{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T23:27:24Z","timestamp":1792106844903,"version":"4.4.0"},"reference-count":42,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T00:00:00Z","timestamp":1782172800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019644","name":"Ministry of Agriculture of the Republic of Kazakhstan","doi-asserted-by":"crossref","award":["BR23591095"],"award-info":[{"award-number":["BR23591095"]}],"id":[{"id":"10.13039\/100019644","id-type":"DOI","asserted-by":"crossref"}]},{"award":["BR23591095"],"award-info":[{"award-number":["BR23591095"]}],"id":[{"id":"https:\/\/ror.org\/03577hm03","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Freshwater amphipods of the genus Gammarus are important trophic components of aquatic ecosystems and are increasingly considered a potential bioresource for aquaculture. However, their role in the maintenance and transmission of infectious agents remains poorly understood. This study evaluated the presence of major crustacean and fish pathogens in Gammarus lacustris populations from Kazakhstan and characterized associated viral communities using metagenomic sequencing. Six pooled samples collected from freshwater ecosystems across Kazakhstan were screened using PCR and RT-PCR assays targeting World Organisation for Animal Health (WOAH)-listed pathogens, including White Spot Syndrome Virus, Taura Syndrome Virus, Infectious Myonecrosis Virus, Aphanomyces astaci, and Aphanomyces invadans. In parallel, high-throughput sequencing (Illumina NovaSeq) was performed to assess virome composition and structure. No WOAH-listed pathogens were detected, suggesting a low detectable occurrence of major notifiable agents under the conditions of the present study. Metagenomic analysis revealed a virome dominated by RNA viruses, particularly picorna-like viruses (Picornaviridae), Dicistroviridae, and Marnaviridae. Phylogenetic and genome organization analyses identified potentially novel or highly divergent viral lineages within Picornavirales. Collectively, these findings suggest a favorable epizootiological profile of G. lacustris populations while highlighting freshwater amphipods as hosts of diverse and partially uncharacterized viral communities relevant to aquatic disease surveillance and aquaculture biosecurity.<\/jats:p>","DOI":"10.3390\/pathogens15070663","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T05:48:16Z","timestamp":1782366496000},"page":"663","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Metagenomic Characterization and Molecular Screening of Pathogens in Freshwater Amphipods (Gammarus lacustris) from Kazakhstan: Implications for Aquaculture Biosecurity"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6148-8204","authenticated-orcid":false,"given":"Marat","family":"Kumar","sequence":"first","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Symbat","family":"Suleimenova","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3979-6424","authenticated-orcid":false,"given":"Sardor","family":"Nuralibekov","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8773-4984","authenticated-orcid":false,"given":"Yermukhammet","family":"Kasymbekov","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7564-2097","authenticated-orcid":false,"given":"Temirlan","family":"Sabyrzhan","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuanysh","family":"Isbekov","sequence":"additional","affiliation":[{"name":"Fisheries Research and Production Center, Almaty 050016, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saule","family":"Assylbekova","sequence":"additional","affiliation":[{"name":"Fisheries Research and Production Center, Almaty 050016, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Fefelov","sequence":"additional","affiliation":[{"name":"Fisheries Research and Production Center, Almaty 050016, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9050-1196","authenticated-orcid":false,"given":"Berik","family":"Pangereyev","sequence":"additional","affiliation":[{"name":"Fisheries Research and Production Center, Almaty 050016, Kazakhstan"},{"name":"Depertment of Biotechnology, Farabi University, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0829-3330","authenticated-orcid":false,"given":"Kobey","family":"Karamendin","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aidyn","family":"Kydyrmanov","sequence":"additional","affiliation":[{"name":"Laboratory for Ecology of Viruses, Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.jip.2012.03.013","article-title":"Disease will limit future food supply from the global crustacean fishery and aquaculture sectors","volume":"110","author":"Stentiford","year":"2012","journal-title":"J. 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