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

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 isolatedfrom 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 RNAextraction was performed from the same swab samples. Amplicon based libraries were prepared and sequenced using theIllumina NextSeq platform. Raw sequencing data were processed for variant calling and generating near-complete genomesequences. 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-completegenomes with an average depth of 2616. All three viral genomes carried the D614G variant (G clade according to GISAIDclassification) 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 virusisolates may enable us to understand variations in disease presentation and association with viral factors if there is any. Inaddition, the sequencing of more viral genomes will delineate the spread of disease and will guide and ease the necessarymeasures taken to stem the spread of the novel coronavirus.