z","timestamp":1792174136713,"version":"4.4.0"},"reference-count":38,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,4,30]],"date-time":"2025-04-30T00:00:00Z","timestamp":1745971200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Influenza is a communicable disease caused by RNA viruses. Strains A (affecting animals, humans), B (affecting humans), C (affecting rarely humans and pigs), and D (affecting cattle) comprise a variety of substrains each. Influenza A strain, affecting both humans and animals, is considered the most infectious, causing pandemics. There is an emerging need for the accurate classification of the different influenza A virus (IAV) subtypes, elucidating their mode of infection, as well as their fast and accurate diagnosis. Notably, in recent years, oligomeric sequences (words) that are present in the pathogen genomes and entirely absent from the host human genome were suggested to provide robust biomarkers for virus classification and rapid detection. To this end, we performed updated phylogenetic analyses of the IAV hemagglutinin genes, focusing on the sub H1N1 and H5N1. More importantly, we applied in silico methods to identify minimum length \u201cwords\u201d that exist consistently in the IAV genomes and are entirely absent from the human genome; these sequences identified in our current analysis may represent minimal signatures that can be utilized to distinguish IAV from other influenza viruses, as well as to perform rapid diagnostic tests.<\/jats:p>","DOI":"10.3390\/v17050659","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T11:35:13Z","timestamp":1746185713000},"page":"659","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Novel Minimal Absent Words Detected in Influenza A Virus"],"prefix":"10.3390","volume":"17","author":[{"given":"Elif Z\u00fclal","family":"Bigi\u015f","sequence":"first","affiliation":[{"name":"Izmir Biomedicine and Genome Center, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"},{"name":"Izmir International Biomedicine and Genome Institute, Dokuz Eyl\u00fcl University, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elif","family":"Y\u0131ld\u0131z","sequence":"additional","affiliation":[{"name":"Izmir Biomedicine and Genome Center, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"},{"name":"Izmir International Biomedicine and Genome Institute, Dokuz Eyl\u00fcl University, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Tagka","sequence":"additional","affiliation":[{"name":"First Department of Dermatology-Venereology, Medical School, National and Kapodistrian University of Athens, Andreas Syggros Hospital of Venereal & Dermatological Diseases, 10527 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Athanasia","family":"Pavlopoulou","sequence":"additional","affiliation":[{"name":"Izmir Biomedicine and Genome Center, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"},{"name":"Izmir International Biomedicine and Genome Institute, Dokuz Eyl\u00fcl University, 35340 Bal\u00e7ova, Izmir, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3098-5264","authenticated-orcid":false,"given":"George P.","family":"Chrousos","sequence":"additional","affiliation":[{"name":"University Research Institute of Maternal & Child Health & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Levadeias 8, 10527 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1227-5274","authenticated-orcid":false,"given":"Styliani","family":"Geronikolou","sequence":"additional","affiliation":[{"name":"University Research Institute of Maternal & Child Health & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Levadeias 8, 10527 Athens, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"D49","DOI":"10.1016\/j.vaccine.2008.07.039","article-title":"The biology of influenza viruses","volume":"26","author":"Bouvier","year":"2008","journal-title":"Vaccine"},{"key":"ref_2","unstructured":"(2025, February 13). CDC, Available online: https:\/\/www.cdc.gov\/flu\/about\/viruses-types.html."},{"key":"ref_3","first-page":"153","article-title":"Hippocrates, On Epidemics","volume":"1","author":"Littre","year":"1862","journal-title":"Br. Med. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e05055","DOI":"10.7554\/eLife.05055","article-title":"The contrasting phylodynamics of human influenza B viruses","volume":"4","author":"Vijaykrishna","year":"2015","journal-title":"eLife"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2150443","DOI":"10.1080\/21505594.2022.2150443","article-title":"Epidemiological, serological, and genetic evidence of influenza D virus infection in humans: Is it a justifiable cause for concern?","volume":"14","author":"Ly","year":"2023","journal-title":"Virulence"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Acquisti, C., Poste, G., Curtiss, D., and Kumar, S. (2007). Nullomers: Really a matter of natural selection?. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0001022"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3139","DOI":"10.1093\/nar\/gkab139","article-title":"Significant non-existence of sequences in genomes and proteomes","volume":"49","author":"Koulouras","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Pinho, A.J., Ferreira, P.J., Garcia, S.P., and Rodrigues, J.M. (2009). On finding minimal absent words. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-137"},{"key":"ref_9","unstructured":"Hampikian, G., and Andersen, T. (2007). Absent sequences: Nullomers and primes. Biocomputing, World Scientific."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Alileche, A., and Hampikian, G. (2017). The effect of Nullomer-derived peptides 9R, 9S1R and 124R on the NCI-60 panel and normal cell lines. BMC Cancer, 17.","DOI":"10.1186\/s12885-017-3514-z"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.peptides.2012.09.015","article-title":"Nullomer derived anticancer peptides (NulloPs): Differential lethal effects on normal and cancer cells in vitro","volume":"38","author":"Alileche","year":"2012","journal-title":"Peptides"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1016\/j.jflm.2013.02.003","article-title":"Safeguarding forensic DNA reference samples with nullomer barcodes","volume":"20","author":"Goswami","year":"2013","journal-title":"J. Forensic. Leg. Med."},{"key":"ref_13","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_14","doi-asserted-by":"crossref","unstructured":"Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S., and Tamura, K. (2024). MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing. Mol. Biol. Evol., 41.","DOI":"10.1093\/molbev\/msae263"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1093\/bioinformatics\/14.9.817","article-title":"MODELTEST: Testing the model of DNA substitution","volume":"14","author":"Posada","year":"1998","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1093\/bioinformatics\/btv189","article-title":"Three minimal sequences found in Ebola virus genomes and absent from human DNA","volume":"31","author":"Silva","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5129","DOI":"10.1093\/bioinformatics\/btaa686","article-title":"Persistent minimal sequences of SARS-CoV-2","volume":"36","author":"Pratas","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and Genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res."},{"key":"ref_19","first-page":"406","article-title":"The neighbor-joining method: A new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1111\/apm.13178","article-title":"Zoonotic and reverse zoonotic transmission of viruses between humans and pigs","volume":"129","author":"Glud","year":"2021","journal-title":"Apmis"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e0185621","DOI":"10.1128\/jvi.01856-21","article-title":"Coinfection of Chickens with H9N2 and H7N9 Avian Influenza Viruses Leads to Emergence of Reassortant H9N9 Virus with Increased Fitness for Poultry and a Zoonotic Potential","volume":"96","author":"Bhat","year":"2022","journal-title":"J. Virol."},{"key":"ref_22","unstructured":"(2025, February 13). World Health Organization. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/influenza-(seasonal)."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Kosik, I., and Yewdell, J.W. (2019). Influenza Hemagglutinin and Neuraminidase: Yin\u2013Yang Proteins Coevolving to Thwart Immunity. Viruses, 11.","DOI":"10.3390\/v11040346"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Sederdahl, B.K., and Williams, J.V. (2020). Epidemiology and Clinical Characteristics of Influenza C Virus. Viruses, 12.","DOI":"10.3390\/v12010089"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"162058","DOI":"10.1016\/j.scitotenv.2023.162058","article-title":"Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada","volume":"872","author":"Vo","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_26","first-page":"E19","article-title":"The new pandemic influenza A\/(H1N1)pdm09 virus: Is it really \u201cnew\u201d?","volume":"57","author":"Baldo","year":"2016","journal-title":"J. Prev. Med. Hyg."},{"key":"ref_27","unstructured":"(2025, February 14). ECDC. Available online: https:\/\/www.ecdc.europa.eu\/en\/swine-influenza\/factsheet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3201\/eid1201.051254","article-title":"Influenza pandemics of the 20th century","volume":"12","author":"Kilbourne","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1046\/j.1365-2672.2001.01492.x","article-title":"A history of influenza","volume":"91","author":"Potter","year":"2001","journal-title":"J. Appl. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1093\/molbev\/mst012","article-title":"Building phylogenetic trees from molecular data with MEGA","volume":"30","author":"Hall","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Esposito, M.M., Turku, S., Lehrfield, L., and Shoman, A. (2023). The Impact of Human Activities on Zoonotic Infection Transmissions. Animals, 13.","DOI":"10.3390\/ani13101646"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1109\/TCBB.2021.3136792","article-title":"CD-MAWS: An Alignment-Free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets","volume":"20","author":"Anjum","year":"2023","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/s41586-020-2696-8","article-title":"The native structure of the assembled matrix protein 1 of influenza A virus","volume":"587","author":"Peukes","year":"2020","journal-title":"Nature"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"a038372","DOI":"10.1101\/cshperspect.a038372","article-title":"Structure and Function of Influenza Polymerase","volume":"11","author":"Wandzik","year":"2021","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1093\/molbev\/msv044","article-title":"Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment","volume":"32","author":"Zeldovich","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1101\/gr.163101","article-title":"Genome-scale compositional comparisons in eukaryotes","volume":"11","author":"Gentles","year":"2001","journal-title":"Genome Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9403","DOI":"10.1038\/s41467-024-53658-8","article-title":"Molecular mimicry as a mechanism of viral immune evasion and autoimmunity","volume":"15","author":"Maguire","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_38","first-page":"643","article-title":"Future influenza vaccines and the use of genetic recombinants","volume":"41","author":"Kilbourne","year":"1969","journal-title":"Bull. World Health Organ."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/5\/659\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:25:07Z","timestamp":1760030707000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/5\/659"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,30]]},"references-count":38,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["v17050659"],"URL":"https:\/\/doi.org\/10.3390\/v17050659","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,30]]}}}