{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T15:22:59Z","timestamp":1782400979296,"version":"3.54.5"},"reference-count":30,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,10]]},"abstract":"<jats:p>Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus of the genus <jats:italic>Nairovirus<\/jats:italic> within the family Bunyaviridae. Infection can result in general myalgia, fever, and headache with some patients developing hemorrhagic fever with mortality rates ranging from 5% to 30%. CCHFV has a wide geographic range that includes Africa, Asia, the Middle East, and Europe with nucleotide sequence variation approaching 20% across the three negative-sense RNA genome segments. While phylogenetic clustering generally aligns with geographic origin of individual strains, distribution can be wide due to tick\/CCHFV dispersion via migrating birds. This sequence diversity negatively impacts existing molecular diagnostic assays, leading to false negative diagnostic results. Here, we updated a previously developed CCHFV real-time reverse transcription polymerase chain reaction (RT-PCR) assay to include strains not detected using that original assay. Deep sequencing of eight different CCHFV strains, including three that were not detectable using the original assay, identified sequence variants within this assay target region. New primers and probe based on the sequencing results and newly deposited sequences in GenBank greatly improved assay sensitivity and inclusivity with the exception of the genetically diverse strain AP92. For example, we observed a four log improvement in IbAr10200 detection with a new limit of detection of 256 PFU\/mL. Subsequent comparison of this assay to another commonly used CCHFV real-time RT-PCR assay targeting a different region of the viral genome showed improved detection, and both assays could be used to mitigate CCHFV diversity for diagnostics. Overall, this work demonstrated the importance of continued viral sequencing efforts for robust diagnostic assay development.<\/jats:p>","DOI":"10.4269\/ajtmh.17-0165","type":"journal-article","created":{"date-parts":[[2017,11,21]],"date-time":"2017-11-21T07:01:32Z","timestamp":1511247692000},"page":"211-215","source":"Crossref","is-referenced-by-count":22,"title":["Sequence Optimized Real-Time Reverse Transcription Polymerase Chain Reaction Assay for Detection of Crimean-Congo Hemorrhagic Fever Virus"],"prefix":"10.4269","volume":"98","author":[{"given":"Jeffrey W.","family":"Koehler","sequence":"first","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Korey L.","family":"Delp","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrienne T.","family":"Hall","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott P.","family":"Olschner","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian J.","family":"Kearney","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aura R.","family":"Garrison","sequence":"additional","affiliation":[{"name":"Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis A.","family":"Altamura","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia A.","family":"Rossi","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy D.","family":"Minogue","sequence":"additional","affiliation":[{"name":"Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2795","reference":[{"key":"b1","series-title":"Lancet Infect Dis","first-page":"203","article-title":"Crimean\u2013Congo haemorrhagic fever","volume":"6","author":"Ergonul","year":"2006"},{"key":"b2","series-title":"J Med Virol","first-page":"1690","article-title":"Is there any relationship between toll-like receptor 3 c.1377C\/T and \u22127C\/A polymorphisms and susceptibility to Crimean Congo hemorrhagic fever?","volume":"88","author":"Engin","year":"2016"},{"key":"b3","series-title":"J Med Virol","first-page":"1090","article-title":"Toll-like receptor 7 Gln11Leu, c.4-151A\/G, and +1817G\/T polymorphisms in Crimean-Congo hemorrhagic fever","volume":"87","author":"Arslan","year":"2015"},{"key":"b4","series-title":"Scand J Infect Dis","first-page":"138","article-title":"Relationship between NF-kappaB1 and NF-kappaBIA genetic polymorphisms and Crimean-Congo hemorrhagic fever","volume":"44","author":"Arslan","year":"2012"},{"key":"b5","series-title":"Microbes Infect","first-page":"1071","article-title":"Toll-like receptor 8 and 9 polymorphisms in Crimean-Congo hemorrhagic fever","volume":"12","author":"Engin","year":"2010"},{"key":"b6","series-title":"Trans R Soc Trop Med Hyg","first-page":"503","article-title":"The global distribution of Crimean-Congo hemorrhagic fever","volume":"109","author":"Messina","year":"2015"},{"key":"b7","series-title":"Antiviral Res","first-page":"159","article-title":"Crimean-Congo hemorrhagic fever: history, epidemiology, pathogenesis, clinical syndrome and genetic diversity","volume":"100","author":"Bente","year":"2013"},{"key":"b8","series-title":"Nucleic Acids Res","first-page":"D593","article-title":"ViPR: an open bioinformatics database and analysis resource for virology research","volume":"40","author":"Pickett","year":"2012"},{"key":"b9","series-title":"Future Virol","first-page":"203","article-title":"Therapeutic intervention in Crimean-Congo hemorrhagic fever: where are we now?","volume":"10","author":"Spengler","year":"2015"},{"key":"b10","series-title":"J Clin Microbiol","first-page":"1025","article-title":"Low-density macroarray for rapid detection and identification of Crimean-Congo hemorrhagic fever virus","volume":"47","author":"Wolfel","year":"2009"},{"key":"b11","series-title":"Clin Microbiol Infect","first-page":"E118","article-title":"Molecular diagnostic and genetic characterization of highly pathogenic viruses: application during Crimean-Congo hemorrhagic fever virus outbreaks in eastern Europe and the Middle East","volume":"19","author":"Filippone","year":"2013"},{"key":"b12","series-title":"J Clin Microbiol","first-page":"4279","article-title":"Colorimetric nucleic acid testing assay for RNA virus detection based on circle-to-circle amplification of padlock probes","volume":"49","author":"Ke","year":"2011"},{"key":"b13","series-title":"J Virol Methods","first-page":"4","article-title":"Development and evaluation of loop-mediated isothermal amplification assay for detection of Crimean Congo hemorrhagic fever virus in Sudan","volume":"190","author":"Osman","year":"2013"},{"key":"b14","series-title":"Vector Borne Zoonotic Dis","first-page":"870","article-title":"Development and evaluation of a real-time RT-qPCR for detection of Crimean-Congo hemorrhagic fever virus representing different genotypes","volume":"14","author":"Jaaskelainen","year":"2014"},{"key":"b15","series-title":"Vector Borne Zoonotic Dis","first-page":"786","article-title":"Development of a real-time RT-PCR assay for the detection of Crimean-Congo hemorrhagic fever virus","volume":"12","author":"Atkinson","year":"2012"},{"key":"b16","series-title":"Methods Mol Biol","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1007\/978-1-60761-817-1_19","article-title":"Detection of Crimean-Congo hemorrhagic fever, Hanta, and sandfly fever viruses by real-time RT-PCR","volume":"665","author":"Ibrahim","year":"2011"},{"key":"b17","series-title":"J Virol Methods","first-page":"34","article-title":"A simple-probe real-time PCR assay for genotyping reassorted and non-reassorted isolates of Crimean-Congo hemorrhagic fever virus in southern Africa","volume":"169","author":"Kondiah","year":"2010"},{"key":"b18","series-title":"J Virol Methods","first-page":"175","article-title":"Novel one-step real-time RT-PCR assay for rapid and specific diagnosis of Crimean-Congo hemorrhagic fever encountered in the Balkans","volume":"133","author":"Duh","year":"2006"},{"key":"b19","series-title":"Emerg Infect Dis","first-page":"1958","article-title":"Diagnostic assays for Crimean-Congo hemorrhagic fever","volume":"18","author":"Vanhomwegen","year":"2012"},{"key":"b20","series-title":"Am J Trop Med Hyg","first-page":"514","article-title":"Development of a TaqMan minor groove binding protein assay for the detection and quantification of Crimean-Congo hemorrhagic fever virus","volume":"77","author":"Garrison","year":"2007"},{"key":"b21","series-title":"Euro Surveill","article-title":"Non-fatal case of Crimean-Congo haemorrhagic fever imported into the United Kingdom (ex Bulgaria), June 2014","volume":"19","author":"Lumley","year":"2014"},{"key":"b22","series-title":"J Med Virol","first-page":"501","article-title":"Crimean-Congo hemorrhagic fever nosocomial infection in a immunosuppressed patient, Pakistan: case report and virological investigation","volume":"85","author":"Hasan","year":"2013"},{"key":"b23","series-title":"Genome Announc","article-title":"Genome sequence of Ex-Afghanistan Crimean-Congo hemorrhagic fever virus SCT strain, from an imported United Kingdom case in October 2012","volume":"1","author":"Chamberlain","year":"2013"},{"key":"b24","series-title":"Int J Infect Dis","first-page":"e1031","article-title":"Identification and analysis of Crimean-Congo hemorrhagic fever virus from human sera in Tajikistan","volume":"17","author":"Atkinson","year":"2013"},{"key":"b25","series-title":"Vector Borne Zoonotic Dis","first-page":"722","article-title":"Crimean-Congo hemorrhagic fever in Tajikistan","volume":"12","author":"Tishkova","year":"2012"},{"key":"b26","series-title":"Euro Surveill","article-title":"Sequencing and phylogenetic characterisation of a fatal Crimean\u2013Congo hemorrhagic fever case imported into the United Kingdom, October 2012","volume":"17","author":"Atkinson","year":"2012"},{"key":"b27","series-title":"Genome Announc","article-title":"Draft genome sequences of eight Crimean-Congo hemorrhagic fever virus strains","volume":"5","author":"Koehler","year":"2017"},{"key":"b28","series-title":"J Virol","first-page":"8834","article-title":"Crimean-Congo hemorrhagic fever virus genomics and global diversity","volume":"80","author":"Deyde","year":"2006"},{"key":"b29","series-title":"Science","first-page":"1369","article-title":"Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak","volume":"345","author":"Gire","year":"2014"},{"key":"b30","series-title":"MBio","article-title":"Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics","volume":"6","author":"Kugelman","year":"2015"}],"container-title":["The American Journal of Tropical Medicine and Hygiene"],"original-title":[],"link":[{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/98\/1\/article-p211.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.ajtmh.org\/downloadpdf\/journals\/tpmd\/98\/1\/article-p211.xml","content-type":"text\/html","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/www.ajtmh.org\/downloadpdf\/journals\/tpmd\/98\/1\/article-p211.xml","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T22:58:26Z","timestamp":1722466706000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/98\/1\/article-p211.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,10]]},"references-count":30,"journal-issue":{"issue":"1"},"URL":"https:\/\/doi.org\/10.4269\/ajtmh.17-0165","relation":{},"ISSN":["0002-9637","1476-1645"],"issn-type":[{"value":"0002-9637","type":"print"},{"value":"1476-1645","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,10]]}}}