{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:17:45Z","timestamp":1783487865666,"version":"3.55.0"},"reference-count":100,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Metaviromic sequencing is prone to artifacts, necessitating orthogonal validation. This study evaluates a targeted proteogenomic approach for verifying viral presence initially detected by NGS.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We analyzed oropharyngeal\/anal swabs and feces from hedgehogs, where NGS indicated viruses from the\n                      <jats:italic>Coronaviridae<\/jats:italic>\n                      ,\n                      <jats:italic>Picornaviridae<\/jats:italic>\n                      ,\n                      <jats:italic>Flaviviridae<\/jats:italic>\n                      , and\n                      <jats:italic>Astroviridae<\/jats:italic>\n                      families. For verification, mass spectrometry was applied using sample-specific databases derived from NGS-assembled contigs.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Proteomic analysis confirmed\n                      <jats:italic>Coronaviridae<\/jats:italic>\n                      presence in NGS-positive animals, primarily detecting structural virion proteins in anal and fecal samples. However, proteomic evidence for\n                      <jats:italic>Picornaviridae<\/jats:italic>\n                      ,\n                      <jats:italic>Flaviviridae<\/jats:italic>\n                      , and\n                      <jats:italic>Astroviridae<\/jats:italic>\n                      was not obtained despite their genomic detection.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      Phylogenetic analysis of two complete\n                      <jats:italic>Picornaviridae<\/jats:italic>\n                      genomes assembled from the NGS data \u2013 one closely related to a UK rodent virus and another distantly related to Chinese bat viruses \u2013 supports the authenticity of the NGS findings. The results demonstrate that this two-stage pipeline provides critical orthogonal validation for metaviromic studies but also defines a practical sensitivity limit for the proteomic verification of some viral families. Combining NGS with proteomics significantly enhances the reliability of viral confirmation in complex samples, thereby strengthening ecological and zoonotic inferences.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1814090","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T04:44:10Z","timestamp":1783485850000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Combined NGS and proteomics improves viral diagnostics in wildlife: coronaviruses confirmed in hedgehogs"],"prefix":"10.3389","volume":"16","author":[{"given":"Ivan","family":"Chudinov","sequence":"first","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]},{"name":"Moscow Center for Advanced Studies","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Korneenko","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irina","family":"Rog","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Lukina-Gronskaya","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexey","family":"Kovalenko","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika","family":"Gremyacheva","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Butenko","sequence":"additional","affiliation":[{"name":"Laboratory of Multiomics Research, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Vasileva","sequence":"additional","affiliation":[{"name":"Laboratory of Simple Systems, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]},{"name":"Burnasyan Federal Medical Biophysical Center, Federal Biological Agency","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daria","family":"Matyushkina","sequence":"additional","affiliation":[{"name":"Laboratory of Simple Systems, Scientific Research Institute for Systems Biology and Medicine, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Litvinova","sequence":"additional","affiliation":[{"name":"Biological Department, Lomonosov Moscow State University","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Feoktistova","sequence":"additional","affiliation":[{"name":"A.N. 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