• Farzane Zare Ashrafi, Marzieh Mohseni, Maryam Beheshtian, Zohreh Fattahi, Fatemeh Ghodratpour, Fatemeh Keshavarzi, Hanieh Behravan, Marzieh Kalhor, Khadijeh Jalalvand, Maryam Azad, Mahdieh Koshki, Ali Jafarpour, Azam Ghaziasadi, Alireza Abdollahi, Seyed Jalal Kiani, Angila Ataei-Pirkooh, Iman Rezaei Azhar, Farah Bokharaei-Salim, Mohammad Reza Haghshenas, Farhang Babamahmoodi, Zakiye Mokhames, Alireza Soleimani, Masood Ziaee, Davod Javanmard, Shokouh Ghafari, Akram Ezani, Alireza Ansari Moghaddam, Fariba Shahraki-Sanavi, Seyed Mohammad Hashemi Shahri, Azarakhsh Azaran, Farid Yousefi, Afagh Moattari, Mohsen Moghadami, Hamed Fakhim, Behrooz Ataei, Elahe Nasri, Vahdat Poortahmasebi, Mojtaba Varshochi, Ali Mojtahedi, Farid Jalilian, Mohammad Khazeni, Abdolvahab Moradi, Alijan Tabarraei, Ahmad Piroozmand, Yousef Yahyapour, Masoumeh Bayani, Amir Aboofazeli, Parsa Ghafari, Fariba Keramat, Mahsa Tavakoli, Tahmineh Jalali, Mohammad Hassan Pouriayevali, Mostafa Salehi-Vaziri, Hamid Reza Khorram Khorshid, Reza Najafipour, Reza Malekzadeh, Kimia Kahrizi, Seyed Mohammad Jazayeri, and Hossein Najmabadi.
• Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
• Arch Iran Med. 2023 Feb 1; 26 (2): 697569-75.

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.© 2023 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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