Evidence map›Paper›PMID 37543926›Full record

ArticleArchives of Iranian medicine2023

Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations.

Farzane Zare Ashrafi, Marzieh Mohseni, Maryam Beheshtian, Zohreh Fattahi, Fatemeh Ghodratpour, Fatemeh Keshavarzi, Hanieh Behravan, Marzieh Kalhor, Khadijeh Jalalvand, Maryam Azad and 49 more

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Article in Archives of Iranian medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

59 authors.

Farzane Zare AshrafiGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.ORCID 0000-0002-8163-5221
Marzieh MohseniGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.ORCID 0000-0003-1200-4044
Maryam BeheshtianGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Zohreh FattahiGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Fatemeh GhodratpourGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Fatemeh KeshavarziGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Hanieh BehravanGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Marzieh KalhorGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Khadijeh JalalvandGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Maryam AzadKariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.
Mahdieh KoshkiKariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.
Ali JafarpourResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Azam GhaziasadiResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Alireza AbdollahiDepartment of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Iran.
Seyed Jalal KianiDepartment of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
Angila Ataei-PirkoohDepartment of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
Iman Rezaei AzharResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Farah Bokharaei-SalimDepartment of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
Mohammad Reza HaghshenasDepartment of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
Farhang BabamahmoodiDepartment of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
Zakiye MokhamesDepartment of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran.
Alireza SoleimaniDepartment of Infectious Diseases, Imam Ali hospital, Alborz University of Medical Sciences, Karaj, Iran.
Masood ZiaeeInfectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran.
Davod JavanmardInfectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran.
Shokouh GhafariInfectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran.
Akram EzaniQazvin Deputy of Treatment Reference Laboratory, Qazvin University of Medical Sciences, Qazvin, Iran.
Alireza Ansari MoghaddamHealth Promotion Research Center, Zahedan University of Medical Science, Zahedan, Iran.
Fariba Shahraki-SanaviHealth Promotion Research Center, Zahedan University of Medical Science, Zahedan, Iran.
Seyed Mohammad Hashemi ShahriInfection Disease and Tropical Medicine Research Center, Zahedan University of Medical Science, Zahedan, Iran.
Azarakhsh AzaranDepartment of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
Farid YousefiDepartment of Infectious Diseases, School of Medicine, Razi Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
Afagh MoattariDepartment of Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
Mohsen MoghadamiHealth policy research center, Shiraz University of medical sciences, Shiraz, Iran.
Hamed FakhimInfectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
Behrooz AtaeiInfectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
Elahe NasriInfectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
Vahdat PoortahmasebiDepartment of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
Mojtaba VarshochiInfectious and Tropical Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran.
Ali MojtahediMicrobiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
Farid JalilianDepartment of Medical Virology, Faculty of Medicine, Hamadan University of Medical sciences, Hamadan, Iran.
Mohammad KhazeniBooali lab, Molecular & Virology Diagnostic Section, Qom, Iran.
Abdolvahab MoradiGolestan University of Medical Sciences, Gorgan, Iran.
Alijan TabarraeiGolestan University of Medical Sciences, Gorgan, Iran.
Ahmad PiroozmandDepartment of Microbiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
Yousef YahyapourInfectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.
Masoumeh BayaniInfectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.
Amir AboofazeliResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Parsa GhafariResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Fariba KeramatBrucellosis Research Center, Hamedan University of Medical Science, Hamadan, Iran.
Mahsa TavakoliCOVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
Tahmineh JalaliCOVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
Mohammad Hassan PouriayevaliCOVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
Mostafa Salehi-VaziriCOVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
Hamid Reza Khorram KhorshidGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Reza NajafipourGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Reza MalekzadehDigestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
Kimia KahriziGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
Seyed Mohammad JazayeriResearch Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
Hossein NajmabadiGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.ORCID 0000-0002-6084-7778

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundGlobal real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings.

methodsWe used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021.

resultsIn total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants.

conclusionOur proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.

Indexed as

COVID-19SARS-CoV-2Disease OutbreaksHumansLaboratoriesMutationCOVID-19Nested RT-PCRSanger sequencingSARS-CoV-2 variantsSpike gene

Identifiers

PMID37543926
PMCPMC10685895

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