Geospatial Dynamics of SARS-CoV-2 Variants during the Fifth Wave of COVID-19 in Punjab, Pakistan

Muhammad Mubashar Beig, Muhammad Asad Ali, Hasnain Javed, Tahir Yaqub, Asim Khalid Mehmood, Muhammad Nawaz, Sohail Raza, Muhammad Adnan Ashraf, Muhammad Abu Bakar Shabbir, Nadia Mukhtar, Muhammad Imran Najeeb, Waqar Aziz, Adnan Mehmood, Hamza Raza, Awais Masud, Rida Basharat, Aftab Ahmad Anjum

Abstract


Background: The study was conducted in the various districts of Punjab, Pakistan, to ascertain the incidence and epidemiology of SARS-CoV-2 variants circulating in the population during the fifth wave of COVID-19.

Method: A total of 9603 nasopharyngeal swab samples of suspected patients were collected from the different districts of Punjab from December 2021 to April 2022. In the BSL-3 facility, an auto-extractor (Uni-medica) was used to extract the RNA genome. Viral detection and quantification were performed using real-time reverse transcriptase PCR. Multiplex PCR was used to target different mutations of the spike protein in order to identify SARS-CoV-2 variants.

Results: 711 samples were found to be positive from a total of 9603. The Omicron variant of concern (VOC) was the predominant lineage of SARS-CoV-2 circulating at the time of sampling. Ninety-one percent proportion of COVID-19 was caused by the Omicron, followed by the wild variant (3.80%) and Delta (68.11%). Men were found to have a greater Omicron prevalence (47.96%) than women (42.05%). Furthermore, compared to older individuals (32.07%) and younger kids (10.55%), adults had the higher percentage of Omicron (47.39%).

Conclusion: This study brought attention to the Omicron variant's circulation in Punjab Province, Pakistan, during the COVID-19 fifth wave.

Keywords: Coronavirus; Omicron; Delta; Variant of Concern; Multiplex PCR; Punjab; Pandemic  


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References


Worldometer. COVID LIVE-Coronavirus Statistics. 2024 28 March 2024; Available from: https://www.worldometers.info/coronavirus/.

Rehman Z, Umair M, Ikram A, Fahim A, Salman M. Footprints of SARS-CoV-2 genome diversity in Pakistan, 2020–2021. Virologica Sinica, (2022); 37(1): 153.

Department PW (2022) Population Profile Punjab. Population Welfare Department.

Pakistan, G.o. Punjab Cases Details. 2024; Available from: https://covid.gov.pk/stats/punjab.

Saddique A, Adnan S, Bokhari H, Azam A, Rana MS, et al. Prevalence and Associated Risk Factor of COVID-19 and Impacts of Meteorological and Social Variables on Its Propagation in Punjab, Pakistan. Earth Systems and Environment, (2021); 5(3): 785-798.

Haq M, Rehman A, Ahmad J, Zafar U, Ahmed S, et al. SARS-CoV-2: big seroprevalence data from Pakistan—is herd immunity at hand? Infection, (2021); 49(5): 983-988.

Holmes KV. CORONAVIRUSES (CORONAVIRIDAE). Encyclopedia of virology, (1999); 291-298.

Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virology Journal, (2019); 16(1): 69.

van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJM, et al. Identification of a new human coronavirus. Nature medicine, (2004); 10(4): 368-373.

Zhang Y-y, Li B-r, Ning B-t. The Comparative Immunological Characteristics of SARS-CoV, MERS-CoV, and SARS-CoV-2 Coronavirus Infections. Frontiers in Immunology, (2020); 11 : 563286.

Zhang Y-Z, Holmes EC. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell, (2020); 181(2): 223-227.

Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R, et al. SARS-CoV-2, SARS-CoV, and MERS-COV: a comparative overview. Le Infezioni in Medicina, (2020); 28(2): 174-184.

Li W, Moore MJ, Vasilieva N, Sui J, Wong SK, et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature, (2003); 426(6965): 450-454.

Beumer J, Geurts MH, Lamers MM, Puschhof J, Zhang J, et al. A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses. Nature communications, (2021); 12(1): 1-12.

Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. Journal of Virology, (2010); 84(19): 9733-9748.

Koyama T, Weeraratne D, Snowdon JL, Parida L. Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Pathogens, (2020); 9(5): 324.

Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nature reviews Microbiology, (2021); 19(7): 409-424.

Tian D, Sun Y, Zhou J, Ye Q. The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape. Frontiers in Immunology, (2021); 12: 751778.

Callaway E (2021) Heavily mutated Omicron variant puts scientists on alert. Nature Magazine. 2021; 600(7887): 21 .

Li Q, Zhang L, Liang Z, Wang N, Liu S, et al. Cross-reactivity of eight SARS-CoV-2 variants rationally predicts immunogenicity clustering in sarbecoviruses. Signal Transduct Target Ther, (2022); 7(1): 1-11.

Shah M, Woo HG. Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Frontiers in Immunology, (2022); 12: 830527.

Klein S, Müller TG, Khalid D, Sonntag-Buck V, Heuser A-M, et al. SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP. Viruses, (2020); 12(8): 863.

Ambrosi C, Prezioso C, Checconi P, Scribano D, Sarshar M, et al. SARS-CoV-2: Comparative analysis of different RNA extraction methods. Journal of Virologoical Methods, (2021); 287114008.

Coryell MP, Iakiviak M, Pereira N, Murugkar PP, Rippe J, et al. A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study. The Lancet Microbe, (2021); 2(6): e259-e266.

Seegene (2022) Novaplex™ SARS-CoV-2 Variants Assays. Seegene.

Mohapatra RK, Tiwari R, Sarangi AK, Sharma SK, Khandia R, et al. Twin combination of Omicron and Delta variants triggering a tsunami wave of ever high surges in COVID‐19 cases: a challenging global threat with a special focus on the Indian subcontinent. Journal of Medical Virology, (2022); 94(5): 1761-1765.

Mohapatra RK, Sarangi AK, Kandi V, Azam M, Tiwari R, et al. Omicron (B. 1.1. 529 variant of SARS‐CoV‐2); an emerging threat: current global scenario. Journal of Medical Virology, (2022); 94(5): 1780-1783.

Cedro-Tanda A, Gómez-Romero L, de Anda-Jauregui G, Garnica-López D, Alfaro-Mora Y, et al. Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Viruses, (2022); 14(3): 545.

Nasir A, Aamir UB, Kanji A, Samreen A, Ansar Z, et al. SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan. medRxiv, (2022).

Khan A, Waris H, Rafique M, Suleman M, Mohammad A, et al. The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data. International journal of biological macromolecules, (2022); 200438-448.

Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, et al. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell, (2020); 182(5): 1295-1310.e1220.

Leung K, Shum MH, Leung GM, Lam TT, Wu JT. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Eurosurveillance, (2021); 26(1): 2002106.

Sabino EC, Buss LF, Carvalho MP, Prete CA, Crispim MA, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet, (2021); 397(10273): 452-455.

Fratev F. The N501Y and K417N mutations in the spike protein of SARS-CoV-2 alter the interactions with both hACE2 and human derived antibody: A Free energy of perturbation study. bioRxiv, (2020); 2020.2012.2023.424283.

Wan S, Xiang Y, Fang W, Zheng Y, Li B, et al. Clinical features and treatment of COVID-19 patients in northeast Chongqing. Journal of Medical Virology, (2020); 92(7): 797-806.

Wu J, Liu J, Zhao X, Liu C, Wang W, et al. Clinical Characteristics of Imported Cases of Coronavirus Disease 2019 (COVID-19) in Jiangsu Province: A Multicenter Descriptive Study. Clinical Infectious Diseases, (2020); 71(15): 706-712.

Mo P, Xing Y, Xiao Y, Deng L, Zhao Q, et al. Clinical Characteristics of Refractory Coronavirus Disease 2019 in Wuhan, China. Clinical Infectious Diseases, (2020); 73(11): e4208-e4213.

Chen N, Zhou M, Dong X, Qu J, Gong F, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet, (2020); 395(10223): 507-513.

Umair M, Ikram A, Rehman Z, Haider SA, Badar N, et al. Detection and upsurge of SARS-CoV-2 Omicron variant in Islamabad Pakistan. medRxiv, (2022).

Fonager J, Bennedbæk M, Bager P, Wohlfahrt J, Ellegaard KM, et al. Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022. Eurosurveillance, (2022); 27(10): 2200181.

Ulloa AC, Buchan SA, Daneman N, Brown KA. Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada. Jama, (2022); 327(13): 1286-1288.

Sama IE, Ravera A, Santema BT, van Goor H, ter Maaten JM, et al. Circulating plasma concentrations of angiotensin-converting enzyme 2 in men and women with heart failure and effects of renin–angiotensin–aldosterone inhibitors. The European Heart Journal, (2020); 41(19): 1810-1817.

Klein SL, Marriott I, Fish EN. Sex-based differences in immune function and responses to vaccination. Trans R Soc Trop Med Hyg, (2015); 109(1): 9-15.

Jin J-M, Bai P, He W, Wu F, Liu X-F, et al. Gender Differences in Patients With COVID-19: Focus on Severity and Mortality. Frontiers in Public Health, (2020); 8: 545030.

Mai PHV, Hong TUT, Le Khanh HN, Thanh TN, Le Thi T, et al. Missed detections of influenza A (H1) pdm09 by real-time RT–PCR assay due to haemagglutinin sequence mutation, December 2017 to March 2018, northern Viet Nam. Western Pacific surveillance and response journal (2019); 10(1): 32.

Bolotin S, Robertson AV, Eshaghi A, De Lima C, Lombos E, et al. Development of a novel real-time reverse-transcriptase PCR method for the detection of H275Y positive influenza A H1N1 isolates. Journal of Virological Methods, (2009); 158(1-2): 190-194.

van der Vries E, Jonges M, Herfst S, Maaskant J, Van der Linden A, et al. Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Journal of Clinical Virology, (2010); 47(1): 34-37.




DOI: http://dx.doi.org/10.62940/als.v11i2.2872

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