About: The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey

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About: The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey
Creator	Alkurt, Gizem Aydin, Mehtap Can, Nisan Demirkol, Yasemin Dogan, Ozlem Doganay, Gizem Doganay, Levent Irvem, Arzu Karacan, Ilker Kose, Betsi Yildiz, Jale Akgun, Kizilboga Altunal, L Bugra Agaoglu, † Egitim, Umraniye Hastanesi, Arastirma Klinigi, Hepatoloji Serra Ozel, A Tugba, † Universitesi, Bilimleri Ve, Gastroenteroloji
Source	Medline; PMC; WHO
abstract	OBJECTIVE: Turkey is one of the latest countries that COVID-19 disease was reported, with the first case on March 11, 2020, and since then, Istanbul became the epicenter of the pandemic in Turkey. Here, we reveal sequences of the virus isolated from three different patients with various clinical presentations. METHODS: Nasopharyngeal swab specimens of the patients were tested positive for the COVID-19 by qRT-PCR. Viral RNA extraction was performed from the same swab samples. Amplicon based libraries were prepared and sequenced using the Illumina NextSeq platform. Raw sequencing data were processed for variant calling and generating near-complete genome sequences. All three genomes were evaluated and compared with other worldwide isolates. RESULTS: The patients showed various clinics (an asymptomatic patient, patient with mild disease, and with severe pulmonary infiltration). Amplicon-based next-generation sequencing approach successfully applied to generate near-complete genomes with an average depth of 2.616. All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread first through China to Europe then to Istanbul. CONCLUSION: Here, we report the viral genomes circulating in Istanbul for the first time. Further sequencing of the virus isolates may enable us to understand variations in disease presentation and association with viral factors if there is any. In addition, the sequencing of more viral genomes will delineate the spread of disease and will guide and ease the necessary measures taken to stem the spread of the novel coronavirus.
has issue date	2020-05-15(xsd:dateTime)
bibo:doi	10.14744/nci.2020.90532
bibo:pmid	32478289
has license	cc-by-nc-sa
sha1sum (hex)	83308c9224ce2092bc2c3aa9cb57ffe67462a301
schema:url	https://doi.org/10.14744/nci.2020.90532
resource representing a document's title	The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey
has PubMed Central identifier	PMC7251277
has PubMed identifier	32478289
schema:publication	North Clin Istanb
resource representing a document's body	covid:83308c9224ce2092bc2c3aa9cb57ffe67462a301#body_text
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