Whole Genome Sequencing and Phylogenetic Analysis of SARS‑CoV‑2 strains in Turkey

Tokgün, Onur; Çalışkan, Ahmet; Coşkun, Çağıl; Tokgün, Pervin Elvan; Akça, Hakan

doi:10.3855/jidc.14560

Cited by 4 publications

(5 citation statements)

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“…Overall, our findings indicate that there were multiple introductions of the viruses from outside Kenya, resulting in community transmission that contributed to the large number of new infections observed during the study period. This As reported elsewhere and as a common feature of the SARS-CoV-2 Alpha, Beta, and Delta lineages [22,41], all the local strains harbored the D614G mutation in the spike glycoprotein, associated with increased infectivity [9,[46][47][48]. Interestingly, all of the Alpha (B.1.1.7) viruses in this study had the 69-70del and Y144del deletions in the spike protein, which are linked to increased infectivity and decreased monoclonal antibody binding [49][50][51][52].…”

Section: Discussionsupporting

confidence: 81%

“…Sixty-four SARS-CoV-2 genome sequences were obtained over the study period. Of these, forty-one [41] were found to belong to the Alpha (B.1.1.7) lineage, twenty-two [22] to Delta (B.1.617.2), and one (1) to Beta (B.1.351). The majority of the individuals from which viral sequences were obtained were male (n = 43; 68.3%).…”

Section: Resultsmentioning

confidence: 99%

“…Surveillance of the SARS-CoV-2 by whole genome sequencing is crucial in providing insights into its transmission and evolutionary dynamics [4,22]. It's equally valuable in identifying potential variants and virulence determinants [4,41,42]. This type of information is critical in evaluating vaccine effectiveness and guiding the design of drugs or diagnostics [41].…”

Section: Discussionmentioning

confidence: 99%

“…It's equally valuable in identifying potential variants and virulence determinants [4,41,42]. This type of information is critical in evaluating vaccine effectiveness and guiding the design of drugs or diagnostics [41]. In this study, we investigated sixty-four (N = 64) genome sequences of SARS-CoV-2 VOCs in Nairobi and neighboring counties in Kenya between March 2021 and July 2021, utilizing various bioinformatics approaches.…”

Section: Discussionmentioning

confidence: 99%

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Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Khamadi

Opanda

Symekher

et al. 2022

Virol J

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The emergence and rapid spread of SARS-CoV-2 variants of concern (VOC) have been linked to new waves of COVID-19 epidemics occurring in different regions of the world. The VOC have acquired adaptive mutations that have enhanced virus transmissibility, increased virulence, and reduced response to neutralizing antibodies. Kenya has experienced six waves of COVID-19 epidemics. In this study, we analyzed 64 genome sequences of SARS-CoV-2 strains that circulated in Nairobi and neighboring counties, Kenya between March 2021 and July 2021. Viral RNA was extracted from RT-PCR confirmed COVID-19 cases, followed by sequencing using the ARTIC network protocol and Oxford Nanopore Technologies. Analysis of the sequence data was performed using different bioinformatics methods. Our analyses revealed that during the study period, three SARS-CoV-2 variants of concern (VOC) circulated in Nairobi and nearby counties in Kenya. The Alpha (B.1.1.7) lineage predominated (62.7%), followed by Delta (B.1.617.2, 35.8%) and Beta (B.1.351, 1.5%). Notably, the Alpha (B.1.1.7) VOC were most frequent from March 2021 to May 2021, while the Delta (B.1.617.2) dominated beginning June 2021 through July 2021. Sequence comparisons revealed that all the Kenyan viruses were genetically similar to those that circulated in other regions. Although the majority of Kenyan viruses clustered together in their respective phylogenetic lineages/clades, a significant number were interspersed among foreign strains. Between March and July 2021, our study's findings indicate the prevalence of multiple lineages of SAR-CoV-2 VOC in Nairobi and nearby counties in Kenya. The data suggest that the recent increase in SARS-CoV-2 infection, particularly in Nairobi and Kenya as a whole, is attributable to the introduction and community transmission of SARS-CoV-2 VOC among the populace. In conclusion, the findings provide a snapshot of the SARS-CoV-2 variants that circulated in Kenya during the study period.

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Section: Discussionsupporting

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Khamadi

Opanda

Symekher

et al. 2022

Virol J

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“…Names of the clades are designed as memorable and informative enough, consisting of the year it arose and a letter (24). SARS-CoV-2 genome analyses with patient information (demographic) in Turkey has done with small number of viral genomes (26)(27)(28)(29)(30). Our main objective was to perform wholegenome sequencing of 1000 samples collected from different regions of Turkey in order to characterize SARS-CoV-2 genomes.…”

Section: Introductionmentioning

confidence: 99%

Tracking the circulating SARS-CoV-2 variants in Turkey: Complete genome sequencing and molecular characterization of 1000 SARS-CoV-2 samples

Akcesme

Köprülü

Erkal

et al. 2022

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease, named ‘coronavirus disease 2019’ (COVID-19). COVID-19 has a deep impact on public health as one of the most serious pandemics in the last century. Tracking SARS-CoV-2 is important for monitoring and assessing its evolution. This is only possible by detecting all mutations in the viral genome through genomic sequencing. Moreover, accurate detection of SARS-CoV-2 and tracking its mutations is also required for its correct diagnosis. Potential effects of mutations on the prognosis of the disease can be observed. Assignment of epidemiological lineages in an emerging pandemic requires efforts. To address this, we collected 1000 SARS-CoV-2 samples from different geographical regions in Turkey and analyze their genome comprehensively. To track the virus across Turkey we focus on 10 distinct cities in different geographic regions. Each SARS-CoV-2 genome was analyzed and named according to the nomenclature system of Nextclade and Pangolin Lineage. Furthermore, the frequency of the variations observed in 10 months was also determined by region. In this way, we have observed how the virus mutations and what kind of transmission mechanism it has. The effects of age and disease severity on lineage distribution were other considered parameters. The temporal rates of SARS-CoV-2 variants by time in Turkey were close to the global trend. This study is one of the most comprehensive whole genome analyses of SARS-CoV-2 that represents a general picture of the distribution of SARS-CoV-2 variations in Turkey in 2021.Author SummarySince the outbreak of the COVID-19 pandemic in 2019, the viral genome of SARS-CoV-2 was analysed intensively all over the world both to detect its zoonotic origin and the emerging variants worldwide together with the variants’ effect on the prognosis and treatment, respectively, of the infection. Remarkable COVID-19 studies were also made in Turkey as it was in the rest of the world. To date, indeed, almost all studies on COVID-19 in Turkey either sequenced only a small number of the viral genome or analysed the viral genome which was obtained from online databases. In respect thereof, our study constitutes a milestone regarding both the huge sample size consisting of 1000 viral genomes and the widespread geographic origin of the viral genome samples. Our study provides new insights both into the SARS-CoV-2 landscape of Turkey and the transmission of the emerging viral pathogen and its interaction with its vertebrate host.

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Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye

Akçeşme,

Köprülü,

Çam

et al. 2024

Biochem Genet

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Whole Genome Sequencing and Phylogenetic Analysis of SARS‑CoV‑2 strains in Turkey

Cited by 4 publications

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Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Tracking the circulating SARS-CoV-2 variants in Turkey: Complete genome sequencing and molecular characterization of 1000 SARS-CoV-2 samples

Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye

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