SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran

• Published in: Infection, genetics and evolution Vol. 84; p. 104387
• Main Authors: Tabibzadeh, Alireza, Zamani, Farhad, Laali, Azadeh, Esghaei, Maryam, Safarnezhad Tameshkel, Fahimeh, Keyvani, Hossein, Jamshidi Makiani, Mahin, Panahi, Mahshid, Motamed, Nima, Perumal, Dhayaneethie, Khoonsari, Mahmoodreza, Ajdarkosh, Hossein, Sohrabi, Masuodreza, Ghanbari, Behrooz, Savaj, Shokoufeh, Mosavi-Jarrahi, Alireza, Karbalaie Niya, Mohammad Hadi
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2020; Published by Elsevier B.V
• Subjects: Aged; Base Sequence; Betacoronavirus - classification; Betacoronavirus - genetics; Betacoronavirus - pathogenicity; Coronavirus Infections - diagnosis; Coronavirus Infections - epidemiology; Coronavirus Infections - pathology; Coronavirus Infections - virology; Coronavirus RNA-Dependent RNA Polymerase; COVID-19; Female; Genome, Viral; High-Throughput Nucleotide Sequencing; Humans; Iran - epidemiology; Male; Middle Aged; Molecular Epidemiology; Pandemic; Pandemics; Phylogeny; Pneumonia, Viral - diagnosis; Pneumonia, Viral - epidemiology; Pneumonia, Viral - pathology; Pneumonia, Viral - virology; Real-Time Polymerase Chain Reaction; RNA-Dependent RNA Polymerase - genetics; SARS-CoV-2; Sequence Alignment; Spike Glycoprotein, Coronavirus - genetics; Viral infection; Viral Nonstructural Proteins - genetics; Iran; COVID-19; Pandemic; Phylogeny; Viral infection
• DOI: 10.1016/j.meegid.2020.104387
• ISSN: 1567-1348

The aim of the current study was to investigate and track the SARS-CoV-2 in Iranian Coronavirus Disease 2019 (COVID-19) patients using molecular and phylogenetic methods. We enrolled seven confirmed cases of COVID-19 patients for the phylogenetic assessment of the SARS-CoV-2 in Iran. The nsp-2, nsp-12, and S genes were amplified using one-step RT-PCR and sequenced using Sanger sequencing method. Popular bioinformatics software were used for sequences alignment and analysis as well as phylogenetic construction. The mean age of the patients in the present study was 60.42 ± 9.94 years and 57.1% (4/7) were male. The results indicated high similarity between Iranian and Chinese strains. We could not find any particular polymorphisms in the assessed regions of the three genes. Phylogenetic trees by neighbor-joining and maximum likelihood method of nsp-2, nsp-12, and S genes showed that there are not any differences between Iranian isolates and those of other countries. As a preliminary phylogenetic study in Iranian SARS-CoV-2 isolates, we found that these isolates are closely related to the Chinese and reference sequences. Also, no sensible differences were observed between Iranian isolates and those of other countries. Further investigations are recommended using more comprehensive methods and larger sample sizes. •SARS-2 genome showed one genetic pattern.•Iran has the same sequence of SARS-2 like other countries isolates.•SNPs in nsp-2 did not show any polymorphisms between this study isolates and other countries.