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This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (\u00b1paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63\u2013159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (&lt;250 copies\/million cells) and longer PCR amplicons (&gt;150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.<\/jats:p>","DOI":"10.3390\/v14010133","type":"journal-article","created":{"date-parts":[[2022,1,12]],"date-time":"2022-01-12T09:10:36Z","timestamp":1641978636000},"page":"133","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6878-5770","authenticated-orcid":false,"given":"Outi I.","family":"Mielonen","sequence":"first","affiliation":[{"name":"Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland"},{"name":"Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-552X","authenticated-orcid":false,"given":"Diogo","family":"Pratas","sequence":"additional","affiliation":[{"name":"Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland"},{"name":"Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal"},{"name":"Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1779-7960","authenticated-orcid":false,"given":"Klaus","family":"Hedman","sequence":"additional","affiliation":[{"name":"Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4117-5248","authenticated-orcid":false,"given":"Antti","family":"Sajantila","sequence":"additional","affiliation":[{"name":"Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland"},{"name":"Forensic Medicine Unit, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9031-4251","authenticated-orcid":false,"given":"Maria F.","family":"Perdomo","sequence":"additional","affiliation":[{"name":"Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1373\/clinchem.2014.223040","article-title":"Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization","volume":"61","author":"Do","year":"2015","journal-title":"Clin. 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