SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran.
Aged
Base Sequence
Betacoronavirus
/ classification
COVID-19
Coronavirus Infections
/ diagnosis
Coronavirus RNA-Dependent RNA Polymerase
Female
Genome, Viral
High-Throughput Nucleotide Sequencing
Humans
Iran
/ epidemiology
Male
Middle Aged
Molecular Epidemiology
Pandemics
Phylogeny
Pneumonia, Viral
/ diagnosis
RNA-Dependent RNA Polymerase
/ genetics
Real-Time Polymerase Chain Reaction
SARS-CoV-2
Sequence Alignment
Spike Glycoprotein, Coronavirus
/ genetics
Viral Nonstructural Proteins
/ genetics
COVID-19
Pandemic
Phylogeny
Viral infection
Journal
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
ISSN: 1567-7257
Titre abrégé: Infect Genet Evol
Pays: Netherlands
ID NLM: 101084138
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
20
05
2020
revised:
26
05
2020
accepted:
27
05
2020
pubmed:
3
6
2020
medline:
3
10
2020
entrez:
3
6
2020
Statut:
ppublish
Résumé
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.
Sections du résumé
BACKGROUND
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.
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.
RESULTS
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.
CONCLUSION
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.
Identifiants
pubmed: 32485332
pii: S1567-1348(20)30218-5
doi: 10.1016/j.meegid.2020.104387
pmc: PMC7832360
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Viral Nonstructural Proteins
0
nsp2 protein, SARS-CoV-2
0
spike protein, SARS-CoV-2
0
Coronavirus RNA-Dependent RNA Polymerase
EC 2.7.7.48
NSP12 protein, SARS-CoV-2
EC 2.7.7.48
RNA-Dependent RNA Polymerase
EC 2.7.7.48
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
104387Informations de copyright
Copyright © 2020. Published by Elsevier B.V.
Déclaration de conflit d'intérêts
Declaration of Competing Interest There is no conflict of interests between authors in the present study.
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