Wajdy J Al-Awaida1, Baker Jawabrah Al Hourani2, Samer Swedan3, Refat Nimer3, Foad Alzoughool4, Hamzeh J Al-Ameer1, Sara E Al Tamam1, Raghad Alashqar1, Omar Al Bawareed5, Yulia Gushchina6, Mohamed Samy Abousenna7, Amani Marwan Ayyash8, Ahmad Sharab1, Sulaiman M Alnaimat9, Amer Imraish10, Muhanad W Akash11, Najah R Hadi12. 1. Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan. 2. Department of Biology and Chemistry, Embry-Riddle Aeronautical University, Prescott, AZ 86301, USA. 3. Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan. 4. Department of Medical Laboratory Sciences, The Hashemite University, Zarqa 13133, Jordan. 5. Department of Normal Physiology, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia. 6. Department of General and Clinical Pharmacology, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia. 7. Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, Cairo 11517, Egypt. 8. Department of Pharmacy, Faculty of Heath Sciences, American University of Madaba, Madaba 11821, Jordan. 9. Biological Department, Faculty of Science, Al Hussein Bin Talal University, Ma'an P.O. Box 20, Jordan. 10. Department of Biology, Faculty of Science, The University of Jordan, Amman 11942, Jordan. 11. Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman 11942, Jordan. 12. Department of Pharmacology and Therapeutics, Faculty of Medicine, University of Kufa, Najaf 540011, Iraq.
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly developed into a worldwide pandemic. Mutations in the SARS-CoV-2 genome may affect various aspects of the disease including fatality ratio. In this study, 553,518 SARS-CoV-2 genome sequences isolated from patients from continents for the period 1 December 2020 to 15 March 2021 were comprehensively analyzed and a total of 82 mutations were identified concerning the reference sequence. In addition, associations between the mutations and the case fatality ratio (CFR), cases per million and deaths per million, were examined. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. In addition, among the identified clades, none showed a significant correlation to CFR. The G, GR, GV, S clades showed a significant positive correlation to deaths per million. The GR and S clades showed a positive correlation to number of cases per million. The clades having the highest frequencies among continents were G, followed by GH and GR. These findings should be taken into consideration during epidemiological surveys of the virus and vaccine development.
The outbreak of coronavirus disease 2019 (n class="Disease">COVID-19), by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly developed into a worldwide pandemic. Mutations in the SARS-CoV-2 genome may affect various aspects of the disease including fatality ratio. In this study, 553,518 SARS-CoV-2 genome sequences isolated from patients from continents for the period 1 December 2020 to 15 March 2021 were comprehensively analyzed and a total of 82 mutations were identified concerning the reference sequence. In addition, associations between the mutations and the case fatality ratio (CFR), cases per million and deaths per million, were examined. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. In addition, among the identified clades, none showed a significant correlation to CFR. The G, GR, GV, S clades showed a significant positive correlation to deaths per million. The GR and S clades showed a positive correlation to number of cases per million. The clades having the highest frequencies among continents were G, followed by GH and GR. These findings should be taken into consideration during epidemiological surveys of the virus and vaccine development.
Entities:
Keywords:
COVID-19; GISAID; SARS-CoV-2; Spearman’s correlation; case fatality ratio; cases per million; deaths per million; genomic variations
Authors: Océane Delandre; Mathieu Gendrot; Priscilla Jardot; Marion Le Bideau; Manon Boxberger; Céline Boschi; Isabelle Fonta; Joel Mosnier; Sébastien Hutter; Anthony Levasseur; Bernard La Scola; Bruno Pradines Journal: Pharmaceuticals (Basel) Date: 2022-04-02