Partial sequence conservation of SARS-CoV-2 NSP-2, NSP-12, and Spike in stool samples from Abadan, Iran.
COVID 19
Iran
SARS coronavirus 2
phylogenetic relationship
spike glycoprotein
viral nonstructural proteins
Journal
Biotechnology and applied biochemistry
ISSN: 1470-8744
Titre abrégé: Biotechnol Appl Biochem
Pays: United States
ID NLM: 8609465
Informations de publication
Date de publication:
Feb 2023
Feb 2023
Historique:
received:
01
11
2021
accepted:
28
02
2022
pubmed:
10
4
2022
medline:
25
2
2023
entrez:
9
4
2022
Statut:
ppublish
Résumé
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID-19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help better understand 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 the SARS-CoV-2 genome presence in stool samples was confirmed by RT-PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT-PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor-joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 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; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS-CoV-2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). 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 VOC in the particular evaluated partial sequences of S, nsp12, and nsp2.
Identifiants
pubmed: 35396867
doi: 10.1002/bab.2343
pmc: PMC9082511
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
201-209Informations de copyright
© 2022 International Union of Biochemistry and Molecular Biology, Inc.
Références
Sanami S, Zandi M, Pourhossein B, Mobini G-R, Safaei M, Abed A, et al. Design of a multi-epitope vaccine against SARS-CoV-2 using immunoinformatics approach. Int J Biol Macromol.2020;164:871-83.
deSouza TH, Nadal JA, Nogueira RJ, Pereira RM, Brandão MB. Clinical manifestations of children with COVID-19: a systematic review. Pediatr Pulmonol.2020;55(8):1892-9.
Behboudi E, Hamidi-Sofiani V, Zeynali P. Review of therapeutic candidates for the new corona virus (COVID-19). RJMS.2020;27(8):65-77.
Fumian TM, Malta FC, Dos Santos DR, Pauvolid-Corrêa A, Fialho AM, Leite JP, et al. SARS-CoV-2 RNA detection in stool samples from acute gastroenteritis cases, Brazil. J Med Virol.2021;93(4):2543-7.
Cheung KS, Hung IF, Chan PP, Lung K, Tso E, Liu R, et al. Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from a Hong Kong cohort: systematic review and meta-analysis. Gastroenterology.2020;159(1):81-95.
Chu H, Chan JF-W, Wang Y, Yuen TT-T, Chai Y, Shuai H, et al. SARS-CoV-2 induces a more robust innate immune response and replicates less efficiently than SARS-CoV in the human intestines: an ex vivo study with implications on pathogenesis of COVID-19. Cell Mol Gastroenterol Hepatol.2021;11(3):771-81.
Wang J, Zhao S, Liu M, Zhao Z, Xu Y, Wang P, et al. ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism. MedRxiv.2020. https://doi.org/10.1101/2020.02.05.20020545.
Bhattacharya S, Basu P, Poddar S. Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic. J Prev Med Hyg.2020;61(2):E130-6.
Speranskaya A, Kaptelova V, Samoilov A, Bukharina AY, Shipulina OY, Korneenko E, et al. Genetic variability of SARS-CoV-2 in biological samples from patients in Moscow. J Microbiol Epidemiol Immunobiol.2021;97(6):511-7.
Sun F, Wang X, Tan S, Dan Y, Lu Y, Zhang J, et al. SARS-CoV-2 quasispecies provides an advantage mutation pool for the epidemic variants. Microbiol Spectr, 2021;9(1):e00261-21.
Vilar S, Isom DG. One year of SARS-CoV-2: how much has the virus changed?Biology.2021;10(2):91.
Poudel S, Ishak A, Perez-Fernandez J, Garcia E, León-Figueroa DA, Romaní L, et al. Highly mutated SARS-CoV-2 Omicron variant sparks significant concern among global experts-What is known so far?Travel Medi Infect Dis.2022;45:102234.
Mercatelli D, Giorgi FM. Geographic and genomic distribution of SARS-CoV-2 mutations. Front Microbiol.2020;11:1800.
Yao H-P, Lu X, Chen Q, Xu K, Chen Y, Cheng L, et al. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discov. 2020;6(1):76.
Masood N, Malik SS, Raja MN, Mubarik S, Yu C. Unraveling the epidemiology, geographical distribution, and genomic evolution of potentially lethal coronaviruses (SARS, MERS, and SARS CoV-2). Front Cell Infect Microbiol. 2020;10:499.doi: 10.3389/fcimb.2020.00499. eCollection 2020.
coronaviruse/whoinhouseassays https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.
Fani M, Zandi M, Soltani S, Abbasi SJB.Future developments in biosensors for field-ready SARS-CoV-2 virus diagnostics. Biotechnol Appl Biochem.2021;68(4):695-9.
Centers for Disease Control and Prevention. Interim guidelines for collecting and handling of clinical specimens for COVID-19 testing. 2020. https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, et al. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. N Engl J Med.2020;383:1283-6.
Szymczak WA, Goldstein DY, Orner EP, Fecher RA, Yokoda RT, Skalina KA, et al. Utility of stool PCR for the diagnosis of COVID-19: comparison of two commercial platforms. J Clin Microbiol.2020;58(9):e01369-20.
Fani M, Zandi M, Ebrahimi S, Soltani S, Abbasi SJFV. The role of miRNAs in COVID-19 disease. Future Virol. 2021;16(4):301-6.
Wu Y, Guo C, Tang L, Hong Z, Zhou J, Dong X, et al. Prolonged presence of SARS-CoV-2 viral RNA in faecal samples. Lancet Gastroenterol Hepatol.2020;5(5):434-5.
Lin L, Jiang X, Zhang Z, Huang S, Zhang Z, Fang Z, et al. Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection. Gut.2020;69(6):997-1001.
Zhang J, Garrett S, Sun J. Gastrointestinal symptoms, pathophysiology, and treatment in COVID-19. Genes Dis.2021;8(4):385-400.
Gu J, Han B, Wang JJG. COVID-19: gastrointestinal manifestations and potential fecal-oral transmission. Gastroenterology. 2020;158(6):1518-9.
Zhang W, Du R-H, Li B, Zheng X-S, Yang X-L, Hu B, et al. Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect.2020;9(1):386-9.
Kim J-M, Kim HM, Lee EJ, Jo HJ, Yoon Y, Lee N-J, et al. Detection and isolation of SARS-CoV-2 in serum, urine, and stool specimens of COVID-19 patients from the Republic of Korea. Osong Public Health Res Perspect.2020;11(3):112-7.
Jackson CB, Farzan M, Chen B, Choe H. Mechanisms of SARS-CoV-2 entry into cells. Nat Rev Mol Cell Biol.2022;23(1):3-20.
Zheng S, Fan J, Yu F, Feng B, Lou B, Zou Q, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ. 2020;369:m1443.
Riphagen S, Gomez X, Gonzalez-Martinez C, Wilkinson N, Theocharis PJTL. Hyperinflammatory shock in children during COVID-19 pandemic. Lancet. 2020;395(10237):1607-8.
Liu W, Tang F, Fontanet A, Zhan L, Zhao Q-M, Zhang P-H, et al. Long-term SARS coronavirus excretion from patient cohort, China. Emerg Infect Dis.2004;10(10):1841-3.
Heller L, Mota CR, DBJSotTE G. COVID-19 faecal-oral transmission: are we asking the right questions?Sci Total Environ.2020;729:138919.
Warish A, Triplett C, Gomi R, Gyawali P, Hodgers L, SJEs T, et al. Assessment of genetic markers for tracking the sources of human wastewater associated Escherichia coli in environmental waters. Environ Sci Technol. 2015;49(15):9341-6.