{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T14:57:37Z","timestamp":1792421857588,"version":"4.5.0"},"reference-count":54,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T00:00:00Z","timestamp":1656892800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Infection and Public Health"],"published-print":{"date-parts":[[2022,8]]},"DOI":"10.1016\/j.jiph.2022.07.002","type":"journal-article","created":{"date-parts":[[2022,7,8]],"date-time":"2022-07-08T02:53:33Z","timestamp":1657248813000},"page":"878-891","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":40,"title":["A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries"],"prefix":"10.1016","volume":"15","author":[{"given":"Syed Umair","family":"Ahmad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bushra","family":"Hafeez Kiani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Abrar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zainab","family":"Jan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Imran","family":"Zafar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasir","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amer M.","family":"Alanazi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdul","family":"Malik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohd Ashraf","family":"Rather","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asrar","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azmat Ali","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"2","key":"10.1016\/j.jiph.2022.07.002_bib1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.micinf.2020.02.002","article-title":"The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future","volume":"vol. 22","author":"Li","year":"2020","journal-title":"Microbes Infect"},{"issue":"7798","key":"10.1016\/j.jiph.2022.07.002_bib2","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"vol. 579","author":"Zhou","year":"2020","journal-title":"nature"},{"issue":"7","key":"10.1016\/j.jiph.2022.07.002_bib3","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1001\/jamainternmed.2020.0994","article-title":"Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China","volume":"vol. 180","author":"Wu","year":"2020","journal-title":"JAMA Intern Med"},{"key":"10.1016\/j.jiph.2022.07.002_bib4","doi-asserted-by":"crossref","DOI":"10.4178\/epih.e2020013","article-title":"WHO international health regulations emergency committee for the COVID-19 outbreak","volume":"vol. 42","author":"Jee","year":"2020","journal-title":"Epidemiol Health"},{"key":"10.1016\/j.jiph.2022.07.002_bib5","series-title":"HIVAIDS Care and Counselling: A Multidisciplinary Approach","author":"Van Dyk","year":"2010"},{"key":"10.1016\/j.jiph.2022.07.002_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.intimp.2021.107493","article-title":"SARS-CoV-2: insight in genome structure, pathogenesis and viral receptor binding analysis\u2013an updated review","volume":"vol. 95","author":"Bhat","year":"2021","journal-title":"Int Immunopharmacol"},{"key":"10.1016\/j.jiph.2022.07.002_bib7","article-title":"Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia","author":"Berm\u00fadez","year":"2021","journal-title":"Infect, Genet Evol"},{"issue":"2","key":"10.1016\/j.jiph.2022.07.002_bib8","doi-asserted-by":"crossref","first-page":"192","DOI":"10.3109\/10409238.2013.771132","article-title":"Poly (A)-specific ribonuclease (PARN): an allosterically regulated, processive and mRNA cap-interacting deadenylase","volume":"vol. 48","author":"Virtanen","year":"2013","journal-title":"Crit Rev Biochem Mol Biol"},{"issue":"5","key":"10.1016\/j.jiph.2022.07.002_bib9","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nrm3785","article-title":"The dynamic epitranscriptome: N 6-methyladenosine and gene expression control","volume":"vol. 15","author":"Meyer","year":"2014","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"6","key":"10.1016\/j.jiph.2022.07.002_bib10","article-title":"Novel coronavirus (Sars-cov-2): molecular biology, pathogenesis, pathobiology and advances in treatment of covid-19 patients\u2013an update","volume":"vol. 8","author":"Tripathi","year":"2020","journal-title":"J Exp Biol Agric Sci"},{"key":"10.1016\/j.jiph.2022.07.002_bib11","series-title":"in The Coronaviridae","first-page":"115","article-title":"The Coronavirus Membrane Glycoprotein","author":"Rottier","year":"1995"},{"key":"10.1016\/j.jiph.2022.07.002_bib12","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.ijbiomac.2020.06.007","article-title":"Corona virus versus existence of human on the earth: a computational and biophysical approach","volume":"vol. 161","author":"Zehra","year":"2020","journal-title":"Int J Biol Macromol"},{"issue":"1","key":"10.1016\/j.jiph.2022.07.002_bib13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41541-020-0170-0","article-title":"The outbreak of SARS-CoV-2 pneumonia calls for viral vaccines","volume":"vol. 5","author":"Shang","year":"2020","journal-title":"npj Vaccin"},{"key":"10.1016\/j.jiph.2022.07.002_bib14","unstructured":"W. Wodarg, Dangerous side effects of genetically induced production of SARS CoV-2 spike proteins."},{"key":"10.1016\/j.jiph.2022.07.002_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.142746","article-title":"The novel SARS-CoV-2 pandemic: possible environmental transmission, detection, persistence and fate during wastewater and water treatment","volume":"vol. 765","author":"Mohapatra","year":"2021","journal-title":"Sci Total Environ"},{"key":"10.1016\/j.jiph.2022.07.002_bib16","series-title":"in Intelligent Data Analysis for COVID-19 Pandemic","first-page":"115","article-title":"Artificial Intelligence and Big Data Solutions for COVID-19","author":"Rayan","year":"2021"},{"issue":"50","key":"10.1016\/j.jiph.2022.07.002_bib17","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.15585\/mmwr.mm7050e1","article-title":"SARS-CoV-2 B. 1.1. 529 (Omicron) Variant\u2014United States, December 1\u20138, 2021","volume":"vol. 70","author":"COVID","year":"2021","journal-title":"Morb Mortal Wkly Rep"},{"key":"10.1016\/j.jiph.2022.07.002_bib18","article-title":"Omicron variant (B. 1.1. 529) of SARS-CoV-2: Threat assessment and plan of action","volume":"vol. 97","author":"Choudhary","year":"2022","journal-title":"Int J Surg (Lond, Engl)"},{"key":"10.1016\/j.jiph.2022.07.002_bib19","doi-asserted-by":"crossref","DOI":"10.15585\/mmwr.mm705152e3","article-title":"Investigation of a SARS-CoV-2 B. 1.1. 529 (Omicron) Variant Cluster\u2014Nebraska, November\u2013December 2021","volume":"vol. 70","author":"Jansen","year":"2021","journal-title":"Mmwr Morb Mortal Wkly Rep"},{"key":"10.1016\/j.jiph.2022.07.002_bib20","first-page":"2.3","article-title":"Multiple sequence alignment using ClustalW and ClustalX","volume":"no. 1","author":"Thompson","year":"2003","journal-title":"Curr Protoc Bioinforma"},{"issue":"7","key":"10.1016\/j.jiph.2022.07.002_bib21","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"vol. 33","author":"Kumar","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"4","key":"10.1016\/j.jiph.2022.07.002_bib22","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1111\/mec.14000","article-title":"High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin","volume":"vol. 26","author":"Wang","year":"2017","journal-title":"Mol Ecol"},{"issue":"11","key":"10.1016\/j.jiph.2022.07.002_bib23","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1093\/bioinformatics\/btn179","article-title":"Forward-time simulations of non-random mating populations using simuPOP","volume":"vol. 24","author":"Peng","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jiph.2022.07.002_bib24","unstructured":"R.C. Team, R: A language and environment for statistical computing, 2013."},{"key":"10.1016\/j.jiph.2022.07.002_bib25","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.281","article-title":"Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and\/or sexual reproduction","volume":"vol. 2","author":"Kamvar","year":"2014","journal-title":"PeerJ"},{"issue":"3","key":"10.1016\/j.jiph.2022.07.002_bib26","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1093\/bioinformatics\/btp696","article-title":"pegas: an R package for population genetics with an integrated\u2013modular approach","volume":"vol. 26","author":"Paradis","year":"2010","journal-title":"Bioinformatics"},{"issue":"4","key":"10.1016\/j.jiph.2022.07.002_bib27","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1111\/2041-210X.12158","article-title":"PopGenReport: simplifying basic population genetic analyses in R","volume":"vol. 5","author":"Adamack","year":"2014","journal-title":"Methods Ecol Evol"},{"issue":"3","key":"10.1016\/j.jiph.2022.07.002_bib28","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1111\/j.1365-294X.1996.tb00336.x","article-title":"A simple new method for estimating null allele frequency from heterozygote deficiency","volume":"vol. 5","author":"Brookfield","year":"1996","journal-title":"Mol Ecol"},{"issue":"4","key":"10.1016\/j.jiph.2022.07.002_bib29","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1023\/B:COGE.0000041021.91777.1a","article-title":"Counting alleles with rarefaction: private alleles and hierarchical sampling designs","volume":"vol. 5","author":"Kalinowski","year":"2004","journal-title":"Conserv Genet"},{"issue":"8","key":"10.1016\/j.jiph.2022.07.002_bib30","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1111\/2041-210X.12067","article-title":"diveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors","volume":"vol. 4","author":"Keenan","year":"2013","journal-title":"Methods Ecol Evol"},{"issue":"949","key":"10.1016\/j.jiph.2022.07.002_bib31","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1086\/282771","article-title":"Genetic distance between populations","volume":"vol. 106","author":"Nei","year":"1972","journal-title":"Am Nat"},{"issue":"9","key":"10.1016\/j.jiph.2022.07.002_bib32","doi-asserted-by":"crossref","first-page":"6513","DOI":"10.1007\/s11033-021-06630-4","article-title":"Pandemic COVID-19 caused by SARS-CoV-2: genetic structure, vaccination, and therapeutic approaches","volume":"vol. 48","author":"Marei","year":"2021","journal-title":"Mol Biol Rep"},{"issue":"12","key":"10.1016\/j.jiph.2022.07.002_bib33","doi-asserted-by":"crossref","first-page":"2638","DOI":"10.3390\/cells9122638","article-title":"Comprehensive structural and molecular comparison of spike proteins of SARS-CoV-2, SARS-CoV and MERS-CoV, and their interactions with ACE2","volume":"vol. 9","author":"Hatmal","year":"2020","journal-title":"Cells"},{"key":"10.1016\/j.jiph.2022.07.002_bib34","doi-asserted-by":"crossref","DOI":"10.1016\/j.jgg.2021.12.003","article-title":"Evidence for a mouse origin of the SARS-CoV-2 Omicron variant","author":"Wei","year":"2021","journal-title":"J Genet Genom"},{"issue":"2","key":"10.1016\/j.jiph.2022.07.002_bib35","doi-asserted-by":"crossref","first-page":"301","DOI":"10.13005\/bbra\/2834","article-title":"Genome-wide identification and expression analysis of PPOs and POX gene families in the selected plant species","volume":"vol. 17","author":"Zafar","year":"2020","journal-title":"Biosci Biotechnol Res Asia"},{"issue":"10","key":"10.1016\/j.jiph.2022.07.002_bib36","doi-asserted-by":"crossref","first-page":"1932","DOI":"10.1002\/jmv.25909","article-title":"Understanding evolution of SARS\u2010CoV\u20102: a perspective from analysis of genetic diversity of RdRp gene","volume":"vol. 92","author":"Kasibhatla","year":"2020","journal-title":"J Med Virol"},{"key":"10.1016\/j.jiph.2022.07.002_bib37","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.ijid.2020.11.190","article-title":"Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences","volume":"vol. 103","author":"Motayo","year":"2021","journal-title":"Int J Infect Dis"},{"issue":"2","key":"10.1016\/j.jiph.2022.07.002_bib38","first-page":"95","article-title":"The statistical treatment of data and the analysis of molecular variance (AMOVA) in molecular microbial ecology","volume":"vol. 52","author":"Mengoni","year":"2002","journal-title":"Ann Microbiol"},{"key":"10.1016\/j.jiph.2022.07.002_bib39","article-title":"Structural-bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B. 1.1","author":"Durmaz","year":"2021","journal-title":"529 spike RBD Comp wild-Type Ref"},{"key":"10.1016\/j.jiph.2022.07.002_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.bspc.2021.103433","article-title":"A fractal scaling analysis of the SARS-CoV-2 genome sequence","volume":"vol. 73","author":"Meraz","year":"2022","journal-title":"Biomed Signal Process Control"},{"issue":"3","key":"10.1016\/j.jiph.2022.07.002_bib41","first-page":"46","article-title":"Whole-genome sequencing-based genetic analysis of influenza A (H3N2) virus strains isolated in Guangzhou city","volume":"vol. 38","author":"Lan","year":"2022","journal-title":"\u4e2d\u56fd\u516c\u5171\u536b\u751f"},{"issue":"1","key":"10.1016\/j.jiph.2022.07.002_bib42","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal Omega for making accurate alignments of many protein sequences","volume":"vol. 27","author":"Sievers","year":"2018","journal-title":"Protein Sci"},{"issue":"4","key":"10.1016\/j.jiph.2022.07.002_bib43","doi-asserted-by":"crossref","first-page":"1627","DOI":"10.1002\/jmv.27515","article-title":"Omicron variant genome evolution and phylogenetics","volume":"vol. 94","author":"Kandeel","year":"2022","journal-title":"J Med Virol"},{"issue":"4","key":"10.1016\/j.jiph.2022.07.002_bib44","doi-asserted-by":"crossref","DOI":"10.1016\/j.jksus.2022.102038","article-title":"Genome-wide identification and analysis of GRF (growth-regulating factor) gene family in Camila sativa through in silico approaches","volume":"vol. 34","author":"Zafar","year":"2022","journal-title":"J King Saud Univ-Sci"},{"key":"10.1016\/j.jiph.2022.07.002_bib45","article-title":"Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)","volume":"vol. 30","author":"Zafar","year":"2021","journal-title":"Biotechnol Rep"},{"key":"10.1016\/j.jiph.2022.07.002_bib46","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2021.105106","article-title":"Alignment-free sequence comparison for virus genomes based on location correlation coefficient","volume":"vol. 96","author":"He","year":"2021","journal-title":"Infect, Genet Evol"},{"key":"10.1016\/j.jiph.2022.07.002_bib47","first-page":"2021","article-title":"The SARS-CoV-2 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and efficiently uses the endosomal route of entry","author":"Peacock","year":"2022","journal-title":"BioRxiv"},{"key":"10.1016\/j.jiph.2022.07.002_bib48","article-title":"Analysis of SARS-COV2 spike protein variants among Iraqi isolates","volume":"vol. 26","author":"Sabir","year":"2022","journal-title":"Gene Rep"},{"key":"10.1016\/j.jiph.2022.07.002_bib49","article-title":"SARS-CoV-2 B. 1.617","author":"Mlcochova","year":"2021","journal-title":"2 Delta Var \u00c9merg Vaccin Breakthr"},{"issue":"20","key":"10.1016\/j.jiph.2022.07.002_bib50","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1056\/NEJMoa2102214","article-title":"Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B. 1.351 variant","volume":"vol. 384","author":"Madhi","year":"2021","journal-title":"N Engl J Med"},{"issue":"7898","key":"10.1016\/j.jiph.2022.07.002_bib51","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/s41586-021-04386-2","article-title":"Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift","volume":"vol. 602","author":"Cameroni","year":"2022","journal-title":"Nature"},{"issue":"7898","key":"10.1016\/j.jiph.2022.07.002_bib52","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/s41586-021-04388-0","article-title":"Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2","volume":"vol. 602","author":"Liu","year":"2022","journal-title":"Nature"},{"issue":"11","key":"10.1016\/j.jiph.2022.07.002_bib53","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41564-020-0771-4","article-title":"Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic","volume":"vol. 5","author":"Boni","year":"2020","journal-title":"Nat Microbiol"},{"issue":"6","key":"10.1016\/j.jiph.2022.07.002_bib54","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1136\/gutjnl-2020-320926","article-title":"Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms","volume":"vol. 69","author":"Jin","year":"2020","journal-title":"Gut"}],"container-title":["Journal of Infection and Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1876034122001800?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1876034122001800?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T15:14:55Z","timestamp":1761750895000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1876034122001800"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8]]},"references-count":54,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2022,8]]}},"alternative-id":["S1876034122001800"],"URL":"https:\/\/doi.org\/10.1016\/j.jiph.2022.07.002","relation":{},"ISSN":["1876-0341"],"issn-type":[{"value":"1876-0341","type":"print"}],"subject":[],"published":{"date-parts":[[2022,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries","name":"articletitle","label":"Article Title"},{"value":"Journal of Infection and Public Health","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jiph.2022.07.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Author(s). Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences.","name":"copyright","label":"Copyright"}]}}