tetano
Editor, Senior Moderator
Biotechnol Appl Biochem
. 2022 Apr 9.
doi: 10.1002/bab.2343. Online ahead of print.
The SARS-CoV-2 NSP-2, NSP-12 and Spike partial sequence conservation in stool samples from Abadan, Iran
Milad Zandi[SUP] 1 [/SUP], Saber Soltani[SUP] 1 [/SUP], Alireza Tabibzadeh[SUP] 2 [/SUP], Sepideh Nasimzadeh[SUP] 3 [/SUP], Emad Behboudi[SUP] 4 [/SUP], Armin Zakeri[SUP] 5 [/SUP], Yousef Erfani[SUP] 6 [/SUP], Shokrollah Salmanzadeh[SUP] 7 [/SUP], Samaneh Abbasi[SUP] 8 [/SUP]
Affiliations
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there are many reports on gastrointestinal symptoms in COVID-19 patients. This study aimed to perform a detailed phylogenetic study and assessment of different SNVs on the RNA genome of virus isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help to better understand the viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID-19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and confirmed the SARS-CoV-2 genome presence in stool samples by RT-PCR assay. Three viral genes S, nsp12, and nsp2 were amplified using the RT-PCR method and specific primers. The multiple sequencing alignment (MSA) was performed in the CLC word bench and phylogenetic tree generated by the MEGA X based on the neighbor-joining method. Of all cases, 11(55%) were male. The mean age of patients was 33.6 years. Diabetes (70%) and blood pressure (55%) had the most prevalent comorbidities. All of 20 patients were positive for SARS-CoV-2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS-CoV-2 genome was found among 10 stool samples and only 3 samples were used for sequencing. The polymorphism and phylogenetic analysis in the SARS-CoV-2 showed a great similarity between all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOC). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS-CoV-2 isolates with the Wuhan reference sequence and all of the current variants of concern (VOC) in the particular evaluated partial sequences of S, nsp12 and nsp2. This article is protected by copyright. All rights reserved.
Keywords: COVID 19; Islamic Republic of Iran; Phylogenetic Relationship; SARS Coronavirus 2; Viral Non-Structural Proteins; spike glycoprotein.
. 2022 Apr 9.
doi: 10.1002/bab.2343. Online ahead of print.
The SARS-CoV-2 NSP-2, NSP-12 and Spike partial sequence conservation in stool samples from Abadan, Iran
Milad Zandi[SUP] 1 [/SUP], Saber Soltani[SUP] 1 [/SUP], Alireza Tabibzadeh[SUP] 2 [/SUP], Sepideh Nasimzadeh[SUP] 3 [/SUP], Emad Behboudi[SUP] 4 [/SUP], Armin Zakeri[SUP] 5 [/SUP], Yousef Erfani[SUP] 6 [/SUP], Shokrollah Salmanzadeh[SUP] 7 [/SUP], Samaneh Abbasi[SUP] 8 [/SUP]
Affiliations
- PMID: 35396867
- DOI: 10.1002/bab.2343
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there are many reports on gastrointestinal symptoms in COVID-19 patients. This study aimed to perform a detailed phylogenetic study and assessment of different SNVs on the RNA genome of virus isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help to better understand the viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID-19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and confirmed the SARS-CoV-2 genome presence in stool samples by RT-PCR assay. Three viral genes S, nsp12, and nsp2 were amplified using the RT-PCR method and specific primers. The multiple sequencing alignment (MSA) was performed in the CLC word bench and phylogenetic tree generated by the MEGA X based on the neighbor-joining method. Of all cases, 11(55%) were male. The mean age of patients was 33.6 years. Diabetes (70%) and blood pressure (55%) had the most prevalent comorbidities. All of 20 patients were positive for SARS-CoV-2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS-CoV-2 genome was found among 10 stool samples and only 3 samples were used for sequencing. The polymorphism and phylogenetic analysis in the SARS-CoV-2 showed a great similarity between all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOC). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS-CoV-2 isolates with the Wuhan reference sequence and all of the current variants of concern (VOC) in the particular evaluated partial sequences of S, nsp12 and nsp2. This article is protected by copyright. All rights reserved.
Keywords: COVID 19; Islamic Republic of Iran; Phylogenetic Relationship; SARS Coronavirus 2; Viral Non-Structural Proteins; spike glycoprotein.