Academy of Medical Sciences of I.R. Iran Archives of Iranian Medicine 1029-2977 26 2 2023 02 01 Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations 69 75 10.34172/aim.2023.12 EN Farzane Zare Ashrafi https://orcid.org/0000-0002-8163-5221 Marzieh Mohseni https://orcid.org/0000-0003-1200-4044 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 Hossein Najmabadi https://orcid.org/0000-0002-6084-7778 Journal Article 10.34172/aim.2023.12 2022 07 12 2022 11 16 Background: Global 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. Methods: We 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. Results: In 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. Conclusion: Our 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.