Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey

Abstract

COVID-19 has effectively spread worldwide. As of May 2020, Turkey is 3 among the top ten countries with the most cases. A comprehensive genomic 4 characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a 5 phylogenetic tree with 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-6 CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in 7 comparison with the previously annotated classifications. We performed a phylogenetic 8 analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. Our 9 results suggest that the first introduction of the virus to the country is earlier than the first 10 reported case of infection. Virus genomes isolated from Turkey are dispersed among most 11 types in the phylogenetic tree. Two of the seventeen sub-clusters were found enriched 12 with the isolates of Turkey, which likely have spread expansively in the country. Finally, 13 we traced virus genomes based on their phylogenetic placements. This analysis suggested 14 multiple independent international introductions of the virus and revealed a hub for the 15 inland transmission. We released a web application to track the global and interprovincial 16 virus spread of the isolates from Turkey in comparison to thousands of genomes 17 worldwide. 18 19 20 24 SARS-CoV genome, the reason behind it's pandemic behaviour is still unclear. Genome 25 sequences around the world were revealed and deposited into public databases such as 26 GISAID (Shu and McCauley 2017). It is crucial to reveal the evolutionary events of 27 SARS-CoV-2 to understand the types of the circulating genomes as well as in which parts 28 of the genome differ across these types. 29 30 The SARS-CoV-2 virus originated from SARS-CoV, and the intermediate versions 31 between two human viruses were found in bats and pangolins (Li, et al. 2020). The virus 32 has been under a strong purifying selection (Li, et al. 2020). With the genomes obtained 33 so far, the sequences of SARS-CoV-2 genomes showed more than 99.9% percent identity 34 suggesting a recent shift to the human species (Tang, et al. 2020). Still, there are clear 35 evolutionary clusters in the genome pool. Various studies use different methods such as 36 SNP based (Tang, et al. 2020) or entropy (Zhao, et al. 2020) based to identify evolving 37 virus strains to reveal genomic regions responsible for transmission and evolution of the 38 virus. Tang et. al identified S and L strains among 103 SARS-CoV-2 genomes based on 39 two SNPs at ORF1ab and ORF8 regions which encode replicase/transcriptase and ATF6, 40 respectively (Tang, et al. 2020). Entropy-based approach generated informative subtype 41 markers from 17 informative positions to cluster evolving virus genomes (Zhao, et al.42 2020). Another study defined a competitive subtype based on D614G mutation at spike 43 59 2.1. Data retrieval, multiple sequence alignment and phylogenomic tree 60 generation 61The entire SARS-CoV-2 genome sequences, along with their metadata were retriev...

Stability of SARS-CoV-2 Phylogenies

“…Extremely rapid whole genome sequencing has enabled nearly real-time tracing of the evolution of the SARS-CoV-2 pandemic [1][2][3][4][5] . By leveraging sequence data produced by labs throughout the world, researchers can trace transmission of the virus across human populations [6][7][8][9][10][11][12][13][14] . Typically, viral evolution is encapsulated by a phylogenetic tree relating all of the virus samples in a large set to one another [5,[15][16][17][18][19] .…”

Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR−/- mice

“…We have not performed a comprehensive phylogenetic evaluation in this study. Nevertheless, a recent analysis, albeit with a lower number of genomes, suggested multiple independent international virus introductions in Anatolia and inland spread ( Adebalı et al., 2020 ).…”

The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents

“…A phylogenetic analysis carried out in Turkey, with the first 30 genomes isolated from SARS-CoV-2 in this region, showed that the introduction of the virus in the country occurred before the first reported case of infection. The study demonstrated that the virus circulated in Turkey from several independent international introductions and revealed a hub for inland transmission [ 139 ].…”