{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:54:12Z","timestamp":1789692852270,"version":"4.0.1"},"reference-count":35,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,12,8]],"date-time":"2022-12-08T00:00:00Z","timestamp":1670457600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Research Foundation (DFG)","award":["GR 980\/5-1"],"award-info":[{"award-number":["GR 980\/5-1"]}]},{"name":"German Research Foundation (DFG)","award":["AHHFLI001\/2019"],"award-info":[{"award-number":["AHHFLI001\/2019"]}]},{"name":"German Research Foundation (DFG)","award":["AA-OR12-370.43"],"award-info":[{"award-number":["AA-OR12-370.43"]}]},{"name":"German Research Foundation (DFG)","award":["EBO-SURSY"],"award-info":[{"award-number":["EBO-SURSY"]}]},{"name":"Federal Ministry for Economic Cooperation and Development of Germany (BMZ)","award":["GR 980\/5-1"],"award-info":[{"award-number":["GR 980\/5-1"]}]},{"name":"Federal Ministry for Economic Cooperation and Development of Germany (BMZ)","award":["AHHFLI001\/2019"],"award-info":[{"award-number":["AHHFLI001\/2019"]}]},{"name":"Federal Ministry for Economic Cooperation and Development of Germany (BMZ)","award":["AA-OR12-370.43"],"award-info":[{"award-number":["AA-OR12-370.43"]}]},{"name":"Federal Ministry for Economic Cooperation and Development of Germany (BMZ)","award":["EBO-SURSY"],"award-info":[{"award-number":["EBO-SURSY"]}]},{"name":"Federal Foreign Office of Germany","award":["GR 980\/5-1"],"award-info":[{"award-number":["GR 980\/5-1"]}]},{"name":"Federal Foreign Office of Germany","award":["AHHFLI001\/2019"],"award-info":[{"award-number":["AHHFLI001\/2019"]}]},{"name":"Federal Foreign Office of Germany","award":["AA-OR12-370.43"],"award-info":[{"award-number":["AA-OR12-370.43"]}]},{"name":"Federal Foreign Office of Germany","award":["EBO-SURSY"],"award-info":[{"award-number":["EBO-SURSY"]}]},{"name":"World Organisation for Animal Health (WOAH)","award":["GR 980\/5-1"],"award-info":[{"award-number":["GR 980\/5-1"]}]},{"name":"World Organisation for Animal Health (WOAH)","award":["AHHFLI001\/2019"],"award-info":[{"award-number":["AHHFLI001\/2019"]}]},{"name":"World Organisation for Animal Health (WOAH)","award":["AA-OR12-370.43"],"award-info":[{"award-number":["AA-OR12-370.43"]}]},{"name":"World Organisation for Animal Health (WOAH)","award":["EBO-SURSY"],"award-info":[{"award-number":["EBO-SURSY"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean\u2013Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses.<\/jats:p>","DOI":"10.3390\/pathogens11121502","type":"journal-article","created":{"date-parts":[[2022,12,9]],"date-time":"2022-12-09T01:51:26Z","timestamp":1670550686000},"page":"1502","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6958-5874","authenticated-orcid":false,"given":"Ansgar","family":"Schulz","sequence":"first","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Balal","family":"Sadeghi","sequence":"additional","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franziska","family":"Stoek","sequence":"additional","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1857-7660","authenticated-orcid":false,"given":"Jacqueline","family":"King","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8707-3442","authenticated-orcid":false,"given":"Kerstin","family":"Fischer","sequence":"additional","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5318-665X","authenticated-orcid":false,"given":"Anne","family":"Pohlmann","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1197-8288","authenticated-orcid":false,"given":"Martin","family":"Eiden","sequence":"additional","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0215-185X","authenticated-orcid":false,"given":"Martin H.","family":"Groschup","sequence":"additional","affiliation":[{"name":"Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.onehlt.2017.06.001","article-title":"Emerging arboviruses: Why today?","volume":"4","author":"Gould","year":"2017","journal-title":"One Health"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1038\/nature06536","article-title":"Global trends in emerging infectious diseases","volume":"451","author":"Jones","year":"2008","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.coviro.2017.11.004","article-title":"Assessing the zoonotic potential of arboviruses of African origin","volume":"28","author":"Venter","year":"2018","journal-title":"Curr. 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