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J Pediatr Infect Dis 2021; 16(06): 296-302
DOI: 10.1055/s-0041-1736561
Original Article

SARS-CoV-2 Genome Analysis of Pediatric Patients in Konya Region, Turkey

Fatma Esenkaya Tasbent 
1   Department of Medical Microbiology, Meram Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
,
Mehmet Özdemir 
2   Department of Medical Microbiology, Division of Medical Virology, Meram Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
,
Özge M. Akcan
3   Department of Pediatric Infectious Diseases, Meram Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
,
Esma K. Kurt 
4   Department of Infectious Diseases and Clinical Microbiology, Meram Faculty of Medicine, Necmettin Erbakan University, Konya, Turkey
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Abstract

Objective Genome sequencing is useful for following the change in mutation and variants in viral agent during pandemics. In this study, we performed next-generation sequencing of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) complete genomes on pediatric patients.

Methods Six pediatric patients aged 0 to 18 years who were positive for SARS-CoV-2 by reverse transcription polymerase chain reaction were included in this study. SARS-CoV-2 genome sequencing was performed using Oxford Nanopore Technologies MinION, following the ARTIC Network protocols. Sequencing data were obtained using the FASTQ program and quality assessment was evaluated. The sequence information of all samples was uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) database. Genome, variant, clade, and phylogenetic tree analyses were performed with bioinformatic analysis.

Results Two of these six samples were at 20A, two were at 20B, and two were at 19A in the nextstrain clade. According to Pango lineages, B.1.36, B.1.218, B.1, and B.1.260 lineages were detected. A total of 84 mutations were observed in all samples. None of the variants were classified as variants of concern (VOC) nor variants of interest (VOI) according to the Pango database.

Conclusion This study is the first comprehensively sequence analysis registered in the GISAID database reported from the Konya region in Turkey. Similar studies will be informative to track changes in the virus genome, obtain epidemiological data, guide studies on diagnosis and treatment, and evaluate vaccine efficacy.

Keywords

COVID-19 - SARS CoV-2 - variation - genome sequencing - clade


Publication History

Received: 18 August 2021

Accepted: 16 September 2021

Article published online:
21 October 2021

© 2021. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 

  • References

  • 1 Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 2019; 17 (03) 181-192
    CrossrefPubMedGoogle Scholar
  • 2 Demİr AB, Benvenuto D, AbacioĞlu H, Angeletti S, Ciccozzi M. Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Turk J Biol 2020; 44 (03) 178-184
    CrossrefPubMedGoogle Scholar
  • 3 Aleem A, Akbar Samad AB, Slenker AK. Emerging variants of SARS-CoV-2 and novel therapeutics against coronavirus (COVID-19). In: StatPearls. Treasure Island (FL): StatPearls Publishing; 2021
    Google Scholar
  • 4 United Nations Geoscheme. COVID-19 coronavirus pandemic. Accessed August 11, 2021 at: www.worldometers.info/coronavirus
    PubMedGoogle Scholar
  • 5 Karacan I, Akgun TK, Agaoglu NB. et al. The origin of SARS-CoV-2 in Istanbul: sequencing findings from the epicenter of the pandemic in Turkey. North Clin Istanb 2020; 7 (03) 203-209
    PubMedGoogle Scholar
  • 6 Durmaz B, Abdulmajed O, Durmaz R. Mutations observed in the SARS-CoV-2 spike glycoprotein and their effects in the interaction of virus with ACE-2 receptor. Medeni Med J 2020; 35 (03) 253-260
    PubMedGoogle Scholar
  • 7 Chen ZM, Fu JF, Shu Q. et al. Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus. World J Pediatr 2020; 16 (03) 240-246
    CrossrefPubMedGoogle Scholar
  • 8 World Health Organization. Clinical management of COVID-19: interim guidance. Geneva, Switzerland: World Health Organization; 2020
    PubMedGoogle Scholar
  • 9 GISAID. Global influenza surveillance & response system. Accessed August 12, 2021 at: https://www.gisaid.org
    PubMedGoogle Scholar
  • 10 Nextstrain. Genomic epidemiology of novel coronavirus—global subsampling. Accessed August 16, 2021 at: https://nextstrain.org/ncov/gisaid/global?tl=clade_membership
    PubMedGoogle Scholar
  • 11 Takenouchi T, Iwasaki YW, Harada S. et al. Clinical utility of SARS-CoV-2 whole genome sequencing in deciphering source of infection. J Hosp Infect 2021; 107: 40-44
    CrossrefPubMedGoogle Scholar
  • 12 PANGO lineages. Accessed August 11, 2021 at: https://cov-lineages.org/global_report.html
    PubMedGoogle Scholar
  • 13 Demir AB, Bulgurcu A, Appak Ö, Sayıner AA. Analysis of nucleotide changes in RT-PCR primer/probe binding regions in SARS-CoV-2 isolates reported from Turkey [in Turkish]. Mikrobiyol Bul 2021; 55 (03) 311-326
    CrossrefPubMedGoogle Scholar
  • 14 Adebalİ O, Bİrcan A, Çİrcİ D. et al. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey. Turk J Biol 2020; 44 (03) 146-156
    CrossrefPubMedGoogle Scholar
  • 15 Maison DP, Ching LL, Shikuma CM, Nerurkar VR. Genetic characteristics and phylogeny of 969-bp S gene sequence of SARS-CoV-2 from Hawai'i reveals the worldwide emerging P681H mutation. Hawaii J Health Soc Welf 2021; 80 (03) 52-61
    PubMedGoogle Scholar
  • 16 Phan T. Genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol 2020; 81: 104260
    CrossrefPubMedGoogle Scholar
  • 17 Liu Y, Liu J, Plante KS. et al. The N501Y spike substitution enhances SARS-CoV-2 transmission. bioRxiv 2021; DOI: 10.1101/2021.03.08.434499.
    CrossrefPubMedGoogle Scholar
  • 18 Fırat M, Yücesan B, Özkan Ö. SARS-CoV-2 variants of concern detected in Turkey -overview of pandemia in Cankiri. Eurasian JHS 2021; 4 (02) 138-144
    PubMedGoogle Scholar