tetano
Editor, Senior Moderator
North Clin Istanb
. 2020 May 15;7(3):203-209.
doi: 10.14744/nci.2020.90532. eCollection 2020.
The Origin of SARS-CoV-2 in Istanbul: Sequencing Findings From the Epicenter of the Pandemic in Turkey
Ilker Karacan[SUP] 1 2 [/SUP], Tugba Kizilboga Akgun[SUP] 1 [/SUP], N Bugra Agaoglu[SUP] 1 3 [/SUP], Arzu Irvem[SUP] 4 [/SUP], Gizem Alkurt[SUP] 1 [/SUP], Jale Yildiz[SUP] 1 [/SUP], Betsi Kose[SUP] 1 [/SUP], A Serra Ozel[SUP] 5 [/SUP], L Nilsun Altunal[SUP] 5 [/SUP], Nisan Denizce Can[SUP] 6 [/SUP], Yasemin Kendir Demirkol[SUP] 1 7 [/SUP], Mehtap Aydin[SUP] 5 [/SUP], Ozlem Akgun Dogan[SUP] 1 7 [/SUP], Levent Doganay[SUP] 1 [/SUP], Gizem Dinler Doganay[SUP] 6 [/SUP]
Affiliations
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.
Keywords: COVID-19; SARS-CoV-2; whole-genome sequencing.
. 2020 May 15;7(3):203-209.
doi: 10.14744/nci.2020.90532. eCollection 2020.
The Origin of SARS-CoV-2 in Istanbul: Sequencing Findings From the Epicenter of the Pandemic in Turkey
Ilker Karacan[SUP] 1 2 [/SUP], Tugba Kizilboga Akgun[SUP] 1 [/SUP], N Bugra Agaoglu[SUP] 1 3 [/SUP], Arzu Irvem[SUP] 4 [/SUP], Gizem Alkurt[SUP] 1 [/SUP], Jale Yildiz[SUP] 1 [/SUP], Betsi Kose[SUP] 1 [/SUP], A Serra Ozel[SUP] 5 [/SUP], L Nilsun Altunal[SUP] 5 [/SUP], Nisan Denizce Can[SUP] 6 [/SUP], Yasemin Kendir Demirkol[SUP] 1 7 [/SUP], Mehtap Aydin[SUP] 5 [/SUP], Ozlem Akgun Dogan[SUP] 1 7 [/SUP], Levent Doganay[SUP] 1 [/SUP], Gizem Dinler Doganay[SUP] 6 [/SUP]
Affiliations
- PMID: 32478289
- PMCID: PMC7251277
- DOI: 10.14744/nci.2020.90532
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.
Keywords: COVID-19; SARS-CoV-2; whole-genome sequencing.