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Quarleri J, Delpino MV, Galvan V. Anticipating the future of the COVID-19 pandemic: insights into the emergence of SARS-CoV-2 variant JN.1 and its projected impact on older adults. GeroScience 2024; 46:2879-2883. [PMID: 38198026 PMCID: PMC11009205 DOI: 10.1007/s11357-024-01066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Affiliation(s)
- Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Ciencias Médicas, Universidad de Buenos Aires-Consejo de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, C1121ABG, Buenos Aires, Argentina.
| | - M Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Ciencias Médicas, Universidad de Buenos Aires-Consejo de Investigaciones Científicas y Técnicas (CONICET), Paraguay 2155, Piso 11, C1121ABG, Buenos Aires, Argentina
| | - Veronica Galvan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veterans Affairs, Oklahoma City VA Health Care System, Oklahoma City, OK, USA
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Vermeulen M, Mhlanga L, Sykes W, Cable R, Coleman C, Pietersen N, Swanevelder R, Glatt TN, Bingham J, van den Berg K, Grebe E, Welte A. The evolution and interpretation of seroprevalence of SARS-CoV-2 antibodies among South African blood donors from the Beta to Omicron variant-driven waves. Vox Sang 2024; 119:242-251. [PMID: 38156504 DOI: 10.1111/vox.13571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND AND OBJECTIVES Confirmed COVID-19 diagnoses underestimate the total number of infections. Blood donors can provide representative seroprevalence estimates, which can be leveraged into reasonable estimates of total infection counts and infection fatality rate (IFR). MATERIALS AND METHODS Blood donors who donated after each of three epidemic waves (Beta, Delta and first Omicron waves) were tested for anti-SARS-CoV-2 nucleocapsid antibodies using the Roche Elecsys anti-SARS-CoV-2 total immunoglobulin assay. Roche Elecsys anti-spike antibody testing was done for the post-Omicron sampling. Prevalence of antibodies was estimated by age, sex, race and province and compared to official case reporting. Province and age group-specific IFRs were estimated using external excess mortality estimates. RESULTS The nationally weighted anti-nucleocapsid seroprevalence estimates after the Beta, Delta and Omicron waves were 47% (46.2%-48.6%), 71% (68.8%-73.5%) and 87% (85.5%-88.4%), respectively. There was no variation by age and sex, but there were statistically and epidemiologically significant differences by province (except at the latest time point) and race. There was a 13-fold higher seroprevalence than confirmed case counts at the first time point. Age-dependent IFR roughly doubled for every 10 years of age increase over 6 decades from 0.014% in children to 6.793% in octogenarians. CONCLUSION Discrepancies were found between seroprevalence and confirmed case counts. High seroprevalence rates found among Black African donors can be ascribed to historical inequities. Our IFR estimates were useful in refining previous large disagreements about the severity of the epidemic in South Africa. Blood donor-based serosurveys provided a valuable and efficient way to provide near real-time monitoring of the ongoing SARS-CoV-2 outbreak.
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Affiliation(s)
- Marion Vermeulen
- South African National Blood Service, Johannesburg, South Africa
- University of the Free State, Bloemfontein, South Africa
| | - Laurette Mhlanga
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Northwestern University, Chicago, Illinois, USA
| | - Wendy Sykes
- South African National Blood Service, Johannesburg, South Africa
| | | | - Charl Coleman
- South African National Blood Service, Johannesburg, South Africa
| | | | | | - Tanya Nadia Glatt
- South African National Blood Service, Johannesburg, South Africa
- University of Johannesburg, Johannesburg, South Africa
| | - Jeremy Bingham
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Karin van den Berg
- South African National Blood Service, Johannesburg, South Africa
- University of the Free State, Bloemfontein, South Africa
- University of Cape Town, Rondebosch, South Africa
| | - Eduard Grebe
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Vitalant Research Institute, San Francisco, California, USA
- University of California San Francisco, San Francisco, California, USA
| | - Alex Welte
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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Chen L, He Y, Liu H, Shang Y, Guo G. Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants. Front Immunol 2024; 15:1339660. [PMID: 38464527 PMCID: PMC10924305 DOI: 10.3389/fimmu.2024.1339660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.
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Affiliation(s)
- Luyi Chen
- Chongqing Nankai Secondary School, Chongqing, China
| | - Ying He
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Hongye Liu
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Yongjun Shang
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Guoning Guo
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
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Jin B, Oyama R, Tabe Y, Tsuchiya K, Hando T, Wakita M, Yan Y, Saita M, Takei S, Horiuchi Y, Miida T, Naito T, Takahashi K, Ogawa H. Investigation of the individual genetic evolution of SARS-CoV-2 in a small cluster during the rapid spread of the BF.5 lineage in Tokyo, Japan. Front Microbiol 2023; 14:1229234. [PMID: 37744926 PMCID: PMC10516552 DOI: 10.3389/fmicb.2023.1229234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
There has been a decreasing trend in new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases and fatalities worldwide. The virus has been evolving, indicating the potential emergence of new variants and uncertainties. These challenges necessitate continued efforts in disease control and mitigation strategies. We investigated a small cluster of SARS-CoV-2 Omicron variant infections containing a common set of genomic mutations, which provided a valuable model for investigating the transmission mechanism of genetic alterations. We conducted a study at a medical center in Japan during the Omicron surge (sub-lineage BA.5), sequencing the entire SARS-CoV-2 genomes from infected individuals and evaluating the phylogenetic tree and haplotype network among the variants. We compared the mutations present in each strain within the BA.5 strain, TKYnat2317, which was first identified in Tokyo, Japan. From June 29th to July 4th 2022, nine healthcare workers (HCWs) tested positive for SARS-CoV-2 by real-time PCR. During the same period, five patients also tested positive by real-time PCR. Whole genome sequencing revealed that the infected patients belonged to either the isolated BA.2 or BA.5 sub-lineage, while the healthcare worker infections were classified as BF.5. The phylogenetic tree and haplotype network clearly showed the specificity and similarity of the HCW cluster. We identified 12 common mutations in the cluster, including I110V in nonstructural protein 4 (nsp4), A1020S in the Spike protein, and H47Y in ORF7a, compared to the BA.5 reference. Additionally, one case had the extra nucleotide-deletion mutation I27* in ORF10, and low frequencies of genetic alterations were also found in certain instances. The results of genome sequencing showed that the nine HCWs shared a set of genetic mutations, indicating transmission within the cluster. Minor mutations observed in five HCW individuals suggested the emergence of new virus variants. Five amino acid substitutions occurred in nsp3, which could potentially affect virus replication or immune escape. Intra-host evolution also generated additional mutations. The cluster exhibited a mild disease course, with individuals in this case, recovering without requiring any medical treatments. Further investigation is needed to understand the relationship between the genetic evolution of the virus and the symptoms.
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Affiliation(s)
- Bo Jin
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Rieko Oyama
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Tabe
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Koji Tsuchiya
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Tetsuya Hando
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Mitsuru Wakita
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Yan Yan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mizue Saita
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki Horiuchi
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshio Naito
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideoki Ogawa
- Department of Dermatology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Juhász V, Csulak E, Szabó L, Ocsovszky Z, Balla D, Nagy G, Zorzi A, Hoepelman AIM, Merkely B, Vágó H, Sydó N. Retrospective study of COVID-19 experiences in elite multinational aquatic athletes. Sci Rep 2023; 13:13978. [PMID: 37633994 PMCID: PMC10460449 DOI: 10.1038/s41598-023-40821-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023] Open
Abstract
This study assessed the experiences of elite aquatic athletes with coronavirus disease 2019 (COVID-19) during the first World Championship conducted without social distancing and an isolation "bubble". An online questionnaire was completed by 812 athletes (22.7 ± 5.9 years, 467 females) to provide data on demographics, sports activity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates, symptoms, reinfection, vaccination status, and psychological aspects. The answers revealed that 49.4% of athletes had experienced SARS-CoV-2 infection. The infection rates varied significantly across different aquatic sports, with open water swimmers having the lowest (28%) and water polo players (67%) and artistic swimmers (61%) having the highest infection rates (p < 0.0001). The majority reported mild (51%) or moderate (27%) symptoms, while 16% remained asymptomatic. Reinfection occurred in 13%, and 10% of initial infections led to long COVID, with fatigue (65%) and shortness of breath (48%) being the most common long-term symptoms. Significantly, 92% of athletes received at least two vaccine doses and reported a positive vaccination experience (median score of 8 out of 10 for each shot). Mood changes and subjective performance drops significantly correlated with the overall experience scores (rho: 0.617, p < 0.0001, and rho: 0.466, p < 0.0001, respectively). In conclusion, most athletes experienced a benign disease course despite a relatively high infection rate. This study provides valuable insights into the COVID-19 experiences of elite aquatic athletes. The findings emphasize the importance of vaccination initiatives, monitoring psychological well-being and the need to fortify athletes' resilience in the face of future health challenges.
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Affiliation(s)
- Vencel Juhász
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | - Emese Csulak
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | - Liliána Szabó
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | - Zsófia Ocsovszky
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | - Dorottya Balla
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | - György Nagy
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
| | | | | | - Béla Merkely
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
- Department of Sports Medicine, Semmelweis University, Budapest, 1122, Hungary
| | - Hajnalka Vágó
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary.
- Department of Sports Medicine, Semmelweis University, Budapest, 1122, Hungary.
| | - Nóra Sydó
- Heart and Vascular Center, Semmelweis University, 68 Városmajor Street, Budapest, 1122, Hungary
- Department of Sports Medicine, Semmelweis University, Budapest, 1122, Hungary
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Bozidis P, Petridi E, Gartzonika K. An ARMS-Multiplex PCR Targeting SARS-CoV-2 Omicron Sub-Variants. Pathogens 2023; 12:1017. [PMID: 37623977 PMCID: PMC10459702 DOI: 10.3390/pathogens12081017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
As of November 2021, the SARS-CoV-2 Omicron variant had made its appearance, gradually replacing the predominant Delta variant. Since its emergence, the Omicron variant has been continuously evolving through more than 500 strains, most of which belong to five sub-variants known as BA.1, BA.2, BA.3, BA.4, and BA.5. The aim of this study was to develop a multiplex polymerase chain reaction (PCR) that will be able to distinguish the basic sub-variants of Omicron in a rapid and specific way. Full genome sequences of Omicron strains with high frequency and wide geographical distribution were retrieved by the NCBI Virus and ENA databases. These sequences were compared to each other in order to locate single nucleotide polymorphisms common to all strains of the same sub-variant. These polymorphisms should also be capable of distinguishing Omicron sub-variants not only from each other but from previously circulating variants of SARS-CoV-2 as well. Thus, specific primers targeting characteristic polymorphisms of the four Omicron main branches BA.1, BA.2, BA.4, and BA.5 were designed according to the principles of the amplification refractory mutation system (ARMS) and with the ability to react under multiplex PCR conditions. According to our results, the ARMS-multiplex PCR could successfully distinguish all Omicron sub-variants that carry the corresponding mutations.
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Affiliation(s)
- Petros Bozidis
- Department of Microbiology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.P.); (K.G.)
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Mondol SM, Hasib M, Limon MBH, Alam ASMRU. Insights into Omicron's Low Fusogenicity through In Silico Molecular Studies on Spike-Furin Interactions. Bioinform Biol Insights 2023; 17:11779322231189371. [PMID: 37529484 PMCID: PMC10387760 DOI: 10.1177/11779322231189371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.
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Affiliation(s)
| | - Md Hasib
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
| | | | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
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Saade M, Ghosh S, Banerjee M, Volpert V. An epidemic model with time delays determined by the infectivity and disease durations. Math Biosci Eng 2023; 20:12864-12888. [PMID: 37501470 DOI: 10.3934/mbe.2023574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We propose an epidemiological model with distributed recovery and death rates. It represents an integrodifferential system of equations for susceptible, exposed, infectious, recovered and dead compartments. This model can be reduced to the conventional ODE model under the assumption that recovery and death rates are uniformly distributed in time during disease duration. Another limiting case, where recovery and death rates are given by the delta-function, leads to a new point-wise delay model with two time delays corresponding to the infectivity period and disease duration. Existence and positiveness of solutions for the distributed delay model and point-wise delay model are proved. The basic reproduction number and the final size of the epidemic are determined. Both, the ODE model and the delay models are used to describe COVID-19 epidemic progression. The delay model gives a better approximation of the Omicron data than the conventional ODE model from the point of view of parameter estimation.
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Affiliation(s)
- Masoud Saade
- Peoples Friendship University of Russia (RUDN University) 6 Miklukho-Maklaya St, Moscow 117198, Russia
| | - Samiran Ghosh
- Department of Mathematics and Statistics, IIT Kanpur, Kanpur 208016, India
| | - Malay Banerjee
- Department of Mathematics and Statistics, IIT Kanpur, Kanpur 208016, India
| | - Vitaly Volpert
- Peoples Friendship University of Russia (RUDN University) 6 Miklukho-Maklaya St, Moscow 117198, Russia
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, Villeurbanne 69622, France
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Wang J, Hu W, Wang K, Yu R, Chang L, Rong Z. Case report: Acute hepatitis in neonates with COVID-19 during the Omicron SARS-CoV-2 variant wave: a report of four cases. Front Pediatr 2023; 11:1179402. [PMID: 37215592 PMCID: PMC10196249 DOI: 10.3389/fped.2023.1179402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), first emerging in December 2019 and continuously evolving, poses a considerable challenge worldwide. It was reported in the literature that neonates had mild upper respiratory symptoms and a better outcome after Omicron SARS-CoV-2 variant infection, but there was insufficient data about complications and prognosis. Case Presentation In this paper, we present the clinical and laboratory characteristics of four COVID-19 neonate patients with acute hepatitis during the Omicron SARS-CoV-2 variant wave. All patients had a clear history of Omicron exposure and were infected via contact with confirmed caregivers. Low to moderate fever and respiratory symptoms were the primary clinical manifestations, and all patients had a normal liver function at the initial stage of the course. Then, the fever lasted 2 to 4 days, and it was noted that hepatic dysfunction might have occurred 5 to 8 days after the first onset of fever, mainly characterized by moderate ALT and AST elevation (>3 to 10-fold of upper limit). There were no abnormalities in bilirubin levels, blood ammonia, protein synthesis, lipid metabolism, and coagulation. All the patients received hepatoprotective therapy, and transaminase levels gradually decreased to the normal range after 2 to 3 weeks without other complications. Conclusions This is the first case series about moderate to severe hepatitis in COVID-19 neonatal patients via horizontal transmission. Besides fever and respiratory symptoms, the clinical doctor should pay much attention to evaluating the risk of liver function injury after SARS-CoV-2 variants infection, which is usually asymptomatic and has a delayed onset.
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Wu Y, Pan Y, Su K, Zhang Y, Jia Z, Yi J, Lv H, Zhang L, Xue M, Cao D, Jiang J. Elder and booster vaccination associates with decreased risk of serious clinical outcomes in comparison of Omicron and Delta variant: A meta-analysis of SARS-CoV-2 infection. Front Microbiol 2023; 14:1051104. [PMID: 37125157 PMCID: PMC10140352 DOI: 10.3389/fmicb.2023.1051104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Background The COVID-19 pandemic brings great pressure to the public health systems. This meta-analysis aimed to compare the clinical outcomes among different virus variants, to clarify their impact on medical resources and to provide evidence for the formulation of epidemic prevention policies. Methods A systematic literature search was performed in the PubMed, Embase, and Cochrane Library databases using the key words "Omicron" and "Delta." The adjusted Risk ratios (RRs), Odds ratios (ORs) and Hazard ratios (HRs) were extracted, and RRs and Rate difference % (RD%) were used to interpret the risk estimates of the outcomes ultimately. Results Forty-three studies were included, with 3,812,681 and 14,926,841 individuals infected with SARS-CoV-2 Delta and Omicron variant, respectively. The relative risks of hospitalization, death, ICU admission, and mechanical ventilation use after infection with the Omicron variant were all significantly reduced compared those after infection with the Delta variant (RRhospitalization = 0.45, 95%CI: 0.40-0.52; RRdeath = 0.37, 95%CI: 0.30-0.45; RRICU = 0.35, 95%CI: 0.29-0.42; RRmechanical ventilation = 0.33, 95%CI: 0.25-0.44). The change of both absolute and relative risks for hospitalization was more evident (RR = 0.47, 95%CI: 0.42-0.53;RD% =10.61, 95%CI: 8.64-12.59) and a significant increase was observed for the absolute differences in death in the elderly (RD% = 5.60, 95CI%: 4.65-6.55); the change of the absolute differences in the risk of hospitalization and death were most markedly observed in the patients with booster vaccination (RD%hospitalization = 8.60, 95CI%: 5.95-11.24; RD%death = 3.70, 95CI%: 0.34-7.06). Conclusion The ability of the Omicron variant to cause severe clinical events has decreased significantly, as compared with the Delta variant, but vulnerable populations still need to be vigilant. There was no interaction between the vaccination doses and different variants.
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Affiliation(s)
- Yanhua Wu
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yuchen Pan
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Kaisheng Su
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yangyu Zhang
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Zhifang Jia
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jiaxin Yi
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Haiyong Lv
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Lihuan Zhang
- The Second Hospital of Jilin University, Changchun, China
| | - Mingyang Xue
- School of Public Health, Jilin University, Changchun, China
| | - Donghui Cao
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jing Jiang
- Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
- Department of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
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Dörr R. Protecting healthcare personnel and patients over 3 years of COVID-19 : Effective protection by masks and hygiene: What else was effective? Herz 2023:10.1007/s00059-023-05169-3. [PMID: 37010567 PMCID: PMC10069352 DOI: 10.1007/s00059-023-05169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 04/04/2023]
Abstract
Healthcare professionals, particularly those in test centers, laboratories, or specialized COVID-19 wards, are in danger of becoming infected. Patients with special underlying health conditions are at an increased risk of getting very sick, being hospitalized, or dying from COVID-19. Age is a leading risk factor in this context. Currently, FFP2 (Filtering Facepiece 2, European standard), N95 (US standard), and KN95 (Chinese standard) face masks remain the simplest measure of protection. Coronavirus warning apps installed on smartphones have been recommended for anonymous contact tracing and quickly disrupting chains of infection. Preventive testing two to three times per week for healthcare personnel, on the day of hospital admission for patients, and upon facility entry for visitors has been routinely performed or has been requested from external test centers in most medical institutions. However, vaccination is regarded the most effective protective measure against COVID-19. The general recommendation of the World Health Organization is that countries continue to work toward vaccinating at least 70% of their populations, prioritizing the vaccination of 100% of healthcare workers and 100% of the most vulnerable groups, including people who are over 60 years of age and those who are immunocompromised or have underlying health conditions. The most vulnerable individuals among patients and healthcare workers should be identified and then their vaccination status should be checked and, if necessary, optimized by booster administration. In Germany, seasonal and institutional recommendations for individual protection by face masks, for hygiene measures, and for preventive testing must follow the updated coronavirus protection regulations (Coronavirus-Schutzverordnungen).
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Affiliation(s)
- Rolf Dörr
- MVZ Praxisklinik Herz und Gefäße, Forststraße 3, 01099, Dresden, Germany.
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12
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Kumar R, Srivastava Y, Muthuramalingam P, Singh SK, Verma G, Tiwari S, Tandel N, Beura SK, Panigrahi AR, Maji S, Sharma P, Rai PK, Prajapati DK, Shin H, Tyagi RK. Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses 2023; 15:856. [PMID: 37112836 PMCID: PMC10142771 DOI: 10.3390/v15040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.
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Affiliation(s)
- Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Yogesh Srivastava
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Sunil Kumar Singh
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Geetika Verma
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Savitri Tiwari
- Division of Life Sciences, Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Gautam Buddha Nagar, Greater Noida 201310, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG Highway, Gujarat 382481, India
| | - Samir Kumar Beura
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | | | - Somnath Maji
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prakriti Sharma
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, IIET, Invertis University, Bareilly 243001, India
| | | | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Rajeev K. Tyagi
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
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13
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Wang X, Li J, Liu H, Hu X, Lin Z, Xiong N. SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments. Microorganisms 2023; 11:580. [PMID: 36985154 PMCID: PMC10051779 DOI: 10.3390/microorganisms11030580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time.
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14
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Das NC, Chakraborty P, Bayry J, Mukherjee S. Comparative Binding Ability of Human Monoclonal Antibodies against Omicron Variants of SARS-CoV-2: An In Silico Investigation. Antibodies (Basel) 2023; 12:antib12010017. [PMID: 36975364 PMCID: PMC10045060 DOI: 10.3390/antib12010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023] Open
Abstract
Mutation(s) in the spike protein is the major characteristic trait of newly emerged SARS-CoV-2 variants such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Delta-plus. Omicron (B.1.1.529) is the latest addition and it has been characterized by high transmissibility and the ability to escape host immunity. Recently developed vaccines and repurposed drugs exert limited action on Omicron strains and hence new therapeutics are immediately needed. Herein, we have explored the efficiency of twelve therapeutic monoclonal antibodies (mAbs) targeting the RBD region of the spike glycoprotein against all the Omicron variants bearing a mutation in spike protein through molecular docking and molecular dynamics simulation. Our in silico evidence reveals that adintivimab, beludivimab, and regadanivimab are the most potent mAbs to form strong biophysical interactions and neutralize most of the Omicron variants. Considering the efficacy of mAbs, we incorporated CDRH3 of beludavimab within the framework of adintrevimab, which displayed a more intense binding affinity towards all of the Omicron variants viz. BA.1, BA.2, BA.2.12.1, BA.4, and BA.5. Furthermore, the cDNA of chimeric mAb was cloned in silico within pET30ax for recombinant production. In conclusion, the present study represents the candidature of human mAbs (beludavimab and adintrevimab) and the therapeutic potential of designed chimeric mAb for treating Omicron-infected patients.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Pritha Chakraborty
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
| | - Jagadeesh Bayry
- Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Palakkad 678 623, India
- Correspondence: (J.B.); or (S.M.)
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, India
- Correspondence: (J.B.); or (S.M.)
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15
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Mohamed EAR, Abdel-Rahman IM, Zaki MEA, Al-Khdhairawi A, Abdelhamid MM, Alqaisi AM, Rahim LBA, Abu-Hussein B, El-Sheikh AAK, Abdelwahab SF, Hassan HA. In silico prediction of potential inhibitors for SARS-CoV-2 Omicron variant using molecular docking and dynamics simulation-based drug repurposing. J Mol Model 2023; 29:70. [PMID: 36808314 PMCID: PMC9939377 DOI: 10.1007/s00894-023-05457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND In November 2021, variant B.1.1.529 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified by the World Health Organization (WHO) and designated Omicron. Omicron is characterized by a high number of mutations, thirty-two in total, making it more transmissible than the original virus. More than half of those mutations were found in the receptor-binding domain (RBD) that directly interacts with human angiotensin-converting enzyme 2 (ACE2). This study aimed to discover potent drugs against Omicron, which were previously repurposed for coronavirus disease 2019 (COVID-19). All repurposed anti-COVID-19 drugs were compiled from previous studies and tested against the RBD of SARS-CoV-2 Omicron. METHODS As a preliminary step, a molecular docking study was performed to investigate the potency of seventy-one compounds from four classes of inhibitors. The molecular characteristics of the best-performing five compounds were predicted by estimating the drug-likeness and drug score. Molecular dynamics simulations (MD) over 100 ns were performed to inspect the relative stability of the best compound within the Omicron receptor-binding site. RESULTS The current findings point out the crucial roles of Q493R, G496S, Q498R, N501Y, and Y505H in the RBD region of SARS-CoV-2 Omicron. Raltegravir, hesperidin, pyronaridine, and difloxacin achieved the highest drug scores compared with the other compounds in the four classes, with values of 81%, 57%, 18%, and 71%, respectively. The calculated results showed that raltegravir and hesperidin had high binding affinities and stabilities to Omicron with ΔGbinding of - 75.7304 ± 0.98324 and - 42.693536 ± 0.979056 kJ/mol, respectively. Further clinical studies should be performed for the two best compounds from this study.
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Affiliation(s)
- Eslam A. R. Mohamed
- Department of Chemistry, Faculty of Science, Minia University, Minia, 61511 Egypt
| | - Islam M. Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, 61519 Minia Egypt
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Mahmoud M. Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Asyut, 71524 Egypt
| | - Ahmad M. Alqaisi
- Chemistry Department, University of Jordan, Amman, 11942 Jordan
- Present Address: School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287 USA
| | - Lyana binti Abd Rahim
- Department of Medicine, Hospital Tuanku Ampuan Najihah, Kuala Pilah, Negeri Sembilan Malaysia
| | - Bilal Abu-Hussein
- Albayader Specialty Hospital, Amman, Jordan
- Present Address: Department of General Surgery, Cumberland Infirmary Hospital, Carlisle, England
| | - Azza A. K. El-Sheikh
- Basic Health Sciences Department, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. 13 Box 84428, Riyadh, 11671 Saudi Arabia
| | - Sayed F. Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, PO Box 11099, Taif, 21944 Saudi Arabia
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, 82524 Egypt
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16
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Mohseni Afshar Z, Tavakoli Pirzaman A, Karim B, Rahimipour Anaraki S, Hosseinzadeh R, Sanjari Pireivatlou E, Babazadeh A, Hosseinzadeh D, Miri SR, Sio TT, Sullman MJM, Barary M, Ebrahimpour S. SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13. [PMID: 36766664 DOI: 10.3390/diagnostics13030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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17
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Chavda VP, Balar P, Vaghela D, Solanki HK, Vaishnav A, Hala V, Vora L. Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management. Vaccines (Basel) 2023; 11. [PMID: 36680006 DOI: 10.3390/vaccines11010160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes of omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts of India. Further studies are required for a better understanding of the new immersing SARS-CoV-2 subvariant of the omicron. They differ in the mutation of the spike proteins, which alters their attachment to the host receptor and hence modifies their virulence and adaptability. Delta variants have a great disastrous influence on the entire world, especially in India. While overcoming it, another mutant catches the pace. The Indian population is highly affected by omicron variants. It alters the entire management and diagnosis system against COVID-19. It demanded forcemeat in the health care system, both qualitatively and quantitively, to cope with the omicron wave. The alteration in spike protein, which is the major target of vaccines, leads to varied immunization against the subvariants. The efficacy of vaccines against the new variant was questioned. Every vaccine had a different shielding effect on the new variant. The hesitancy of vaccination was a prevalent factor in India that might have contributed to its outbreak. The prevalence of omicron, monkeypox, and tomato flu shared some similarities and distinct features when compared to their influence on the Indian population. This review emphasizes the changes omicron brings with it and how the Indian health care system outrage this dangerous variant.
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18
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Haque MA, Tanbir M, Ahamed B, Hossain MJ, Roy A, Shahriar M, Bhuiyan MA, Islam MR. Comparative Performance Evaluation of Personal Protective Measures and Antiviral Agents Against SARS-CoV-2 Variants: A Narrative Review. Clin Pathol 2023; 16:2632010X231161222. [PMID: 36938514 PMCID: PMC10014419 DOI: 10.1177/2632010x231161222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023]
Abstract
Scientists identified SARS-CoV-2 in December 2019 in Wuhan city of China. Soon after its identification, Covid-19 spreads almost everywhere. The World Health Organization (WHO) declared the Covid-19 outbreak as a pandemic on March 11, 2020. Countries are facing multiple waves due to the different variants of the coronavirus. Personal preventive measures, vaccines, and antiviral drugs are the approaches to control Covid-19. However, these approaches are being implemented in different countries at different levels because of the availability of personal protective measures and antiviral agents. The objective of this study was to evaluate the effectiveness of practicing measures to fight the Covid-19 pandemic. Here we searched relevant literature from PubMed and Scopus using the keywords such as personal protective measures, antiviral agents, and vaccine effectiveness. According to the present findings, protective measures were found comparatively less effective. Nevertheless, these measures can be used to limit the spreading of Covid-19. Antiviral agents can reduce the hospitalization rate and are more effective than personal protective measures. The most effective strategy against Covid-19 is early vaccination or multiple vaccination dose. The respective authorities should ensure equal distribution of vaccines, free availability of antiviral drugs, and personal protective measure in poor and developing countries. We recommend more studies to describe the effectiveness of practicing preventive measures and antiviral agents against recent variants of the coronavirus.
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Affiliation(s)
- Md Anamul Haque
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md Tanbir
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Bulbul Ahamed
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Arpita Roy
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, India
| | - Mohammad Shahriar
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | | | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
- Md Rabiul Islam, Department of Pharmacy, University of Asia Pacific, 74/A Green Road, Farmgate, Dhaka1205, Bangladesh.
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Kishimoto T, Tasato D, Nagasawa Y, Higure Y, Setoguti M, Tibana R, Yamashiro A, Miyazato T, Shokita H. Vaccination, regular exercise, and prevention of chronic lung disease reduce exacerbation of COVID-19 severity in northern Okinawa, Japan: A cross-sectional study. Environ Health Prev Med 2023; 28:73. [PMID: 38008444 PMCID: PMC10685076 DOI: 10.1265/ehpm.23-00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/27/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND As at June 14, 2023, the coronavirus disease 2019 (COVID-19) pandemic had affected more than 767 million people and caused more than 6.9 million deaths worldwide. This study aimed to clarify the lifestyle factors that influence the exacerbation of COVID-19 severity. METHODS This was a cross-sectional study of patients with COVID-19 whose severity classification of "moderate or severe" (COVID-19 exacerbation) was defined as an objective variable. The 1,353 participants were selected from 4,899 patients with COVID-19 between August 10, 2020 and December 10, 2022. Participants who underwent a specific health checkup before the date for a COVID-19 consultation were included. Using binominal logistic regression analysis, we evaluated the odds ratios (ORs) for COVID-19 exacerbation according to lifestyle-related factors. Limitations were discussed using a target trial emulation framework which clarifies problems in observational studies. RESULTS The explanatory variables extracted as factors that exacerbated COVID-19 severity were gender (OR [man vs. woman]: 2.533, 95% confidence interval [CI] 1.484-4.322); age (OR [50s vs. 10s, 20s, or 30s]: 4.858, 95% CI 2.319-10.177; OR [60s]: 9.738, 95% CI 4.355-21.777; OR [70s + 80s + 90s]: 8.327, 95% CI 3.224-21.507); and comorbid chronic lung disease (OR ['yes' vs. 'no']: 2.892, 95% CI 1.227-6.818). The explanatory variables extracted as factors that reduce the severity of COVID-19 were hospital consultation year (OR [2022, predominantly Omicron variant prevalent vs. 2020, predominantly Alpha variant prevalent]: 0.180, 95% CI 0.058-0.559); number of vaccinations (OR [2 doses vs. 0 or one doses]: 0.223, 95% CI 0.114-0.436; OR [≥3 doses vs. 0 or one doses]: 0.090, 95% CI 0.035-0.229); regular exercise (exercising ≥2 days/week ≥30 minutes each at an intensity that causes a slight sweat for ≥1 year) (OR ['yes' vs. 'no']: 0.458, 95% CI 0.242-0.866). CONCLUSIONS These results suggest the importance of vaccination, regular exercise, and prevention of chronic lung disease as measures against exacerbation of COVID-19 severity.
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Affiliation(s)
- Takuji Kishimoto
- Department of Health Screening, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Daisuke Tasato
- Department of Respiratory and Infectious Diseases, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Yoshitaka Nagasawa
- Department of Endocrinology, Metabolism and Dialysis, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Yuri Higure
- Department of Respiratory and Infectious Diseases, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Michika Setoguti
- Department of Respiratory and Infectious Diseases, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Rin Tibana
- Department of Respiratory and Infectious Diseases, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Akihiro Yamashiro
- Department of Health Screening, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Tatsuya Miyazato
- Department of Health Screening, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
| | - Hayashi Shokita
- Department of Gastroenterology, Okinawa North Medical Association Hospital, 1712-3 Nago City, Okinawa 905-8611, Japan
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20
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Elssaig EH, Alnour TM, Ullah MF, Ahmed-Abakur EH. Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern. Pol J Microbiol 2022; 71:577-587. [PMID: 36537060 PMCID: PMC9944972 DOI: 10.33073/pjm-2022-053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/12/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).
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Affiliation(s)
- Elmutuz H. Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
| | - Tarig M.S. Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan, T.M.S. Alnour, Department of Medical Laboratory Technology (FAMS), University of Tabuk, Saudi Arabia; Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia; Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan;
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Eltayib H. Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
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21
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Abstract
The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
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Affiliation(s)
- Anshika Srivastava
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| | - Jill A. Hollenbach
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
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22
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Chen Q, Zhu K, Liu X, Zhuang C, Huang X, Huang Y, Yao X, Quan J, Lin H, Huang S, Su Y, Wu T, Zhang J, Xia N. The Protection of Naturally Acquired Antibodies Against Subsequent SARS-CoV-2 Infection: A Systematic Review and Meta-Analysis. Emerg Microbes Infect 2022; 11:793-803. [PMID: 35195494 PMCID: PMC8920404 DOI: 10.1080/22221751.2022.2046446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The specific antibodies induced by SARS-CoV-2 infection may provide protection against a subsequent infection. However, the efficacy and duration of protection provided by naturally acquired immunity against subsequent SARS-CoV-2 infection remain controversial. We systematically searched for the literature describing COVID-19 reinfection published before 07 February 2022. The outcomes were the pooled incidence rate ratio (IRR) for estimating the risk of subsequent infection. The Newcastle–Ottawa Scale (NOS) was used to assess the quality of the included studies. Statistical analyses were conducted using the R programming language 4.0.2. We identified 19 eligible studies including more than 3.5 million individuals without the history of COVID-19 vaccination. The efficacy of naturally acquired antibodies against reinfection was estimated at 84% (pooled IRR = 0.16, 95% CI: 0.14-0.18), with higher efficacy against symptomatic COVID-19 cases (pooled IRR = 0.09, 95% CI = 0.07-0.12) than asymptomatic infection (pooled IRR = 0.28, 95% CI = 0.14-0.54). In the subgroup analyses, the pooled IRRs of COVID-19 infection in health care workers (HCWs) and the general population were 0.22 (95% CI = 0.16-0.31) and 0.14 (95% CI = 0.12-0.17), respectively, with a significant difference (P = 0.02), and those in older (over 60 years) and younger (under 60 years) populations were 0.26 (95% CI = 0.15–0.48) and 0.16 (95% CI = 0.14-0.19), respectively. The risk of subsequent infection in the seropositive population appeared to increase slowly over time. In conclusion, naturally acquired antibodies against SARS-CoV-2 can significantly reduce the risk of subsequent infection, with a protection efficacy of 84%. Registration number: CRD42021286222
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Kongxin Zhu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Xiaohui Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Chunlan Zhuang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Xingcheng Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Yue Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Xingmei Yao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Jiali Quan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Hongyan Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Shoujie Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Yingying Su
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Ting Wu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, School of Public Health, Xiamen University, Xiamen City, Fujian Province, People's Republic of China.,The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen City, Fujian Province, People's Republic of China
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23
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Sarkar MS, Madabhavi I. SARS-CoV-2 variants of concern: a review. Monaldi Arch Chest Dis 2022. [DOI: 10.4081/monaldi.2022.2337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The virus that causes severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family Coronaviridae. The SARS-CoV-2 virus is a positive sense, non-segmented single-strand RNA virus that causes coronavirus disease 2019 (COVID-19), which was first reported in December 2019 in Wuhan, China. COVID-19 is now a worldwide pandemic. Globally, several newer variants have been identified; however, only a few of them are of concern (VOCs). VOCs differ in terms of infectivity, transmissibility, disease severity, drug efficacy, and neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. VOCs reported from various parts of the world include B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron). These VOCs are the result of mutations, with some based on spike proteins. Mutations may also cause molecular diagnostic tests to fail to detect the few VOCs, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, Stanford variants database, and CINAHL from December 2019 to February 2022 using the following search terms: Variant of Concern, SARS-CoV-2, Omicron, etc. All types of research were chosen. All research methods were considered. This review discusses the various VOCs, as well as their mutations, infectivity, transmissibility, and neutralization efficacy.
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24
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022; 44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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25
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Konyak BM, Sharma M, Kharia S, Pandey RP, Chang C. A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies. Vaccines (Basel) 2022; 10:1468. [PMID: 36146546 PMCID: PMC9503441 DOI: 10.3390/vaccines10091468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/18/2023] Open
Abstract
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another variant of concern, with a total of 50 mutations, 30 of which are present on its spike protein alone. These mutations have led to immune escape and more transmissibility compared to other variants, including the Delta variant. A cluster of mutations (H655Y, N679K, and P681H) present in the Omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of the anti-viral and mAbs drugs. However, two monoclonal antibody drugs, Sotrovimab and Evusheld, are authorized for emergency use in COVID-19 patients. This virus is not fading away soon. The easiest solution and least expensive measure to fight against this pandemic are to follow the appropriate COVID-19 protocols. There is a need to strengthen the level of research for the development of potential vaccines and anti-viral drugs. It is also important to monitor and expand the genomic surveillance to keep track of the emergence of new variants, thus avoiding the spread of new diseases worldwide. This article highlights the emergence of the new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), and the vast number of mutations in its protein. In addition, recent advancements in drugs approved by FDA to treat COVID patients have been listed and focused in this paper.
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26
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Basavanna PN, Basavanagowdappa H, Siddaiah A, Patra A, Srinivasan V, Janardhan SM, Pasi R, Ravi KS. Omicron and vaccine booster dose – an update. Indian J Community Health 2022. [DOI: 10.47203/ijch.2022.v34i02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mutations in coronavirus is not unheard off. The variant, Omicron B.1.1.529 has overall 50 mutations and is considered as a variant of concern. Though the new variant has shown changes throughout its genome, S gene changes predominate. Significant changes in the S encoding gene, S gene, influences not only the transmissibility properties of SARS-CoV-2 but also the efficacy of existing vaccines. Increased transmissibility and ability of this variant to evade host immune responses conferred either due to past infections or due to vaccination driving increase in number of infections. However, the severity of the infections is low in comparison to its predecessors. A meta-analysis of ten studies analyzing the effect of COVID-19 vaccine booster dose, it was found studies report 10-to-42-fold increase in omicron neutralization. COVID appropriate behaviors, if followed rigidly can bring a meaningful change in the viral spread and resultant health impacts.
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27
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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28
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Mezger MC, Conzelmann C, Weil T, von Maltitz P, Albers DPJ, Münch J, Stamminger T, Schilling EM. Inhibitors of Activin Receptor-like Kinase 5 Interfere with SARS-CoV-2 S-Protein Processing and Spike-Mediated Cell Fusion via Attenuation of Furin Expression. Viruses 2022; 14:v14061308. [PMID: 35746781 PMCID: PMC9228453 DOI: 10.3390/v14061308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/18/2023] Open
Abstract
Screening of a protein kinase inhibitor library identified SB431542, targeting activin receptor-like kinase 5 (ALK5), as a compound interfering with SARS-CoV-2 replication. Since ALK5 is implicated in transforming growth factor β (TGF-β) signaling and regulation of the cellular endoprotease furin, we pursued this research to clarify the role of this protein kinase for SARS-CoV-2 infection. We show that TGF-β1 induces the expression of furin in a broad spectrum of cells including Huh-7 and Calu-3 that are permissive for SARS-CoV-2. The inhibition of ALK5 by incubation with SB431542 revealed a dose-dependent downregulation of both basal and TGF-β1 induced furin expression. Furthermore, we demonstrate that the ALK5 inhibitors SB431542 and Vactosertib negatively affect the proteolytic processing of the SARS-CoV-2 Spike protein and significantly reduce spike-mediated cell-cell fusion. This correlated with an inhibitory effect of ALK5 inhibition on the production of infectious SARS-CoV-2. Altogether, our study shows that interference with ALK5 signaling attenuates SARS-CoV-2 infectivity and cell-cell spread via downregulation of furin which is most pronounced upon TGF-β stimulation. Since a TGF-β dominated cytokine storm is a hallmark of severe COVID-19, ALK5 inhibitors undergoing clinical trials might represent a potential therapy option for COVID-19.
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Affiliation(s)
- Maja C. Mezger
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Dan P. J. Albers
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (C.C.); (T.W.); (P.v.M.); (D.P.J.A.); (J.M.)
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
- Correspondence: ; Tel.: +49-731-50065100
| | - Eva-Maria Schilling
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany; (M.C.M.); (E.-M.S.)
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29
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Luna N, Muñoz M, Ramírez AL, Patiño LH, Castañeda SA, Ballesteros N, Ramírez JD. Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries. Viruses 2022; 14:v14061234. [PMID: 35746705 PMCID: PMC9230695 DOI: 10.3390/v14061234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/21/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage's genomic and epidemiological characteristics. However, in South America, this variant's arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.
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Affiliation(s)
- Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Angie L. Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Luz H. Patiño
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Sergio Andres Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología—UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (N.L.); (M.M.); (A.L.R.); (L.H.P.); (S.A.C.); (N.B.)
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or
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30
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Szargut M, Cytacka S, Serwin K, Urbańska A, Gastineau R, Parczewski M, Ossowski A. SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains. Viruses 2022; 14:1230. [PMID: 35746701 PMCID: PMC9227152 DOI: 10.3390/v14061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/14/2022] [Accepted: 06/04/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.
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Islam F, Dhawan M, Nafady MH, Emran TB, Mitra S, Choudhary OP, Akter A. Understanding the omicron variant (B.1.1.529) of SARS-CoV-2: Mutational impacts, concerns, and the possible solutions. Ann Med Surg (Lond) 2022; 78:103737. [PMID: 35571678 PMCID: PMC9078452 DOI: 10.1016/j.amsu.2022.103737] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 01/18/2023] Open
Abstract
Despite many nations' best efforts to contain the so-called COVID-19 pandemic, the emergence of the SARS-CoV-2 Omicron strain (B.1.1.529) has been identified as a serious concern. After more than two years of COVID-19 pandemic and more than a year of worldwide vaccination efforts, the globe will not be free of COVID-19 variants such as Delta and Omicron variants. According to current statistics, the Omicron variant has more than 30 mutations when contrasted to other VOCs such as Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). High numbers of changes, particularly in the spike protein (S-Protein), raise worries about the virus's capacity to resist pre-existing immunity acquired by vaccination or spontaneous infection and antibody-based therapy. The Omicron variant raised international concerns, resuming travel bans and coming up with many questions about its severity, transmissibility, testing, detection, and vaccines efficiency against it. Additionally, inadequate health care infrastructures and many immunocompromised individuals increase the infection susceptibility. The current status of low vaccination rates will play a significant role in omicron spreading and create a fertile ground for producing new variants. As a result, this article emphasizes the mutational changes and their consequences. In addition, the potential preventing measures have been examined in detail. In South Africa, WHO designated the first cases of the SARS-CoV-2 Omicron variant (B.1.1.529). This variation is notable for having an extremely high number of spike protein mutations. Omicron has about 50 mutations, particularly 32 spike protein mutations. Omicron considers the most common variant in South Africa as an alternative to Delta.
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Kumar A, Parihar A, Panda U, Parihar DS. Microfluidics-Based Point-of-Care Testing (POCT) Devices in Dealing with Waves of COVID-19 Pandemic: The Emerging Solution. ACS Appl Bio Mater 2022; 5:2046-2068. [PMID: 35473316 PMCID: PMC9063993 DOI: 10.1021/acsabm.1c01320] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/11/2022] [Indexed: 02/08/2023]
Abstract
Recent advances in microfluidics-based point-of-care testing (POCT) technology such as paper, array, and beads have shown promising results for diagnosing various infectious diseases. The fast and timely detection of viral infection has proven to be a critical step for deciding the therapeutic outcome in the current COVID-19 pandemic, which in turn not only enhances the patient survival rate but also reduces the disease-associated comorbidities. In the present scenario, rapid, noninvasive detection of the virus using low cost and high throughput microfluidics-based POCT devices embraces the advantages over existing diagnostic technologies, for which a centralized lab facility, expensive instruments, sample pretreatment, and skilled personnel are required. Microfluidic-based multiplexed POCT devices can be a boon for clinical diagnosis in developing countries that lacks a centralized health care system and resources. The microfluidic devices can be used for disease diagnosis and exploited for the development and testing of drug efficacy for disease treatment in model systems. The havoc created by the second wave of COVID-19 led several countries' governments to the back front. The lack of diagnostic kits, medical devices, and human resources created a huge demand for a technology that can be remotely operated with single touch and data that can be analyzed on a phone. Recent advancements in information technology and the use of smartphones led to a paradigm shift in the development of diagnostic devices, which can be explored to deal with the current pandemic situation. This review sheds light on various approaches for the development of cost-effective microfluidics POCT devices. The successfully used microfluidic devices for COVID-19 detection under clinical settings along with their pros and cons have been discussed here. Further, the integration of microfluidic devices with smartphones and wireless network systems using the Internet-of-things will enable readers for manufacturing advanced POCT devices for remote disease management in low resource settings.
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Affiliation(s)
- Avinash Kumar
- Department of Mechanical Engineering,
Indian Institute of Information Technology Design & Manufacturing
Kancheepuram, Chennai 600127, India
| | - Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials,
CSIR-Advanced Materials and Processes Research Institute
(AMPRI), Hoshangabad Road, Bhopal, Madhya Pradesh 462026,
India
| | - Udwesh Panda
- Department of Mechanical Engineering,
Indian Institute of Information Technology Design & Manufacturing
Kancheepuram, Chennai 600127, India
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Halder B. Evaluating the risk factor of novel public health disaster “Omicron” variant: an Indian prospective. Model Earth Syst Environ 2022. [PMID: 35469271 PMCID: PMC9022065 DOI: 10.1007/s40808-022-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/01/2022] [Indexed: 01/18/2023]
Abstract
COVID-19 epidemic is destroying world health and gradually increasing the mortality rate. The economy was also affected due to the spreading of the newly developed virus. The named COVID-19 progressively develops and affecting in the human body. The new Delta variant Omicron is first noticed in South Africa. After that many cases are recorded worldwide and finally India has recorded the first case of Omicron on 24 November 2021 from Karnataka. This study is to identify the Omicron variant affected states and UTs in India. The graphical results indicate the geographical location-wise spreading of the Omicron virus in India. The destibution of confirmed and death cases indicate the speed of spreading this health disaster in India. After that total of 781 cases were registered and 241 people were discharged from this. Mostly affected states and UTs are Delhi, Maharashtra, Karnataka, Telangana, Kerala, and Rajasthan, where Tripura, Bihar, Jharkhand, Assam, and Sikkim have not any Omicron recorded. Delhi (238), Maharashtra (167), Gujarat (73), and Kerala (65), where Himachal Pradesh, Goa, Manipur, and Ladakh have recorded one case each. The correlation between total cases and discharge is very high and the R2 value is strong positive (0.80). This situation is indicating that Omicron is gripped by public health. If we don’t maintain the social distancing and WHO notified guidelines, this condition may more harmful for human livelihood and increase the health emergency very soon.
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Chekol Abebe E, Tiruneh G/Medhin M, Behaile T/Mariam A, Asmamaw Dejenie T, Mengie Ayele T, Tadele Admasu F, Tilahun Muche Z, Asmare Adela G. Mutational Pattern, Impacts and Potential Preventive Strategies of Omicron SARS-CoV-2 Variant Infection. Infect Drug Resist 2022; 15:1871-1887. [PMID: 35450114 PMCID: PMC9017707 DOI: 10.2147/idr.s360103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/08/2022] [Indexed: 01/18/2023] Open
Abstract
Since the emergence of COVID 19, the authentic SARS-CoV-2 has evolved into a range of novel variants that are of more global concern. In late November 2021, the Omicron (lineage B.1.1.529) variant was identified as a new variant and considered as the fifth variant of concern. Omicron harbors a genetic profile that is exceedingly unusual, with a huge number of mutations. Above thirty mutations are localized in the S protein, while some are found in other structural and non-structural proteins. Half of the mutations in the S protein are in the RBD, which is a major target of antibodies, showing that Omicron mutations may affect antibody binding affinity to the S protein. The Omicron variant has been found to result in immune escape, therapeutic or vaccine escape, as well as increased transmissibility and reinfection risk, explaining its rapid international spread that sparks a global alarm even more serious than the previously reported variants. Omicron has the capability to bypass at least some of the multi-faceted immune responses induced by prior infection or vaccination. It is shown to extensively escape neutralizing antibodies while evading cell mediated immune defense to a lesser extent. The efficacy of COVID 19 vaccines against Omicron variant is decreased with primary vaccination, showing that the vaccine is less efficient in preventing Omicron infections. However, after receiving a booster vaccine dose, the immunological response to Omicron significantly improved and hold promising results. Despite the mild nature of the disease in most vaccinated people, the rapid spread of Omicron, as well as the increased risk of re-infection, poses yet another major public health concern. Therefore, effort should be devoted to maintaining the existing COVID 19 preventive measures as well as developing new vaccination strategies in order to control the fast dissemination of Omicron.
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Affiliation(s)
- Endeshaw Chekol Abebe
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Markeshaw Tiruneh G/Medhin
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Awgichew Behaile T/Mariam
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Teklie Mengie Ayele
- Department of Pharmacy, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Fitalew Tadele Admasu
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Zelalem Tilahun Muche
- Department of Physiology, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Getachew Asmare Adela
- Department of Reproductive Health and Nutrition, School of Public Health, Wolaita Sodo University, Wolaita Sodo, Ethiopia
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Vo GV, Bagyinszky E, An SSA. COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development. Microorganisms 2022; 10:microorganisms10030598. [PMID: 35336173 PMCID: PMC8954257 DOI: 10.3390/microorganisms10030598] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
In the two years since the SARS-CoV-2 pandemic started, it has caused over 5 million deaths and 400 million infected cases, and the world continues to be on high alert for COVID-19. Among the variants of interest and concern of SARS-CoV-2, the current Omicron (B.1.1.529) and stealth Omicron (BA.2) raised serious concerns due to rapid rates of infection caused by numerous mutations in the spike protein, which could escape from the antibody-mediated neutralization and increase the risk of reinfections. Hence, this work aims to describe the most relevant mutations in the SARS-CoV-2 spike protein, discuss vaccine against variant of concerns, describe rare adverse events after COVID-19 vaccination, introduce the most available promising COVID-19 vaccine candidates, and provide few perspectives of the future variants.
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Affiliation(s)
- Giau Van Vo
- Department of Biomedical Engineering, School of Medicine, Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam;
- Research Center for Genetics and Reproductive Health (CGRH), School of Medicine, Vietnam National University, Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam
- Vietnam National University Ho Chi Minh City (VNU-HCM), Ho Chi Minh City 70000, Vietnam
| | - Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam 13120, Korea
- Correspondence: (E.B.); (S.S.A.A.)
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam 13120, Korea
- Correspondence: (E.B.); (S.S.A.A.)
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Samanta A, Alam SSM, Ali S, Hoque M. Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant. EXCLI J 2022; 21:610-620. [PMID: 35651657 PMCID: PMC9149974 DOI: 10.17179/excli2022-4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/25/2022] [Indexed: 01/18/2023]
Abstract
The newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has steered concerns across the world due to the possession of a large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in spike (S) protein alone. The viral infectivity is determined mainly by the ability of S protein Receptor Binding Domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARS-CoV-2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. This unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants.
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Affiliation(s)
- Arijit Samanta
- Applied Bio-Chemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | | | - Safdar Ali
- Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | - Mehboob Hoque
- Applied Bio-Chemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
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Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G, Chakraborty C. Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. GeroScience 2022. [PMID: 35258772 DOI: 10.1007/s11357-022-00532-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant has been detected in nearly 150 countries. We analyzed the mutational landscape of Omicron throughout the genome, focusing the S-glycoprotein. We also evaluated mutations in the antibody-binding regions and observed some important mutations overlapping those of previous variants including N501Y, D614G, H655Y, N679K, and P681H. Various new receptor-binding domain mutations were detected, including Q493K, G496S, Q498R, S477N, G466S, N440K, and Y505H. New mutations were found in the NTD (Δ143-145, A67V, T95I, L212I, and Δ211) including one new mutation in fusion peptide (D796Y). There are several mutations in the antibody-binding region including K417N, E484A, Q493K, Q498R, N501Y, and Y505H and several near the antibody-binding region (S477N, T478K, G496S, G446S, and N440K). The impact of mutations in regions important for the affinity between spike proteins and neutralizing antibodies was evaluated. Furthermore, we examined the effect of significant antibody-binding mutations (K417N, T478K, E484A, and N501Y) on antibody affinity, stability to ACE2 interaction, and possibility of amino acid substitution. All the four mutations destabilize the antibody-binding affinity. This study reveals future directions for developing neutralizing antibodies against the Omicron variant.
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Al-Tawfiq JA, Hoang VT, Le Bui N, Chu DT, Memish ZA. The Emergence of the Omicron (B.1.1.529) SARS-CoV-2 Variant: What is the Impact on the Continued Pandemic? J Epidemiol Glob Health 2022; 12:143-146. [PMID: 35089588 PMCID: PMC8795715 DOI: 10.1007/s44197-022-00032-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Van-Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Nhat Le Bui
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Ziad A Memish
- Director Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia.
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Araf Y, Akter F, Tang YD, Fatemi R, Parvez SA, Zheng C, Hossain G. Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines. J Med Virol 2022; 94:1825-1832. [PMID: 35023191 PMCID: PMC9015557 DOI: 10.1002/jmv.27588] [Citation(s) in RCA: 430] [Impact Index Per Article: 215.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 01/18/2023]
Abstract
Currently, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has spread worldwide as an Omicron variant. This variant is a heavily mutated virus and designated as a variant of concern by the World Health Organization (WHO). WHO cautioned that the Omicron variant of SARS‐CoV‐2 held a very high risk of infection, reigniting anxieties about the economy's recovery from the 2‐year pandemic. The extensively mutated Omicron variant is likely to spread internationally, posing a high risk of infection surges with serious repercussions in some areas. According to preliminary data, the Omicron variant of SARS‐CoV‐2 has a higher risk of reinfection. On the other hand, whether the current COVID‐19 vaccines could effectively resist the new strain is still under investigation. However, there is very limited information on the current situation of the Omicron variant, such as genomics, transmissibility, efficacy of vaccines, treatment, and management. This review focused on the genomics, transmission, and effectiveness of vaccines against the Omicron variant, which will be helpful for further investigation of a new variant of SARS‐CoV‐2. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron variant is a heavily mutated virus and designated as a variant of concern. This variant may evade vaccine‐induced immunity. There might have increased risk of SARS‐CoV‐2 reinfection by the Omicron variant.
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Affiliation(s)
- Yusha Araf
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Fariya Akter
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Rabeya Fatemi
- Department of Genetic Engineering and Biotechnology, East-West University, Dhaka, 1212, Bangladesh
| | - Sorwer Alam Parvez
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Golzar Hossain
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
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