Meerjady Sabrina Flora

Pragya D. Yadav

Sanjay Kumar

Éric Bergeron

Frontiers in Medicine

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TYPE EditorialPUBLISHED 29 March 2023DOI 10.3389/fmed.2023.1178696OPEN ACCESSEDITED AND REVIEWED BYMarc Jean Struelens,Université Libre de Bruxelles, Belgium*CORRESPONDENCEPragya D. Yadavhellopragya22@gmail.comSPECIALTY SECTIONThis article was submitted toInfectious Diseases: Pathogenesis and Therapy,a section of the journalFrontiers in MedicineRECEIVED 03 March 2023ACCEPTED 17 March 2023PUBLISHED 29 March 2023CITATIONYadav PD, Kumar S, Bergeron É and Flora MS(2023) Editorial: Emerging SARS-CoV-2variants: Genomic variations, transmission,pathogenesis, clinical impact and interventions.Front. Med. 10:1178696.doi: 10.3389/fmed.2023.1178696COPYRIGHT© 2023 Yadav, Kumar, Bergeron and Flora. Thisis an open-access article distributed under theterms of the Creative Commons AttributionLicense (CC BY). The use, distribution orreproduction in other forums is permitted,provided the original author(s) and thecopyright owner(s) are credited and that theoriginal publication in this journal is cited, inaccordance with accepted academic practice.No use, distribution or reproduction ispermitted which does not comply with theseterms.Editorial: Emerging SARS-CoV-2variants: Genomic variations,transmission, pathogenesis,clinical impact and interventionsPragya D. Yadav1*, Sanjay Kumar2, Éric Bergeron3 andMeerjady Sabrina Flora41Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India,2Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces MedicalCollege (AFMC), Pune, India, 3Centers for Disease Control and Prevention (CDC), Atlanta, GA,United States, 4Directorate General of Health Services, Dhaka, BangladeshKEYWORDSgenomic variations, transmission, pathogenesis, clinical impact, interventionEditorial on the Research TopicEmerging SARS-CoV-2 variants: Genomic variations, transmission,pathogenesis, clinical impact and interventionsSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) originated in Wuhanin December 2019 and rapidly spread across the globe, with the World Health Organization(WHO) declaring it a pandemic in March 2020. Since early 2021, multiple SARS-CoV-2variants have emerged in various countries around the world (1). Among these, the “Variantof Concern” has been reported to be highly transmissible, infectious, and capable of evadingthe natural or vaccine-induced immune response. The rapid spread of these variants hasresulted in a daily increase in SARS-CoV-2 cases, which are associated with severe morbidityand mortality, exacerbating the pandemic situation (2). The newly emerged variants havebecome a serious threat to the global COVID-19 vaccination program due to their reducedsusceptibility to currently available vaccines (3). It is critical to conduct active genomicsurveillance of SARS-CoV-2 variants in order to better understand their transmission,pathogenesis, and the efficacy of vaccines and other therapeutics against these variants.This Research Topic was created to explore the global emergence and prevalence ofSARS-CoV-2 variants, key mutations impacting transmission, infectivity, pathogenicity, andassociated immune escape against vaccines and other therapeutics. The 64 papers thatcomprise this Research Topic, accepted by authors of various countries and continents,investigate mainly genomic variations of SARS-CoV-2, the clinical impact of COVID-19,and the interventions to control the pandemic.The mutational landscape on the SARS-CoV-2 structural and non-structural proteinsand their impact on diagnostics, therapeutics, and vaccines have been studied acrossdifferent geographical locations worldwide. Many of the authors tried to determine the maincharacteristics of the emerging various variants of SARS-CoV-2, including their distribution,mutations, transmissibility, severity, and susceptibility to immune responses. All thesestudies revealed different mutational patterns and their impact on diagnostics, their role inimmune evasion, pathogenesis, and advanced research on current vaccines and therapeutics,i.e., the emergence of Variants of Concern and Variants of Interest, novel mutations, rareFrontiers inMedicine 01 frontiersin.orgYadav et al. 10.3389/fmed.2023.1178696double-deletion variation in the spike region (68-76del+spike675−679del), dynamism in intrahost single nucleotide variants(iSNVs) in the severe and mild infection cohorts, immune evasionof the Mu variant and a derivative of the Delta strain with E484Kand N501Y mutations, increased virulence and transmission, andthe functional role of ORF8a in viral pathogenesis (Agius et al.;Biswas et al.; Bittar et al.; Cheng et al.; Deval et al.; Ha et al.;Huang et al.; Jiang et al.; Khan et al.; Levi et al.; Li T. et al.;Liu C. et al.; Liu L.-T. et al.; Miyakawa et al.; Mostefai et al.;Negrón et al.; Osman et al.; Qin et al.; Smith et al.; Takatsukaet al.; Thakur et al.; Zhang, Ejikemeuwa et al.; Zhang, Hu et al.;Zimerman et al.). In addition, these many studies also reportedshedding of SARS-CoV-2, nosocomial transmission in a clusterof children with underlying malignancy, isolation of SARS-CoV-2 variants and assessment of their genetic diversity, cell tropismand interaction with proteins that promote virus entry, and animalpathogenesis with SARS-CoV-2 variants (Ding et al.; Fernandez etal.; Lavania et al.; Madi et al.; Mostefai et al.; Praharaj et al.; Putri etal.; Rodriguez-Sevilla et al.; Singh et al.; Zhang Y.-D. et al.). Thesefindings will be of value to the development of next-generationvaccines and therapeutic antibodies.Ending the COVID-19 pandemic necessitates a sharedunderstanding of the SARS-CoV-2 and COVID-19 mechanisms.The studies demonstrated the weighted network modeling offrequency trajectories of mutations (FTMs), the Global Evaluationof SARS-CoV-2/hCoV-19 Sequences 2 (GESS v2), and how IdbSVand logistic regression models enable us to rapidly and easily trackdown SARS-CoV-2 variants, identify SNVs, and spike bindingparameters of ACE2 (Essabbar et al.; Huang et al.; Li K. et al.).Various studies have also reported the usefulness of real-timeRT-PCRs for the detection of the relevant mutations/deletionspresent in the Spike protein in VOC/VOIs, amplicon-basedgenome sequencing with MinION, utilizing the ARTIC V4 primersfor improving genome recovery of SARS-CoV-2 variants, andHiSpike, a method for high-throughput cost-effective targetednext-generation sequencing of the spike gene. These studieshighlight the importance of whole genome sequencing andexpanded real-time monitoring of diagnostic PCR assays during apandemic (Angulo et al.; Castro et al.; Fass et al.; Lambisia et al.;Park et al.; Rafiqul Islam et al.).The COVID-19 pandemic has been a great challenge topublic health systems. The factors associated with a higher riskof death were those related to coinfection and comorbidities(Alfonso-Sanchez et al.; Angulo et al.; Hosch et al.; Pang et al.).Although the emergence of vaccines may reduce the threat posedby SARS-CoV-2 variants, these variants are still very importantand need to be studied. Many of the studies focused on thevarious aspects of COVID-19, mainly a wide range of clinicalpresentations, viral transmissibility, viral load, disease severity,lethality, breakthrough infections, reinfections, waning responsewith natural or vaccine-induced immunity, and the need forbooster vaccination (Colavita et al.; da Silva et al.; Guo et al.;Hu et al.; Isnaini et al.; Koyama et al.; Li R. et al.; Xu et al.;Shastri et al.; Temsah et al.; Thangaraj et al.). Moreira-Soto et al.also demonstrated that the equine polyclonal antibodies (pAbs)efficiently neutralize the variants of concern alpha, beta, epsilon,gamma, and delta.Few studies demonstrated the usefulness of fluorescentlylabeled lateral flow assays enabling rapid detection of SARS-CoV-2 under field or at-home conditions and in-house IgG ELISAand PRNT in vaccine efficacy studies (Auerswald et al.; Gestoet al.; Walish et al.). Some research findings also revealed theineffectiveness of red blood cell distribution width (RDW) asa prognostic factor for COVID-19 severity, potential adverseperinatal outcomes with the Gamma variant, and the importanceof a booster vaccination in patients with rheumatoid arthritis(Fernandez et al.; Zhang, Ejikemeuwa et al.; Zhao et al.).The outcome of SARS-CoV-2 infection varies fromasymptomatic, symptomatic to fatal cases. This data highlightsthe importance of better-adapted non-pharmacological measuresand clinical discharge of patients in order to prevent the spread ofSARS-CoV-2 to the general population (Cunha et al.). Currentlyavailable COVID-19 vaccines are still effective against the SARS-CoV-2 variant. If vaccine effectiveness against SARS-CoV-2variants continues to deteriorate, the pandemic could worsen. Toaddress the new challenges posed by new SARS-CoV-2 variants,multiple measures should be implemented, including public healthinterventions, vaccination expansion, and the development of anew vaccine booster.All these research findings emphasized the importanceof monitoring vaccine breakthrough infections, through thecharacterization of virological, immunological, and clinical featuresassociated with these events, in order to tune prevention measuresin the next phase of the COVID-19 pandemic.Author contributionsPY wrote the first draft. All authors reviewed and approved thefinal manuscript.AcknowledgmentsWe thank all the authors of 64 papers that comprise thisResearch Topic, accepted by authors of various countries andcontinents, who investigate mainly genomic variations of SARS-CoV-2 and the clinical impact of COVID-19 and interventions tocontrol the pandemic.Conflict of interestThe authors declare that the research was conducted in theabsence of any commercial or financial relationships that could beconstrued as a potential conflict of interest.Publisher’s noteAll claims expressed in this article are solely those of theauthors and do not necessarily represent those of their affiliatedorganizations, or those of the publisher, the editors and thereviewers. Any product that may be evaluated in this article, orclaim that may be made by its manufacturer, is not guaranteed orendorsed by the publisher.Frontiers inMedicine 02 frontiersin.orgYadav et al. 10.3389/fmed.2023.1178696References1. Hu B, Guo H, Zhou P, Shi ZL. Characteristics of SARS-CoV-2 andCOVID-19. Nat Rev Microbiol. (2021) 19:141–54. doi: 10.1038/s41579-020-00459-72. Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J,COVID-19 Genomics UK Consortium et al. SARS-CoV-2 variant biology:immune escape, transmission and fitness. Nat Rev Microbiol. (2023).21:162–77. doi: 10.1038/s41579-022-00841-73. Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immuneevasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther. (2022)7:202. doi: 10.1038/s41392-022-01039-2Frontiers inMedicine 03 frontiersin.org

Editorial: Emerging SARS-CoV-2 variants: Genomic variations, transmission, pathogenesis, clinical impact and interventions

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Editorial: Emerging SARS-CoV-2 variants: Genomic variations, transmission, pathogenesis, clinical impact and interventions

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