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Rath SL, Padhi AK, Mandal N. Scanning the RBD-ACE2 molecular interactions in Omicron variant. Biochem Biophys Res Commun 2022; 592:18-23. [PMID: 35007846 PMCID: PMC8732900 DOI: 10.1016/j.bbrc.2022.01.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [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] [Received: 12/22/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022]
Abstract
The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.
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Affiliation(s)
- Soumya Lipsa Rath
- National Institute of Technology, Warangal, Telangana, 506004, India.
| | - Aditya K Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Nabanita Mandal
- National Institute of Technology, Warangal, Telangana, 506004, India
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202
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Narikot A, Pardeshi VC, Shubha AM, Iyengar A, Vasudevan A. Deciphering the mutation spectrum in south Indian children with congenital anomalies of the kidney and urinary tract. BMC Nephrol 2022; 23:1. [PMID: 34979951 PMCID: PMC8722277 DOI: 10.1186/s12882-021-02628-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/17/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) cover a spectrum of structural malformations that result from aberrant morphogenesis of kidney and urinary tract. It is the most prevalent cause of kidney failure in children. Hence, it is important from a clinical perspective to unravel the molecular etiology of kidney and urinary tract malformations. Causal variants in genes that direct various stages of development of kidney and urinary tract in fetal life have been identified in 5-20% of CAKUT patients from Western countries. Recent advances in next generation sequencing technology and decreasing cost offer the opportunity to characterize the genetic profile of CAKUT in Indian population and facilitate integration of genetic diagnostics in care of children with CAKUT. METHODS Customized targeted panel sequencing was performed to identify pathogenic variants in 31 genes known to cause human CAKUT in 69 south Indian children with CAKUT. The NGS data was filtered using standardized pipeline and the variants were classified using ACMG criteria. Genotype and phenotype correlations were performed. RESULTS The cohort consisted of children mostly with posterior urethral valve (PUV) (39.1%), vesico-ureteric reflux (VUR) (33.3%) and multi-cystic dysplastic kidney (MCDK) (7.2%). No pathogenic or likely pathogenic variants were identified in the study. Most of our variants (n = 39, 60%) were variants of unknown significance with 25.6% (10/39) of them were identified as potentially damaging but were novel variants. CONCLUSIONS The present study did not identify any disease-causing monogenic variants in the cohort. The absence of genetic cause may be due to limitations of panel-based testing and also due to higher proportion of children with abnormalities in lower urinary tract than hypodysplasia of kidneys. Clinical, larger targeted panel or whole exome sequencing may be a better method to characterize the genetic profile of Indians patients with CAKUT.
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Affiliation(s)
- Ambili Narikot
- Divsion of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bengaluru, India
| | - Varsha Chhotusing Pardeshi
- Divsion of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bengaluru, India
| | - A M Shubha
- Department of Pediatric Surgery, St. John's Medical College, Bengaluru, India
| | - Arpana Iyengar
- Department of Pediatric Nephrology, St. John's Medical College, Bengaluru, 560034, India
| | - Anil Vasudevan
- Divsion of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bengaluru, India.
- Department of Pediatric Nephrology, St. John's Medical College, Bengaluru, 560034, India.
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203
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Dhawan M, Priyanka, Sahni A, Choudhary OP. Vaccine inequity and hesitancy: Dual factors in the emergence of novel SARS-CoV-2 variants. Ann Med Surg (Lond) 2022; 73:103186. [PMID: 34961829 PMCID: PMC8695513 DOI: 10.1016/j.amsu.2021.103186] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
- The Trafford Group of Colleges, Manchester, WA14 5PQ, UK
| | - Priyanka
- Independent Researcher, 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India
| | - Ashima Sahni
- Department Political Science, Kanya Maha Vidyalaya, (Autonomous College), Jalandhar, 144004, Punjab, India
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India
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204
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Choudhary OP, Ali RK, Maulud SQ, Dhawan M, Mohammed TA. Will the next spillover pandemic be deadlier than the COVID-19?: A wake-up call. Int J Surg 2022; 97:106208. [PMID: 34995807 PMCID: PMC8730376 DOI: 10.1016/j.ijsu.2021.106208] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India Department of Biology, College of Education, Salahaddin University, Erbil, Iraq Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India The Trafford Group of Colleges, Manchester, WA14 5PQ, UK Dental Basic Science Department, College of Dentistry, University of Duhok, Duhok, Iraq
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205
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Simnani FZ, Singh D, Kaur R. COVID-19 phase 4 vaccine candidates, effectiveness on SARS-CoV-2 variants, neutralizing antibody, rare side effects, traditional and nano-based vaccine platforms: a review. 3 Biotech 2022; 12:15. [PMID: 34926119 PMCID: PMC8665991 DOI: 10.1007/s13205-021-03076-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Received: 06/18/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has endangered world health and the economy. As the number of cases is increasing, different companies have started developing potential vaccines using both traditional and nano-based platforms to overcome the pandemic. Several countries have approved a few vaccine candidates for emergency use authorization (EUA), showing significant effectiveness and inducing a robust immune response. Oxford-AstraZeneca, Pfizer-BioNTech's BNT162, Moderna's mRNA-1273, Sinovac's CoronaVac, Johnson & Johnson, Sputnik-V, and Sinopharm's vaccine candidates are leading the race. However, the SARS-CoV-2 is constantly mutating, making the vaccines less effective, possibly by escaping immune response for some variants. Besides, some EUA vaccines have been reported to induce rare side effects such as blood clots, cardiac injury, anaphylaxis, and some neurological effects. Although the COVID-19 vaccine candidates promise to overcome the pandemic, a more significant and clear understanding is needed. In this review, we brief about the clinical trial of some leading candidates, their effectiveness, and their neutralizing effect on SARS-CoV-2 variants. Further, we have discussed the rare side effects, different traditional and nano-based platforms to understand the scope of future development.
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Affiliation(s)
| | - Dibyangshee Singh
- KIIT School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Ramneet Kaur
- Department of Life Sciences, RIMT University, Ludhiana, Punjab India
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206
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Noor R, Shareen S, Billah M. COVID-19 vaccines: their effectiveness against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants. Bull Natl Res Cent 2022; 46:96. [PMID: 35431535 PMCID: PMC8991668 DOI: 10.1186/s42269-022-00787-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/31/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND The world has been suffering from the COVID-19 pandemic (officially declared by WHO in March 2020), caused by the severe acute respiratory β-coronavirus 2 (SARS-CoV-2) since the last week of December 2019. The disease was initially designated as a Public Health Emergency of International Concern on January 30, 2020. In order to protect the health of mass public, an array of research on drugs and vaccines against SARS-CoV-2 has been conducted globally. However, the emerging variants of SARS-CoV-2, i.e., Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) variants which evolved in late 2020 and the Omicron variant (B.1.1.529) which emerged in November 2021 along with its subvariant BA.2 which was first identified in India and South Africa in late December 2021, have raised the doubt about the efficiency of the currently used vaccines especially in terms of the consistent potential to produce neutralizing antibodies targeting the viral spike (S) protein. MAIN BODY OF THE ABSTRACT The present review discussed the functional details of major vaccines regarding their efficiency against such variants during the pandemic. Overall, the mRNA vaccines have shown around 94% effectiveness; the adenovector vaccine showed approximately 70% efficacy, whereas Sputnik V vaccines showed around 92% effectiveness; the inactivated whole-virus vaccine CoronaVac/PiCoVacc and BBIBP-CorV showed a varying effectiveness of 65-86% according to the geographic locations; the subunit vaccine NVX-CoV2373 has shown 60-89% effectiveness along with the global regions against the wild-type SARS-CoV-2 strain. However, reduced effectiveness of these vaccines against the SARS-CoV-2 variants was noticed which is suggestive for the further administration of booster dose. SHORT CONCLUSION Maximum variants of SARS-CoV-2 emerged during the second wave of COVID-19; and extensive studies on the viral genomic sequences from all geographical locations around the world have been conducted by an array of groups to assess the possible occurrence of mutations(s) specially within the receptor binding domain of the viral spike (S) protein. Mutational similarities and the new or critical mutations within all variants have been clearly identified so far. The study of effectiveness of the currently used vaccines is also ongoing. The persistence of memory B cell action and the other immune components as well as the administration of booster dose is expected to mitigate the disease.
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Affiliation(s)
- Rashed Noor
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Bangladesh (IUB), Plot 16, Block B, Aftabuddin Ahmed Road, Bashundhara, Dhaka, 1229 Bangladesh
| | - Saadia Shareen
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Bangladesh (IUB), Plot 16, Block B, Aftabuddin Ahmed Road, Bashundhara, Dhaka, 1229 Bangladesh
| | - Muntasir Billah
- Department of Cardiology, Kolling Institute of Medical Research, Northern Sydney Local Health District, St Leonards, NSW 2065 Australia
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207
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Peisahovics F, Rohaim MA, Munir M. Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns. Eur J Cell Biol 2022; 101:151275. [PMID: 36156414 PMCID: PMC9484102 DOI: 10.1016/j.ejcb.2022.151275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 06/18/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 02/08/2023] Open
Abstract
Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination campaigns. The spike (S) glycoprotein of SARS-CoV-2 demonstrated the greatest immunogenicity and amino acid substitution diversity owing to its importance in the interaction with human angiotensin receptor 2 (hACE2). The S protein consistently emerges as an amino acid substitution (AAS) hotspot in all six lineages, however, in Omicron this enrichment is significantly higher. This study attempts to design and validate a method of mapping S-protein substitution profile across variants to identify the conserved and AAS regions. A substitution matrix was created based on publicly available databases, and the substitution localization was illustrated on a cryo-electron microscopy generated S-protein model. Our analyses indicated that the diversity of N-terminal (NTD) and receptor-binding (RBD) domains exceeded that of any other regions but still contained extended low substitution density regions particularly considering significantly broader substitution profiles of Omicron BA.2 and BA.4/5. Finally, the substitution matrix was compared to a random sample alignment of variant sequences, revealing discrepancies. Therefore, it was suggested to improve matrix accuracy by processing a large number of S-protein sequences using an automated algorithm. Several critical immunogenic and receptor-interacting residues were identified in the conserved regions within NTD and RBD. In conclusion, the structural and topological analysis of S proteins of SARS-CoV-2 variants highlight distinctive amino acid substitution patterns which may be foundational in predicting future variants.
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Affiliation(s)
| | | | - Muhammad Munir
- Correspondence to: Lancaster University, Lancaster, United Kingdom
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208
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Coccia M. Preparedness of countries to face COVID-19 pandemic crisis: Strategic positioning and factors supporting effective strategies of prevention of pandemic threats. Environ Res 2022; 203:111678. [PMID: 34280421 PMCID: PMC8284056 DOI: 10.1016/j.envres.2021.111678] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 05/03/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) continues to generate a constant pandemic threat with new mutations of the viral agent (SARS-CoV-2) that create socioeconomic issues. One of the fundamental problems is the evaluation of the preparedness of countries to cope with COVID-19 pandemic crisis to detect and support factors associated with the reduction of mortality and the growth of vaccinations in society. The study here confronts this problem by developing two basic indexes, which measure the performance of countries to face pandemic threats. In particular, the Index r (as resilience) detects the countries having the best performance in the reduction of the negative impact of mortality related to COVID-19 pandemic and the Index p (as preparedness and prevention) assesses best-performer countries to support COVID-19 vaccinations in order to constrain future pandemic threats and support the recovery of socioeconomic systems. Index of resilience is a composite measure based on three indicators associated with COVID-19, given by average mortality, hospital occupancy and Intensive Care Units occupancy per 100 000 people, producing an overall score; Index of preparedness/prevention is a composite measure of two indicators related to COVID-19 vaccinations (i.e., doses of vaccines administered and total vaccinates per 100 000 people), producing also an overall score of performance. The application of these indexes on a case study of European countries, having a homogenous socioeconomic area, shows the strategic positioning of countries to cope with a major pandemic threat. Findings reveal that all countries have some weaknesses and no country has a high preparedness to cope with a major epidemic or pandemic. Moreover, results suggest that best-performer countries to cope with COVID-19 pandemic crisis have a smaller size of population and/or better public governance, associated with high expenditures in health system. These indexes can help policymakers for designing effective strategies to improve preparedness and prevention of countries to face future pandemic threats.
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Affiliation(s)
- Mario Coccia
- CNR -- National Research Council of ITALY, Collegio Carlo Alberto, Via Real Collegio, 30-10024, Moncalieri, Torino, Italy.
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209
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Dhawan M, Priyanka, Parmar M, Angural S, Choudhary OP. Convalescent plasma therapy against the emerging SARS-CoV-2 variants: Delineation of the potentialities and risks. Int J Surg 2022; 97:106204. [PMID: 34974199 PMCID: PMC8717699 DOI: 10.1016/j.ijsu.2021.106204] [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] [Received: 10/02/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has resulted in a catastrophic pandemic and severely impacted people's livelihoods worldwide. In addition, the emergence of SARS-CoV-2 variants has posed a severe threat to humankind. Due to the dearth of therapeutic options during the commencement of the pandemic, convalescent plasma therapy (CPT) played a significant part in the management of patients with severe form of COVID-19. Several recent studies have proposed various protective effects of CPT, such as antiviral, anti-inflammatory, anti-thrombotic, and immunomodulatory actions, curtailing the devastating consequences of the SARS-CoV-2 infection. On the contrary, several clinical studies have raised some serious concerns about the effectiveness and reliability of CPT in the management of patients with COVID-19. The protective effects of CPT in severely ill patients are yet to be proved. Moreover, the emergence of SARS-CoV-2 variants has raised concerns about the effectiveness of CPT against COVID-19. Therefore, to establish concrete evidence of the efficacy of CPT and adjudicate its inclusion in the management of COVID-19, an updated review of present literature is required, which could help in the development of an efficient therapeutic regimen to treat COVID-19 amid the emergence of new viral variants.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India,The Trafford Group of Colleges, Manchester, WA14 5PQ, UK
| | - Priyanka
- Independent Researcher, 07, Type IV Quarter, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India
| | - Manisha Parmar
- Department of Veterinary Microbiology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, Punjab, India
| | - Steffy Angural
- Department of Medical Lab Technology, Faculty of Applied Health Sciences, GNA University, Phagwara-Hoshiarpur Road, Sri Hargobindgarh, 144401, Punjab, India,Corresponding author
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy and Histology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, 796015, Mizoram, India,Corresponding author
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210
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Lina B. [The different phases of molecular and antigenic evolution of SARS-CoV-2 viruses during the 20 months following its emergence]. Bull Acad Natl Med 2022; 206:87-99. [PMID: 34866635 PMCID: PMC8629187 DOI: 10.1016/j.banm.2021.11.002] [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] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023]
Abstract
From its emergence in December 2019 and until the end of the fourth pandemic wave in October 2021, SARS-CoV-2 circulation has been associated with significant molecular evolutions of the virus. These were linked to mutations that have led to new virus linages with replication advantages as a result of increased transmission, or partial immune escape in the context of progressively increasing global immunisation. The pandemic context with large scale epidemics massive outbreaks observed in highly populated areas has favoured this emergence of "variants". During the 20 months period, at least three evolutionary phases have been observed, leading to the situation observed in October 2021. For the first time, an unprecedented worldwide surveillance effort has been conducted to monitor the circulation of the emerging virus, with rapid data sharing. This molecular surveillance system has provided an accurate description of the circulating viruses, and their evolution. The implementation of these tools and skills able to provide SARS-CoV-2 molecular epidemiological data has upgraded the global capacity for surveillance worldwide, and may allow us to be better prepared for a future pandemic episode.
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Affiliation(s)
- B. Lina
- Laboratoire de virologie des HCL, institut des agents infectieux (IAI), CNR des virus à transmission respiratoire (dont la grippe), groupement hospitalier Nord, hôpital de la Croix Rousse, 103, grande rue de la Croix Rousse, 69317 Lyon cedex 04, France,Inserm U1111, laboratoire Virpath, CNRS UMR 5308, ENS de Lyon, UCBL, centre international de recherche en infectiologie (CIRI), université de Lyon, 7–11, rue Guillaume-Paradin, 69372 Lyon cedex 08, France
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211
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Ben-Tov A, Lotan R, Gazit S, Chodick G, Perez G, Mizrahi-Reuveni M, Patalon T. Dynamics in COVID-19 symptoms during different waves of the pandemic among children infected with SARS-CoV-2 in the ambulatory setting. Eur J Pediatr 2022; 181:3309-3318. [PMID: 35778524 PMCID: PMC9395901 DOI: 10.1007/s00431-022-04531-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/22/2022] [Accepted: 06/12/2022] [Indexed: 12/04/2022]
Abstract
UNLABELLED The aim of this real-life, big data population-based study was to evaluate differences in symptomatic presentation of children infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) between the third and fourth waves of the pandemic in Israel, dominated by the Alpha and Delta variants, respectively. Our cohort included all children and adolescents, members of the second-largest Health Maintenance Organization in Israel that had positive real-time polymerase chain reaction (RT-PCR) test during the third and fourth waves of the pandemic (December 1, 2020, to April 30, 2021, and June 1, 2021, to October 10, 2021, respectively). A total of 32,485 and 44,130 children and adolescents in the third and fourth waves were included in the final analysis. The rate of children with symptomatic disease among patients with documented SARS-CoV-2 infection was higher in the fourth wave compared to the third wave (49.9% vs. 37.5%). The most commonly reported symptom and the only symptom that substantially differed between waves was fever, with 33% of SARS-CoV-2 infected children in the fourth wave vs. 13.6% in the third wave. Preschool children had the lowest prevalence of febrile illness compared to other age groups. CONCLUSION Children and adolescents infected during the fourth wave of the pandemic in Israel, a Delta-dominant period, had a significantly higher rate of symptomatic febrile illness than the Alpha-dominant period. This phenomenon occurred across all age groups. WHAT IS KNOWN • There are differences in COVID-19 severity among adults and children during different waves of the pandemic. • There is a paucity of data regarding symptomatic characteristics in children in large-scale cohorts aside from hospital settings. WHAT IS NEW • In a time period dominated by the Delta variant, there were substantially more children with symptomatic disease and febrile illness compared to a period dominated by the alpha variant. • Preschool children had the lowest rate of febrile illness among all age groups.
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Affiliation(s)
- Amir Ben-Tov
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, Israel
- Pediatric Gastroenterology Unit, Dana-Dwek Children’s Hospital, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roni Lotan
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Sivan Gazit
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Gabriel Chodick
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Tel Aviv, Israel
| | - Galit Perez
- Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Tel Aviv, Israel
| | | | - Tal Patalon
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, Israel
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212
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Haque A, Pant AB. Mitigating Covid-19 in the face of emerging virus variants, breakthrough infections and vaccine hesitancy. J Autoimmun 2022; 127:102792. [PMID: 34995958 PMCID: PMC8719928 DOI: 10.1016/j.jaut.2021.102792] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [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] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/06/2023]
Abstract
The emergence and rapid global spread of the new Delta and, more recently, Omicron variants of SARS-CoV-2 pose a daunting public health emergency. Being an RNA virus, the Covid-19 virus is continuing to mutate, resulting in the emergence of new variants with high transmissibility, such as the recently discovered Omicron variant. In this paper, we consider the conditions that may facilitate viral mutations and the emergence of variants with the ability to evade immunity. Here, we have discussed the importance of vaccination with the currently available vaccines. These vaccines are highly effective at preventing serious disease, hospitalization, and death from Covid-19. However, the antibody response induced by these vaccines is short-lasting and there are reports of breakthrough infections. A stable and persistent interaction between T follicular helper cells and germinal center B cells is needed for robust B cell memory response. We discussed the potential reasons behind the breakthrough infections and underscored the importance of developing better second-generation vaccines that may not necessitate frequent booster immunizations and are preventive in nature. This may involve the development of multivalent vaccines and creating vaccines against other viral proteins including conserved proteins. Vaccine hesitancy remains a notable hurdle for implementing vaccination. Furthermore, we recommend different approaches to increase vaccine acceptance, which is a critical translational component of a successful vaccine strategy. These perspectives on overcoming the pandemic's current challenges provide strategies to contain SARS-CoV-2 globally.
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Affiliation(s)
- Azizul Haque
- One Medical Center Drive, Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
| | - Anudeep B Pant
- New Orleans East Hospital, 5620 Read Blvd, New Orleans, LA, 70127, USA.
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213
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Abstract
Real-time quantitative PCR is currently the most widely used method for the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification. Due to the rapid evolution of the SARS-CoV-2 genome, novel mutations on the primer binding sites will cause the failure of PCR. Therefore, in addition to a well-designed primer set, these primers need to be updated and evaluated regularly to ensure that the rapidly evolving genome primers can be amplified. In this protocol, (1) we firstly use assembled genome sequences in the SARS-CoV-2 database to identify and characterize indels and point mutations; (2) design primers skipping the sites of mutations; (3) check the coverage of the primers with the daily update SARS-CoV-2 database; (4) redesign them if novel mutations found in the primer binding sites. Although this protocol takes SARS-CoV-2 as an example, it is suitable for other species that have genomes accumulating mutations over time.
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Rahaman MM, Sarkar MMH, Rahman MS, Islam MR, Islam I, Saha O, Akter S, Banu TA, Jahan I, Habib MA, Goswami B, Bari L, Malek MA, Khan MS. Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach. J Med Virol 2021; 94:1670-1688. [PMID: 34939673 DOI: 10.1002/jmv.27537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Shahina Akter
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Tanjian Akhtar Banu
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Iffat Jahan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Md Ahasan Habib
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Barna Goswami
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Latiful Bari
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Abdul Malek
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Salim Khan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
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Rajpoot S, Solanki K, Kumar A, Zhang KYJ, Pullamsetti SS, Savai R, Faisal SM, Pan Q, Baig MS. In-Silico Design of a Novel Tridecapeptide Targeting Spike Protein of SARS-CoV-2 Variants of Concern. Int J Pept Res Ther 2021; 28:28. [PMID: 34924897 PMCID: PMC8667532 DOI: 10.1007/s10989-021-10339-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
Several mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have increased the transmission and mortality rate of coronavirus disease-19 (COVID-19) across the globe. Although many vaccines have been developed, a large proportion of the global population remains at high risk of infection. The current study aims to develop an antiviral peptide capable of inhibiting the interaction of SARS-CoV-2 spike protein and its six major variants with the host cell angiotensin-converting enzyme 2 (ACE2) receptor. An in-silico approach was employed to design a therapeutic peptide inhibitor against the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 and its variants (B.1.1.7, B.1.351, P.1, B.1.617.1, B.1.617.2 and B.1.617.3). The binding specificity and affinity of our designed peptide inhibitor Mod13AApi (YADKYQKQYKDAY) with wild-type S-RBD and its six variants was confirmed by molecular docking using the HPEPDOCK tool, whereas complex stability was determined by the MD simulation study. The physicochemical and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of inhibitory peptides were determined using the ExPASy tool and pkCSM server. The docking results and its properties from our in-silico analysis present the Mod13AApi, a promising peptide for the rapid development of anti-coronavirus peptide-based antiviral therapy. Blockage of the binding of the spike protein of SARS-CoV-2 variants with ACE2 in the presence of the therapeutic peptide may prevent deadly SARS-CoV-2 variants entry into host cells. Therefore, the designed inhibitory peptide can be utilized as a promising therapeutic strategy to combat COVID-19, as evident from this in-silico study.
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Affiliation(s)
- Sajjan Rajpoot
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552 India
| | - Kundan Solanki
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552 India
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa Japan
| | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Hessen Germany.,Institute for Lung Health (ILH), Justus-Liebig-University Giessen, 35392 Giessen, Hessen Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Hessen Germany.,Institute for Lung Health (ILH), Justus-Liebig-University Giessen, 35392 Giessen, Hessen Germany
| | - Syed M Faisal
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana India
| | - Qiuwei Pan
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Mirza S Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552 India
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216
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Kannan SR, Spratt AN, Sharma K, Chand HS, Byrareddy SN, Singh K. Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies. J Autoimmun 2021; 126:102779. [PMID: 34915422 PMCID: PMC8666303 DOI: 10.1016/j.jaut.2021.102779] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [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: 12/03/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
Abstract
Severe Acute Respiratory Coronavirus (SARS-CoV-2) has been emerging in the form of different variants since its first emergence in early December 2019. A new Variant of Concern (VOC) named the Omicron variant (B.1.1.529) was reported recently. This variant has a large number of mutations in the S protein. To date, there exists a limited information on the Omicron variant. Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. Our analyses show the presence of 46 high prevalence mutations specific to Omicron. Twenty-three of these are localized within the spike (S) protein and the rest localized to the other 3 structural proteins of the virus, the envelope (E), membrane (M), and nucleocapsid (N). Phylogenetic analysis showed that the Omicron is closely related to the Gamma (P.1) variant. The structural analyses showed that several mutations are localized to the region of the S protein that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.
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Affiliation(s)
- Saathvik R Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Kalicharan Sharma
- Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Hitendra S Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, 33199, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA; Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Delhi Pharmaceutical Sciences and Research University, New Delhi, India; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden; Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.
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217
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Wang KN, Chen QQ, Zhu YL, Wang CL. Complete androgen insensitivity syndrome caused by the c.2678C>T mutation in the androgen receptor gene: A case report. World J Clin Cases 2021; 9:11036-11042. [PMID: 35047615 PMCID: PMC8678886 DOI: 10.12998/wjcc.v9.i35.11036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Androgen insensitivity syndrome is an X-linked recessive genetic disease caused by mutations in the androgen receptor gene (AR). However, the underlying molecular mechanisms for the majority of AR variants remain unclear. In this study, we identified a point variant in three patients with complete androgen insensitivity syndrome (CAIS), summarized the correlation analysis, and performed a literature review.
CASE SUMMARY The proband was raised as a girl. In infancy, she was first referred to hospital with a right inguinal hernia. Ultrasonography revealed the absence of a uterus and ovaries, and a testis-like structure located at the inguinal canal. Further diagnostic workup detected a 46, XY karyotype, and fluorescence in situ hybridization analysis showed the presence of the SRY gene. Histological analysis revealed the excised tissue to be testicular. Twelve years later, she was admitted to our hospital with a lack of breast development. Her pubic hair and breasts were Tanner stage I. She had normal female external genitalia. Blood hormone tests showed normal testosterone levels, low estradiol levels, and high gonadotropin levels. Her two siblings underwent similar examinations, and all three had a rare hemizygous missense mutation in AR: c.2678C>T. In vitro functional analyses revealed decreased nuclear translocation in AR-c.2678C>T mutation cells.
CONCLUSION This case of CAIS was caused by an AR variant (c.2678C>T). Functional studies showed impaired nuclear translocation ability of the mutant protein.
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Affiliation(s)
- Ka-Na Wang
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Qing-Qing Chen
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Yi-Lin Zhu
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Chun-Lin Wang
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
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Murugan C, Ramamoorthy S, Kuppuswamy G, Murugan RK, Sivalingam Y, Sundaramurthy A. COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks. Int J Biol Macromol 2021; 193:1165-1200. [PMID: 34710479 PMCID: PMC8545698 DOI: 10.1016/j.ijbiomac.2021.10.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/16/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023]
Abstract
Today, the world population is facing an existential threat by an invisible enemy known as severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) or COVID-19. It is highly contagious and has infected a larger fraction of human population across the globe on various routes of transmission. The detailed knowledge of the SARS-CoV-2 structure and clinical aspects offers an important insight into the evolution of infection, disease progression and helps in executing the different therapies effectively. Herein, we have discussed in detail about the genome structure of SARS-CoV-2 and its role in the proteomic rational spread of different muted species and pathogenesis in infecting the host cells. The mechanisms behind the viral outbreak and its immune response, the availability of existing diagnostics techniques, the treatment efficacy of repurposed drugs and the emerging vaccine trials for the SARS-CoV-2 outbreak also have been highlighted. Furthermore, the possible antiviral effects of various herbal products and their extracted molecules in inhibiting SARS-CoV-2 replication and cellular entry are also reported. Finally, we conclude our opinion on current challenges involved in the drug development, bulk production of drug/vaccines and their storage requirements, logistical procedures and limitations related to dosage trials for larger population.
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Affiliation(s)
- Chandran Murugan
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Sharmiladevi Ramamoorthy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Guruprasad Kuppuswamy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Rajesh Kumar Murugan
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Yuvaraj Sivalingam
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Anandhakumar Sundaramurthy
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India; Department of Chemical Engineering, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India.
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219
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Banks JM, Capistrano K, Thakkar P, Ranade H, Soni V, Datta M, Naqvi AR. Current molecular diagnostics assays for SARS-CoV-2 and emerging variants. Methods Microbiol 2021; 50:83-121. [PMID: 38620738 PMCID: PMC8655725 DOI: 10.1016/bs.mim.2021.10.003] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Since the SARS-CoV-2 virus triggered the beginning of the COVID-19 pandemic, scientists, government officials, and healthcare professionals around the world recognized the need for accessible, affordable, and accurate testing to predict and contain the spread of COVID-19. In the months that followed, research teams designed, tested, and rolled out hundreds of diagnostic assays, each with different sampling methods, diagnostic technologies, and sensitivity levels. However, the contagious virus continued to spread; SARS-CoV-2 travelled through airborne particles and spread rapidly, despite the widening use of diagnostic assays. As the pandemic continued, hundreds of millions of people contracted COVID-19 and millions died worldwide. With so many infections, SARS-CoV-2 received many opportunities to replicate and mutate, and from these mutations emerged more contagious, deadly, and difficult-to-diagnose viral mutants. Each change to the viral genome presented potential added challenges to containing the virus, and as such, researchers have continued developing and improving testing methods to keep up with COVID-19. In this chapter, we examine several SARS-CoV-2 variants that have emerged during the pandemic. Additionally, we discuss a few major COVID-19 diagnostic technique categories, including those involving real-time PCR, serology, CRISPR, and electronic biosensors. Finally, we address SARS-CoV-2 variants and diagnostic assays in the age of COVID-19 vaccines.
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Affiliation(s)
- Jonathan M Banks
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Kristelle Capistrano
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Hemangi Ranade
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Vaidik Soni
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
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220
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Affiliation(s)
- Yousra Kherabi
- AP-HP, Bichat University Hospital, DMU INVICTUS, Infectious Diseases Department, Paris, France
| | - Thibault Fiolet
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussy, "Exposome and Heredity" Team, CESP UMR1018, Villejuif, France
| | - Sacha Rozencwajg
- AP-HP, Bichat University Hospital, DMU PARABOL, Department of Anaesthesiology and Critical Care, Paris, France; Paris University, Paris, France
| | - Jean-Philippe Salaün
- Normandie Univ, UNICAEN, INSERM, GIP Cyceron, Institut Blood and Brain @Caen-Normandie (BB@C), UMR-S U1237, Physiopathology and Imaging of Neurological Disorders (PhIND), Caen, France; CHU Caen, Department of Anaesthesiology and Critical Care Medicine, Caen University Hospital, Avenue de la Côte de Nacre, Caen, France
| | - Nathan Peiffer-Smadja
- AP-HP, Bichat University Hospital, DMU INVICTUS, Infectious Diseases Department, Paris, France; INSERM, IAME, Paris University, Paris, F-75006, France; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK.
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221
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Silva SJRD, Pena L. Collapse of the public health system and the emergence of new variants during the second wave of the COVID-19 pandemic in Brazil. One Health 2021; 13:100287. [PMID: 34222607 PMCID: PMC8240439 DOI: 10.1016/j.onehlt.2021.100287] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 04/16/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 01/30/2023] Open
Abstract
The worldwide spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the most severe public health crisis since the 1918 Spanish influenza pandemic. After the introduction of public health interventions aimed at reducing the number of COVID-19 cases, many countries across the world obtained success at containing the fast spread of SARS-CoV-2 during the first wave of the pandemic. However, the SARS-CoV-2 has resurged in many countries causing a even more devastating second wave. Brazil is one the most affected countries and currently is facing one of the worst public health crises in its history. Here, we discuss the unprecedented challenges faced by the Brazilian public health system in the midst of the second wave of the COVID-19 pandemic, particularly regarding the collapse of the Brazilian health system and the emergence of new variants of concern (VOCs). Finally, we suggest some insights using a one health approach that will help the country to face and overcome the current COVID-19 crisis.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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Metcalf S, Dickerson KL, Milojevich HM, Quas JA. Primary and Secondary Variants of Psychopathic Traits in at-Risk Youth: Links with Maltreatment, Aggression, and Empathy. Child Psychiatry Hum Dev 2021; 52:1060-70. [PMID: 33099658 DOI: 10.1007/s10578-020-01083-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 02/01/2023]
Abstract
The current study examined whether two variants of psychopathic traits (PT) were identifiable in high-risk youth who had not yet been identified as antisocial, some of whom had documented histories of maltreatment (N = 167, Mage = 14.84), and then whether the variants differed in levels of aggression and empathy. High-PT youth with low anxiety and trauma (i.e., primary variant PT) and high anxiety and trauma (i.e., secondary variant PT) were differentiated. The secondary variant group was comprised largely of youth with documented histories of maltreatment. This group of youth also reported higher levels of proactive and reactive aggression than did the primary variant youth and low-PT youth. All youth reported similar levels of affective empathy and only small differences in cognitive empathy emerged: Primary variant youth reported lower cognitive empathy than low-PT youth. Findings support generalization of two variant groups of youth with psychopathic traits to diverse, high-risk samples not already identified as antisocial and have important implications for policy and practice.
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Bhattacharya M, Chatterjee S, Sharma AR, Agoramoorthy G, Chakraborty C. D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Appl Microbiol Biotechnol 2021; 105:9035-9045. [PMID: 34755213 PMCID: PMC8578012 DOI: 10.1007/s00253-021-11676-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 09/13/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
Abstract
The progression of the COVID-19 pandemic has generated numerous emerging variants of SARS-CoV-2 on a global scale. These variants have gained evolutionary advantages, comprising high virulence and serious infectivity due to multiple spike glycoprotein mutations. As a reason, variants are demonstrating significant abilities to escape the immune responses of the host. The D614G mutation in the S-glycoprotein of SARS-CoV-2 variants has shown the most efficient interaction with the ACE2 receptor of the cells. This explicit mutation at amino acid position 614 (aspartic acid-to-glycine substitution) is the prime cause of infection and re-infection. It changes the conformation of RBD and cleavage patterns S-glycoprotein with higher stability, replication fitness, and fusion efficiencies. Therefore, this review aims to provide several crucial pieces of information associated with the D614 mutational occurrence of SARS-CoV-2 variants and their infectivity patterns. This review will also effectively emphasize the mechanism of action of D614G mutant variants, immune escape, and partial vaccine escape of this virus. Furthermore, the viral characteristic changes leading to the current global pandemic condition have been highlighted. Here, we have tried to illustrate a novel direction for future researchers to develop effective therapeutic approaches and counterweight strategies to minimize the spread of COVID-19.Key points• D614G mutation arises within the S-glycoprotein of significant SARS-CoV-2 variants.• The D614G mutation affects infection, re-infection, cleavage patterns of S-glycoprotein, and replication fitness of SARS-CoV-2 variants.• The D614G mutation influences the immunity and partial vaccine escape.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | | | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
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Vasuki KA, Christy HJ. Comprehensive Study of Human FBXW7 Deleterious nsSNP's Functional Inference and Susceptibility to Gynaecological Cancer. Appl Biochem Biotechnol 2021. [PMID: 34817806 DOI: 10.1007/s12010-021-03759-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
Cancer is one of the world's major causes of mortality, and it plays a most important role in the world's declining life expectancy. F-box and WD-40 domain protein 7 (FBXW7), a typical participant of the F-box family of proteins, has been considered as an anti-tumor protein and one of the maximum deregulated ubiquitin-proteasome system proteins in uterine carcinosarcoma, endometrial clear cell carcinoma and cervical carcinoma with the greatest prevalence of alterations. FBXW7 variants with known clinical significance, as well as non-synonymous single nucleotide polymorphisms (nsSNPs) in the F-Box and WD40 domains, were evaluated using functionality prediction web resources. Upon analysing the seventy-three deleterious nsSNP's impact on protein stability and function, we identified that forty-one nsSNPs of WD40 domain and three of F-Box domain imply decreased stability of the FBXW7 structure. Next to TP53 and PTEN, FBXW7 was reported with the highest percentage of arginine substitution among mutations related to cancer. The current research concentrated on two arginine residue locations (Arg465, Arg505) within the WD40-repeat domain, which is vital for substrate binding. Computational analysis revealed significant deviation in stability and structural configuration of mutants R505L, R465H, R465P, R505G, R505C, R465C, R505S and R505L structures. Protein-protein interaction network of FBXW7 populated with promising hub proteins NOTCH1, c-Myc, CCNE1, STYX, KLG5, SREB1, NFKB2, SKP1 and CUL1; thus, alteration in the FBXW7 leads to aberration in their signalling pathways as well as their substrate binding ability makes this protein as attractive target for personalized therapeutic intervention.
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. Methods Microbiol 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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Liu Y, Dai L, Feng X, Gao R, Zhang N, Wang B, Han J, Zou Q, Guo X, Zhu H, Liu J, Qin C, Zhang Y, Bao L, Li M. Fast and long-lasting immune response to S-trimer COVID-19 vaccine adjuvanted by PIKA. Mol Biomed 2021; 2:29. [PMID: 34766005 PMCID: PMC8475395 DOI: 10.1186/s43556-021-00054-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
In the face of the emerging variants of SARS-CoV-2, there is an urgent need to develop a vaccine that can induce fast, effective, long-lasting and broad protective immunity against SARS-CoV-2. Here, we developed a trimeric SARS-CoV-2 S protein vaccine candidate adjuvanted by PIKA, which can induce robust cellular and humoral immune responses. The results showed a high level of neutralizing antibodies induced by the vaccine was maintained for at least 400 days. In the study of non-human primates, PIKA adjuvanted S-trimer induced high SARS-CoV-2 neutralization titers and protected from virus replication in the lung following SARS-CoV-2 challenge. In addition, the long-term neutralizing antibody response induced by S-trimer vaccine adjuvanted by PIKA could neutralize multiple SARS-CoV-2 variants and there is no obvious different among the SARS- CoV-2 variants of interest or concern, including B.1.351, B.1.1.7, P.1, B.1.617.1 and B.1.617.2 variants. These data support the utility of S-trimer protein adjuvanted by PIKA as a potential vaccine candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Yuan Liu
- YishengBio Co., Ltd, Beijing, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Feng
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ran Gao
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | - Bin Wang
- YishengBio Co., Ltd, Beijing, China
| | - Jianbao Han
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qingcui Zou
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiling Guo
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing, China
| | - Hua Zhu
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jiangning Liu
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Chuan Qin
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Yi Zhang
- YishengBio Co., Ltd, Beijing, China
| | - Linlin Bao
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Minghua Li
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Shalabi TA, Amr KS, Shaker MM. Are single nucleotide polymorphisms rs7903146 and rs12255372 in transcription factor 7-like 2 gene associated with an increased risk for gestational diabetes mellitus in Egyptian women? J Genet Eng Biotechnol 2021; 19:169. [PMID: 34724590 PMCID: PMC8560867 DOI: 10.1186/s43141-021-00272-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/01/2021] [Accepted: 10/19/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genetic variants in the transcription factor 7-like 2 (TCF7L2) gene are related with type 2 diabetes (T2D) and gestational diabetes mellitus (GDM) in various populations, but there are not enough statistics regarding GDM among Egyptian women. We aimed by this study to evaluate the effect of two polymorphisms of rs7903146 and rs12255372 in the TCF7L2 gene with the development of GDM among Egyptian women. RESULTS We enrolled 114 pregnant women with normal glucose tolerance and 114 with GDM according to the International Association of Diabetes and Pregnancy Study Groups (IADPSG) guidelines. We gathered records on blood pressure, body mass index (BMI), blood glucose level, hemoglobin A1C (HbA1c), and lipid profile. The genotyping of rs7903146 and rs12255372 polymorphisms was carried out using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The statistical significance of prepregnancy BMI, fasting blood sugar (FBS), HbA1c, low-density lipoprotein (LDL), and total cholesterol (Tch) was higher, P < 0.001, in GDM women in comparison to pregnant women without GDM. CT and TT genotypes in rs7903146 SNP were 46.5% vs. 54%, P <0.04, OR; CI = 1.9 (1.0 to 3.78); TT carriers were 37.7% vs. 9.6%, P <0.001, OR (CI) = 8.9 (3.7-21.1), respectively. For the TCFL2 gene rs12255372 SNP, GT carriers were 48.2% vs. 39.5%, P= 0.004, OR (CI) = 2.3 (1.3-4.2), while TT carriers were 24.6% vs. 7.9%, P < 0.001, OR (CI) = 6 (2.5-14.3). CONCLUSION The study showed there is a significantly higher incidence of CT/TT genotypes in rs7903146 SNP and GT/TT genotypes in rs12255372 SNP in TCF7L2 gene among GDM women in comparison to healthy pregnant women (controls).
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Affiliation(s)
- Taghreed A Shalabi
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mai M Shaker
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
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Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Comput Biol Med 2021; 138:104936. [PMID: 34655895 DOI: 10.1016/j.compbiomed.2021.104936] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 07/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs all-atoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was -31.86 kcal/mol for the wild-type-ACE2 complex, -67.85 kcal/mol for N439K, -69.82 kcal/mol for S477 N, and -69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.
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229
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Sally R, Shaw KS, Pomeranz MK. Benign "lumps and bumps" of the vulva: A review. Int J Womens Dermatol 2021; 7:383-390. [PMID: 34621949 PMCID: PMC8484947 DOI: 10.1016/j.ijwd.2021.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/20/2020] [Revised: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 11/24/2022] Open
Abstract
Vulvar dermatology represents a challenge for many providers. Given that the vulva is both a gynecologic and dermatologic organ, patients with cutaneous lesions involving the vulva may present to primary care, gynecology, or dermatology. Particularly within dermatology, the vulva remains understudied, which can lead to anxiety among providers regarding appropriate next steps in the diagnosis and management of vulvar lesions. Thus, the purpose of this review is to highlight commonly encountered anatomic variants and benign neoplasms of the vulva, distinguish them from key pathologic mimickers, and provide guidance to practicing dermatologists on what may constitute normal vulvar variations.
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Affiliation(s)
- Rachel Sally
- The Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York
| | - Katharina S Shaw
- The Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York
| | - Miriam Keltz Pomeranz
- The Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York
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Jacob JJ, John Fletcher G, Monisha Priya T, Veeraraghavan B, Mutreja A. Relevance of immune response and vaccination strategies of SARS-CoV-2 in the phase of viral red queen dynamics. Indian J Med Microbiol 2021; 39:417-422. [PMID: 34454775 PMCID: PMC8387243 DOI: 10.1016/j.ijmmb.2021.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/05/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Following a relatively mild first wave of coronavirus disease 2019 (COVID-19) in India, a deadly second wave of the pandemic overwhelmed the healthcare system due to the emergence of fast-transmitting SARS-CoV-2 genetic variants. The emergence and spread of the B.1.617.2/Delta variant considered to be driving the devastating second wave of COVID-19 in India. Currently, the Delta variant has rapidly overtaken the previously circulating variants to become the dominant strain. Critical mutations in the spike/RBD region of these variants have raised serious concerns about the virus's increased transmissibility and decreased vaccine effectiveness. As a result, significant scientific and public concern has been expressed about the impact of virus variants on COVID-19 vaccines. OBJECTIVES The purpose of this article is to provide an additional explanation in the context of the evolutionary trajectory of SARS-CoV-2 variants in India, the vaccine-induced immune response to the variants of concern (VOC), and various vaccine deployment strategies to rapidly increase population immunity. CONTENT Phylogenetic analysis of SARS-CoV-2 isolates circulating in India suggests the emergence and spread of B.1.617 variant. The immunogenicity of currently approved vaccines indicates that the majority of vaccines elicit an antibody response and some level of protection. According to current data, vaccines in the pre-fusion configuration (2p substitution) have an advantage in terms of nAb titer, but the duration of vaccine-induced immunity, as well as the role of T cells and memory B cells in protection, remain unknown. Since vaccine efficacy on virus variants is one of the major factors to be considered for achieving herd immunity, existing vaccines need to be improved or effective next-generation vaccines should be developed to cover the new variants of the virus.
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Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - G John Fletcher
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | - T Monisha Priya
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge, UK
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231
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Takáts A, Berke G, Szentesi A, Farkas G, Izbéki F, Erőss B, Czakó L, Vincze Á, Hegyi P, Sahin-Tóth M, Hegyi E. Common calcium-sensing receptor (CASR) gene variants do not modify risk for chronic pancreatitis in a Hungarian cohort. Pancreatology 2021; 21:1305-1310. [PMID: 34481716 PMCID: PMC8663126 DOI: 10.1016/j.pan.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022]
Abstract
The calcium-sensing receptor (CASR) is expressed in the pancreas where it might regulate calcium concentrations in pancreatic secretions. Two independent studies reported conflicting results claiming that commonly occurring missense variants of the CASR gene are risk factors for chronic pancreatitis (CP). Here, we attempted to replicate the association between CASR variants and CP. We analyzed 337 patients and 840 controls from the Hungarian National Pancreas Registry either by direct sequencing of exon 7 and the flanking noncoding regions or by TaqMan SNP genotyping assays. We identified two common missense variants, c.2956G>T (p.A986S), and c.2968A>G (p.R990G), three low-frequency variants, c.3031C>G (p.Q1011E), c.2610G>A (p.E870=) and c.∗60T>A, and 8 rare variants including the novel variant c.1895G>A (p.G632D). When allelic or genotype distributions were considered, none of the CASR variants associated with CP. Subgroup analysis of nonalcoholic versus alcoholic patients revealed no disease association either. Our results demonstrate that common CASR variants do not modify the risk for CP and should not be considered as genetic risk factors in the clinical setting.
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Affiliation(s)
- Amanda Takáts
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Gergő Berke
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; First Department of Medicine, University of Szeged, Szeged, Hungary; Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Gyula Farkas
- Department of Surgery, University of Szeged, Szeged, Hungary
| | - Ferenc Izbéki
- Szent György University Teaching Hospital of Fejér County, Székesfehérvár, Hungary
| | - Bálint Erőss
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - László Czakó
- First Department of Medicine, University of Szeged, Szeged, Hungary
| | - Áron Vincze
- Division of Gastroenterology, First Department of Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary; First Department of Medicine, University of Szeged, Szeged, Hungary; Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Miklós Sahin-Tóth
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Eszter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary.
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Zafar R, Saleem T, Sheikh N, Maqbool H, Mukhtar M, Abbasi M. PRDM16, LRP1 and TRPM8 genetic polymorphisms are risk factor for Pakistani migraine patients. Saudi J Biol Sci 2021; 28:5793-5799. [PMID: 34588893 PMCID: PMC8459056 DOI: 10.1016/j.sjbs.2021.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Migraine is a chronic neurovascular condition characterized by recurring attacks of pulsating headaches. Genome-wide association studies (GWAS) identified many potential loci associated with migraine. To check the association of polymorphisms of PRDM16 (rs2651899), LRP1 (rs11172113), and TRPM8 (rs10166942) with migraine, the first time a case-control study was conducted in understudied Pakistani population. METHODS The study included 127 migraine patients (21 in migraine with aura and 106 with migraine without aura group) and 120 healthy control subjects from different areas of Punjab, Pakistan. Blood samples were collected from all the participants, and DNA was isolated from the lymphocytes by the modified organic method. Sanger's sequencing was done for PRDM16 (rs2651899), LRP1 (rs11172113), and TRPM8 (rs10166942) in all the samples to check the genotype. Logistic regression analysis was done using SPSS 20.0 to check the association of these SNPs with migraine susceptibility. RESULTS We found statistically significant differences between case and control group for PRDM16 (rs2651899) at genotypic level (p < 0.001), allelic level (p < 0.001; OR 3.088; 95% CI 2.082-4.579) and for dominant model (p < 0.001; OR 5.437; 95% CI 3.112-9.498). The major findings of this study suggested that PRDM16 rs2651899 is strongly associated with migraine in overall and subgroup analysis of genotypes. LRP1 (rs11172113) showed significant association with migraine except in subgroup comparison. A similar trend of association was found for TRPM8 (rs10166942) however, significant association was found only at the allelic level but no significant difference was seen at the genotypic level between case and control. One novel mutation c.67 + 4436_67 + 4438delA was also identified in the current study near LRP1 (rs11172113) polymorphic site. CONCLUSION In this first-ever replication report from Pakistan, PRDM16 (rs2651899) was found as a potential genetic marker in migraine susceptibility while LRP1 (rs11172113) and TRPM8 (rs10166942) showed partial association in subgroup analysis.
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Affiliation(s)
- R. Zafar
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore 54590, Pakistan
| | - T. Saleem
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore 54590, Pakistan
| | - N. Sheikh
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore 54590, Pakistan
| | - H. Maqbool
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore 54590, Pakistan
| | - M. Mukhtar
- Cell and Molecular Biology Laboratory, Institute of Zoology, University of the Punjab, Lahore 54590, Pakistan
| | - M.H. Abbasi
- Department of Zoology, University of Okara, Renala Khurd 56300, Pakistan
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Bar-Or I, Weil M, Indenbaum V, Bucris E, Bar-Ilan D, Elul M, Levi N, Aguvaev I, Cohen Z, Shirazi R, Erster O, Sela-Brown A, Sofer D, Mor O, Mendelson E, Zuckerman NS. Detection of SARS-CoV-2 variants by genomic analysis of wastewater samples in Israel. Sci Total Environ 2021; 789:148002. [PMID: 34323811 PMCID: PMC8142738 DOI: 10.1016/j.scitotenv.2021.148002] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 05/12/2023]
Abstract
Investigation of SARS-CoV-2 spread and identification of variants in sewers has been demonstrated to accurately detect prevalence of viral strains and is advantageous to clinical sampling in population catchment size. Herein, we utilized an established nationwide system of wastewater sampling and viral concentration approaches to perform large-scale surveillance of SARS-CoV-2 variants in nine different locations across Israel that were sampled from August 2020 to February 2021 and sequenced (n = 58). Viral sequences obtained from the wastewater samples had high coverages of the genome, and mutation analyses successfully identified the penetration of the B.1.1.7 variant into Israel in December 2020 in the central and north regions, and its spread into additional regions in January and February 2021, corresponding with clinical sampling results. Moreover, the wastewater analysis identified the B.1.1.7 variant in December 2020 in regions in which non-sufficient clinical sampling was available. Other variants of concern examined, including P.1 (Brazil/Manaus), B.1.429 (USA/California), B.1.526 (USA/New York), A.23.1 (Uganda) and B.1.525 (Unknown origin), did not show consistently elevated frequencies. This study exemplifies that surveillance by sewage is a robust approach which allows to monitor the diversity of SARS-CoV-2 strains circulating in the community. Most importantly, this approach can pre-identify the emergence of epidemiologically or clinically relevant mutations/variants, aiding in public health decision making.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Merav Weil
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Victoria Indenbaum
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Elul
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Levi
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Irina Aguvaev
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Zvi Cohen
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Alin Sela-Brown
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
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Khan S, Hussain A, Vahdani Y, Kooshki H, Mahmud Hussen B, Haghighat S, Fatih Rasul M, Jamal Hidayat H, Hasan A, Edis Z, Haj Bloukh S, Kasravi S, Mahdi Nejadi Babadaei M, Sharifi M, Bai Q, Liu J, Hu B, Akhtari K, Falahati M. Exploring the interaction of quercetin-3-O-sophoroside with SARS-CoV-2 main proteins by theoretical studies: A probable prelude to control some variants of coronavirus including Delta. ARAB J CHEM 2021; 14:103353. [PMID: 34909059 PMCID: PMC8317451 DOI: 10.1016/j.arabjc.2021.103353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/18/2023] Open
Abstract
The aim of this study was to investigate the mechanism of interaction between quercetin-3-O-sophoroside and different SARS-CoV-2's proteins which can bring some useful details about the control of different variants of coronavirus including the recent case, Delta. The chemical structure of the quercetin-3-O-sophoroside was first optimized. Docking studies were performed by CoV disease-2019 (COVID-19) Docking Server. Afterwards, the molecular dynamic study was done using High Throughput Molecular Dynamics (HTMD) tool. The results showed a remarkable stability of the quercetin-3-O-sophoroside based on the calculated parameters. Docking outcomes revealed that the highest affinity of quercetin-3-O-sophoroside was related to the RdRp with RNA. Molecular dynamic studies showed that the target E protein tends to be destabilized in the presence of quercetin-3-O-sophoroside. Based on these results, quercetin-3-O-sophoroside can show promising inhibitory effects on the binding site of the different receptors and may be considered as effective inhibitor of the entry and proliferation of the SARS-CoV-2 and its different variants. Finally, it should be noted, although this paper does not directly deal with the exploring the interaction of main proteins of SARS-CoV-2 Delta variant with quercetin-3-O-sophoroside, at the time of writing, no direct theoretical investigation was reported on the interaction of ligands with the main proteins of Delta variant. Therefore, the present data may provide useful information for designing some theoretical studies in the future for studying the control of SARS-CoV-2 variants due to possible structural similarity between proteins of different variants.
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Affiliation(s)
- Suliman Khan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Medical Lab Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Yasaman Vahdani
- Department of Microbiology, Faculty of Pharmaceutical Science, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hamideh Kooshki
- Department of Medical Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Setareh Haghighat
- Department of Microbiology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Science, Tishk International University-Erbil, Kurdistan Region, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Iraq
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Zehra Edis
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University, PO Box 346, Ajman, United Arab Emirates
| | - Samir Haj Bloukh
- Center of Medical and Bio-allied Health Sciences Research, Ajman University, PO Box 346, Ajman, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, PO Box 346, Ajman, United Arab Emirates
| | - Shahab Kasravi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Mahdi Nejadi Babadaei
- Department of Molecular Genetics, Faculty of Biological Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Majid Sharifi
- Department of Medical Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Qian Bai
- Department of Anesthesiology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianbo Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bowen Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Keivan Akhtari
- Department of Physics, University of Kurdistan, Sanandaj, Iran
| | - Mojtaba Falahati
- Department of Medical Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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Abstract
The Sputnik V COVID-19 vaccine is a member of the so-called vector vaccines and uses two different vectors (Ad26 priming and Ad5 boost) to reduce the risk of a reduction in the effectiveness of the vaccination. Real life data indicate an efficacy of the vaccine above 97%. Low cost and no need for ultra-cold storage temperature temperatures are other pluses of the Sputnik V vaccine. However, there are also several important shortcomings that must be considered such as the possible reduction of its immunogenicity in the presence of very high Ad5 neutralizing antibody titres and the decrease with age of the antibody titres neutralizing the virus. Furthermore, there is emerging documentation that Sputnik V has a reduced neutralizing capacity against the Beta variant and all variants with the spike protein carrying the E484K substitution. Nevertheless, due to its characteristics, Sputnik V could be another useful means of satisfying the need for mass vaccination. However, it is imperative to document the efficacy and safety of the Sputnik V vaccine in individuals with high pre-existing anti-Ad26 and Ad5-neutralizing antibody titres and in those under the age of 18 or older than 60 years and be certain that Sputnik V does not cause the rare development of immune thrombotic thrombocytopenia. It is hoped that the now widespread use of this vaccine will generate a large pragmatic real-world study with data accessible to anyone interested in verifying them.
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Affiliation(s)
- Mario Cazzola
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Paola Rogliani
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Filomena Mazzeo
- Department of Science and Technologies, University of Naples "Parthenope", Naples, Italy
| | - Maria Gabriella Matera
- Unit of Pharmacology, Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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236
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Stojanov D. Data on multiple SARS-CoV-2 surface glycoprotein alignments. Data Brief 2021; 38:107414. [PMID: 34584917 PMCID: PMC8459576 DOI: 10.1016/j.dib.2021.107414] [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: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface glycoproteins deposited to the NCBI GenBank from Europe, by the mid of April 2021 (12.04.2021) were analysed. At least one amino acid mutation relative to YP_009724390.1 referent SARS-CoV-2 surface glycoprotein: Wuhan-Hu-1 complete genome (NCBI accession: NC_045512) was found in 788 SARS-CoV-2 surface glycoproteins. Data was computed by NCBI Cobalt multiple alignment tool [1] (one country by another) and structured by special purpose application developed in Visual Studio 2019. Advanced data structures were used to organize computed data. Linked dataset lists program output: SARS-CoV-2 surface glycoprotein mutations per processed protein.
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Affiliation(s)
- Done Stojanov
- Faculty of Computer Science, Goce Delčev University of Štip, Krste Misirkov No.10-A P.O. Box 201, Štip 2000, North Macedonia
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237
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Saffar H, Motevalli D, Seirfar N, Ebrahimi M, Kumar PV, Kosari F, Moradi Tabriz H, Naderi S, Shekarkhar G. Myofibroblastoma of the Breast: A Morphologic and Immunohistochemical Study of Three Cases. Iran J Pathol 2021; 16:451-455. [PMID: 34567197 PMCID: PMC8463761 DOI: 10.30699/ijp.2021.138647.2520] [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] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/16/2021] [Indexed: 11/28/2022]
Abstract
Myofibroblastoma (MFB) of the breast is an uncommon entity of benign spindle neoplasms of the breast. This tumour possesses a broad spectrum of histomorphological patterns. Distinguishing of myofibroblastoma variants from malignant mimics of this benign neoplasm is essential for pathologists to avoid further invasive surgical procedures. In this article, we report the clinical, morphological, and immunohistochemical features of three cases, including two females and one male patient with mammary myofibroblastoma with emphasis on the histomorphological findings. As there is not yet enough information about MFB, more reports of MFB are still required to more clarify the pathogenesis and potential predisposing factors of this rare type of breast tumours.
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Affiliation(s)
- Hiva Saffar
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Dorna Motevalli
- Department of Pathology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasibeh Seirfar
- Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Ebrahimi
- Department of Pathology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Farid Kosari
- Department of Pathology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sadaf Naderi
- School of Medicine (MBBS), University of Central Lancashire, Preston, United Kingdom
| | - Golsa Shekarkhar
- Department of Pathology, Shiraz University of Medical Sciences, Shiraz, Iran
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238
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Mann C, Griffin JH, Downard KM. Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry. Anal Bioanal Chem 2021; 413:7241-7249. [PMID: 34532764 PMCID: PMC8445501 DOI: 10.1007/s00216-021-03649-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
Abstract
Mass mapping using high-resolution mass spectrometry has been applied to identify and rapidly distinguish SARS-CoV-2 coronavirus strains across five major variants of concern. Deletions or mutations within the surface spike protein across these variants, which originated in the UK, South Africa, Brazil and India (known as the alpha, beta, gamma and delta variants respectively), lead to associated mass differences in the mass maps. Peptides of unique mass have thus been determined that can be used to identify and distinguish the variants. The same mass map profiles are also utilized to construct phylogenetic trees, without the need for protein (or gene) sequences or their alignment, in order to chart and study viral evolution. The combined strategy offers advantages over conventional PCR-based gene-based approaches exploiting the ease with which protein mass maps can be generated and the speed and sensitivity of mass spectrometric analysis.
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Affiliation(s)
- Christian Mann
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
| | - Justin H Griffin
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia.
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239
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Li Y, Zhou H, Chen X, Zheng Y, Kang Q, Hao D, Zhang L, Song T, Luo H, Hao Y, Chen R, Zhang P, He S. SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. Genomics Proteomics Bioinformatics 2021; 19:602-610. [PMID: 34536568 PMCID: PMC9039559 DOI: 10.1016/j.gpb.2021.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/30/2022]
Abstract
Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.
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Affiliation(s)
- Yanyan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaomin Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Kang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Di Hao
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingrui Song
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan 528316, China.
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Shunmin He
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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240
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Taha HR, Keewan N, Slati F, Al-Sawalha NA. Remdesivir: A Closer Look at Its Effect in COVID-19 Pandemic. Pharmacology 2021; 106:462-468. [PMID: 34515227 PMCID: PMC8450841 DOI: 10.1159/000518440] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/08/2021] [Indexed: 12/22/2022]
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiology of COVID-19 pandemic, resulted in significant harm to the affected countries in every aspect of life. The virus infected over 139 million patients and resulted in over 2.9 million deaths until April 16, 2021. New variants of this virus were identified that spread rapidly worldwide. Summary Remdesivir, a prodrug of adenosine nucleotide analog, is an antiviral with a broad spectrum of activity that was tested on SARS and Middle East respiratory syndrome infections. In vitro studies conducted on SARS-CoV-2 revealed that remdesivir inhibited viral replication with high selectivity index in cell cultures. In vivo studies showed that remdesivir reduced viral load in bronchoalveolar lavage fluid and attenuated pulmonary infiltrates in infected animals. Further, remdesivir showed promising results in terms of clinical improvement, shortening the recovery time, mortality rate, and the duration of oxygen need, despite that some clinical trials did not reveal significant effect on remdesivir use. Several studies showed positive results of remdesivir against the new variants. Key Messages Remdesivir showed a promising beneficial effect against new variants of SARS-CoV-2, but more clinical evidence is needed to confirm this effect.
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Affiliation(s)
- Huda R Taha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour Keewan
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Farah Slati
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour A Al-Sawalha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan.,Faculty of Pharmacy, Jadara University, Irbid, Jordan
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241
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Kumar S. Vaccines efficacy to SARS-CoV-2 variants require holistic knowledge of viral immunology and protein biochemistry. Hum Vaccin Immunother 2021; 17:4128-4130. [PMID: 34495810 DOI: 10.1080/21645515.2021.1964318] [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] [Indexed: 10/20/2022] Open
Abstract
The article by Abdalla et al., published in the journal on 28 May 2021, raised a concern. The SARS-CoV-2 spike (S) protein is the major targeted surface glycoprotein in COVID-19 vaccines. Many mutations in the S protein of SARS-CoV-2 have been reported across the globe. The S protein plays a crucial role in the induction of neutralizing antibody and protective immunity against SARS-CoV-2 infection. The protein biochemistry and immunology, in addition to conventional virology, will help us to delineate the biology of SARS-CoV-2 variants.
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Affiliation(s)
- Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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242
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Xu X, Lu F, Zhang L, Li H, Du S, Tang J. Novel CLCN4 variant associated with syndromic X-linked intellectual disability in a Chinese girl: a case report. BMC Pediatr 2021; 21:384. [PMID: 34479510 PMCID: PMC8414764 DOI: 10.1186/s12887-021-02860-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/26/2021] [Indexed: 12/17/2022] Open
Abstract
Background The Raynaud-Claes type of X-linked syndromic mental retardation (MRXSRC) is a very rare condition, by intellectual disability ranged from borderline to profound, impaired language development, brain abnormalities, facial dysmorphisms and seizures. MRXSRC is caused by variants in CLCN4 which encodes the 2Cl−/H+ exchanger ClC-4 prominently expressed in brain. Case presentation We present a 3-year-old Chinese girl with intellectual disability, dysmorphic features, brain abnormalities, significant language impairment and autistic features. Brain magnetic resonance imaging (MRI) showed a thin corpus callosum, a mega cisterna magna and ventriculomegaly. Whole exome sequencing (WES) was performed to detect the molecular basis of the disease. It was confirmed that this girl carried a novel heterozygous missense variant (c.1343C > T, p.Ala448Val) of CLCN4 gene, inherited from her mother. This variant has not been registered in public databases and was predicted to be pathogenic by multiple in silico prediction tools. Conclusion Our investigation expands the phenotype spectrum for CLCN4 variants with syndromic X-linked intellectual disability, which help to improve the understanding of CLCN4-related intellectual disability and will help in genetic counselling for this family. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-021-02860-4.
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Affiliation(s)
- Xin Xu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
| | - Fen Lu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
| | - Li Zhang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, Jiangsu Province, China.
| | - Hongying Li
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
| | - Senjie Du
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, No. 72 Guangzhou Road, Nanjing, 210008, Jiangsu Province, China
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Abstract
Mutations in the SARS-CoV-2 genome can affect the gene encoding the Spike (S) antigen, which interacts with the host cell specific receptor, selecting mutant variants with changes in their infective capacity, pathogenic potential and resistance to neutralizing antibodies. The nomenclature to design the variants uses a colloquial form referred to the country or place of detection, a code from the "Pangolin" database and one from the "Nextstrain" page. New variants that have spread include the British B.1.1.7 (20I/501Y.V1), the South African B.1.351 (20H/501.V2), the Brazilian P.1 (20J/501Y.V3), the Californians B.1.427 B.1.429 (20C/S:452R) and the most recent, the Indian B.1.617 (VUI-21APR-01).The gold standard for the identification of the variants is whole genome sequencing. However, real-time PCR techniques have already been developed for the detection of specific mutations that can facilitate their presumptive identification.The impact of these variants on global vaccination programs has raised concern. It is generally thought that, since the response evoked by the vaccine against the S antigen is directed at the entire protein and the mutations only affect specific regions, the escape effect of the vaccine antibodies will be limited. Among the future strategies proposed for immuno-protection, the increase in the number of doses, the alternation of vaccines and the development of specific vaccines against different variants has been suggested.
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Affiliation(s)
- M Pérez-Abeledo
- Unidad de Microbiología Clínica. Laboratorio Regional de Salud Pública de la Comunidad de Madrid. Dirección General de Salud Pública, Consejería de Sanidad. Comunidad de Madrid, Madrid, España
| | - J C Sanz Moreno
- Unidad de Microbiología Clínica. Laboratorio Regional de Salud Pública de la Comunidad de Madrid. Dirección General de Salud Pública, Consejería de Sanidad. Comunidad de Madrid, Madrid, España
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública (CIBERESP), Madrid, España
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Liu J, Bodnar BH, Meng F, Khan AI, Wang X, Saribas S, Wang T, Lohani SC, Wang P, Wei Z, Luo J, Zhou L, Wu J, Luo G, Li Q, Hu W, Ho W. Epigallocatechin gallate from green tea effectively blocks infection of SARS-CoV-2 and new variants by inhibiting spike binding to ACE2 receptor. Cell Biosci 2021; 11:168. [PMID: 34461999 PMCID: PMC8404181 DOI: 10.1186/s13578-021-00680-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [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: 06/24/2021] [Accepted: 08/17/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND As the COVID-19 pandemic rages on, the new SARS-CoV-2 variants have emerged in the different regions of the world. These newly emerged variants have mutations in their spike (S) protein that may confer resistance to vaccine-elicited immunity and existing neutralizing antibody therapeutics. Therefore, there is still an urgent need of safe, effective, and affordable agents for prevention/treatment of SARS-CoV-2 and its variant infection. RESULTS We demonstrated that green tea beverage (GTB) or its major ingredient, epigallocatechin gallate (EGCG), were highly effective in inhibiting infection of live SARS-CoV-2 and human coronavirus (HCoV OC43). In addition, infection of the pseudoviruses with spikes of the new variants (UK-B.1.1.7, SA-B.1.351, and CA-B.1.429) was efficiently blocked by GTB or EGCG. Among the 4 active green tea catechins at noncytotoxic doses, EGCG was the most potent in the action against the viruses. The highest inhibitory activity was observed when the viruses or the cells were pre-incubated with EGCG prior to the infection. Mechanistic studies revealed that EGCG blocked infection at the entry step through interfering with the engagement of the receptor binding domain (RBD) of the viral spikes to angiotensin-converting enzyme 2 (ACE2) receptor of the host cells. CONCLUSIONS These data support further clinical evaluation and development of EGCG as a novel, safe, and cost-effective natural product for prevention/treatment of SARS-CoV-2 transmission and infection.
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Affiliation(s)
- Jinbiao Liu
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.,Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Brittany H Bodnar
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Fengzhen Meng
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Adil I Khan
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Sami Saribas
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Tao Wang
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Saroj Chandra Lohani
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA
| | - Peng Wang
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Zhengyu Wei
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Jinjun Luo
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Lina Zhou
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Jianguo Wu
- Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Guangxiang Luo
- Department of Microbiology, University of Alabama At Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA.
| | - Wenhui Hu
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
| | - Wenzhe Ho
- Department of Pathology and Laboratory Medicine, Center for Metabolic Disease Research, and Department of Neurology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
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Teyssou E, Delagrèverie H, Visseaux B, Lambert-Niclot S, Brichler S, Ferre V, Marot S, Jary A, Todesco E, Schnuriger A, Ghidaoui E, Abdi B, Akhavan S, Houhou-Fidouh N, Charpentier C, Morand-Joubert L, Boutolleau D, Descamps D, Calvez V, Marcelin AG, Soulie C. The Delta SARS-CoV-2 variant has a higher viral load than the Beta and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients. J Infect 2021; 83:e1-3. [PMID: 34419559 DOI: 10.1016/j.jinf.2021.08.027] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
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Pan HX, Wang YG, Zhao YW, Zeng Q, Wang Z, Fang ZH, Zhang Y, Zhou X, He RC, Xu Q, Sun QY, Tan JQ, Yan XX, Li JC, Tang BS, Guo JF. Evaluating the role of ARSA in Chinese patients with Parkinson's disease. Neurobiol Aging 2021; 109:269-272. [PMID: 34531044 DOI: 10.1016/j.neurobiolaging.2021.08.008] [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: 02/24/2021] [Revised: 08/01/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
Recent studies have suggested ARSA, a gene responsible for metachromatic leukodystrophy, could be a genetic modifier of Parkinson's disease (PD) pathogenesis, acting as a molecular chaperone for α-synuclein. To elucidate the role of ARSA variants in PD, we did a comprehensive analysis of ARSA variants by performing next-generation sequencing on 477 PD families, 1440 sporadic early-onset PD patients and 1962 sporadic late-onset PD patients and 2636 controls from Chinese mainland, as well as the association between ARSA variants and cognitive function of PD patients. We identified 2 familial PD following autosomal dominant inherence carrying rare variants of ARSA, but they had limited clinical significance. We detected a total of 81 coding variants of ARSA in our subjects but none of the identified variants were associated with either susceptibility or cognitive performance of PD, while loss-of-function variants showed slightly increased burden in late-onset PD (0.25% vs. 0%, p = 0.08). Our results suggested ARSA may not play important roles in PD of Chinese population.
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Affiliation(s)
- Hong-Xu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi-Ge Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu-Wen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Zeng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zheng-Huan Fang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Run-Cheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi-Ying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie-Qiong Tan
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xin-Xiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jin-Chen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
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Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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Abstract
OBJECTIVES To assess whether regulatory guidance on the use of dexamethasone in hospitalised COVID-19 patients is applicable to the larger population of COVID-19 cases. The surge in worldwide demand for dexamethasone suggests that the guidance, although correct, has not emphasised the danger of its wider use. STUDY DESIGN Data from the Randomised Evaluation of COVID-19 Therapy (RECOVERY) trial and the World Health Organisation (WHO) prospective meta-analysis have been deconstructed and analysed. METHODS To provide context, relevant publications were identified in PubMed using the following keywords: COVID-19, RECOVERY trial, WHO meta-analysis, variants, immunity, public health. RESULTS The WHO guidance 'Corticosteroids for COVID-19' was based on their prospective meta-analysis. This meta-analysis was weighted by data from the RECOVERY trial. CONCLUSIONS In terms of COVID-19, dexamethasone has value in a narrow indication, namely, in hospitalised patients requiring respiratory support. The media blitz likely resulted in the wider use of dexamethasone in outpatients and as a preventive medication. This is reflected in the surge in worldwide demand for dexamethasone. We ask whether the use of steroids, beyond regulatory indications, may be responsible for the recent increase in mortality and especially the emergence of mucormycosis? From the public health standpoint, the current guidance for use of dexamethasone in COVID-19 could benefit from clarification and the addition of a cautionary note.
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Affiliation(s)
- M Fernandes
- Medbase, 114 Milton Avenue, Chapel Hill, NC, 27514, USA.
| | - J Brábek
- Department of Cell Biology, Charles University, Viničná 7, Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, Vestec U Prahy, 25242, Czech Republic
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Roberts NJ, Grant RC, Gallinger S, Klein AP. Germline sequence analysis of RABL3 in a large series of pancreatic ductal adenocarcinoma patients reveals no evidence of deleterious variants. Genes Chromosomes Cancer 2021; 60:559-564. [PMID: 33724601 PMCID: PMC8251898 DOI: 10.1002/gcc.22947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a 5-year survival rate of less than 10%. Individuals with a pathogenic germline variant in a pancreatic cancer susceptibility gene are at an increased risk of developing pancreatic cancer. Understanding the inherited genetic basis of pancreatic tumor development provides a unique opportunity to improve patient care and outcomes. For example, relatives of a patients with PDAC who have a pathogenic germline variant in a pancreatic cancer susceptibility gene are eligible for disease surveillance where cancers may be detected early, and 5-year survival greatly improved. Furthermore, for some patients with PDAC and a pathogenic germline variant in a pancreatic cancer susceptibility gene, their tumors may be susceptible to specific anti-cancer therapies. Recently, RABL3 was identified as a pancreatic cancer susceptibility gene. To validate these findings and inform clinical translation, we determined the prevalence of deleterious RABL3 variants in a large cohort of 1037 patients with PDAC that had undergone either whole genome or whole exome germline sequencing. We identified two synonymous variants and four missense variants classified as variants of unknown significance. We found no pathogenic RABL3 variants, indicating that the maximum prevalence of such variants in patients with PDAC is less than 0.36% (minor allele frequency 0, 97.5% one-sided confidence interval: 0-0.0036). This finding has important implications for germline genetic testing of patients with PDAC.
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Affiliation(s)
- Nicholas J. Roberts
- Department of PathologyThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Sol Goldman Pancreatic Cancer Research CenterThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of OncologyThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Robert C. Grant
- Divison of Medical Oncology and HematologyPrincess Margaret Hospital Cancer CentreTorontoOntarioCanada
- PanCuRx Translational Research InitiativeOntario Institute for Cancer ResearchTorontoOntarioCanada
| | - Steven Gallinger
- PanCuRx Translational Research InitiativeOntario Institute for Cancer ResearchTorontoOntarioCanada
| | - Alison P. Klein
- Department of PathologyThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- The Sol Goldman Pancreatic Cancer Research CenterThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of OncologyThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of EpidemiologyThe Johns Hopkins Bloomberg School of Public HealthBaltimoreMarylandUSA
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Martínez-Casillas KCE, Saucedo-Sariñana AM, Barros-Núñez P, Gallegos-Arreola MP, Pineda-Razo TD, Marín-Contreras ME, Flores-Martínez SE, Rosales-Reynoso MA. MKK4 variants rs3826392 and rs3809728 are associated with susceptibility and clinicopathological features in colorectal cancer patients. Iran J Basic Med Sci 2021; 24:1033-1040. [PMID: 34804420 PMCID: PMC8591758 DOI: 10.22038/ijbms.2021.56874.12690] [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: 04/07/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The mitogen-activated protein kinase kinase 4 (MKK4) plays a key role in several processes like inflammation, apoptosis, and tumorigenesis. Several authors have proposed that genetic variations in these genes may alter their expression with subsequent cancer risk. This study aimed to examine the possible association of MKK4 rs3826392 and rs3809728 variants in Mexican patients with colorectal cancer (CRC). These variants were also compared with clinical features as sex, age, TNM stage, and tumor location. MATERIALS AND METHODS The study included genomic DNA from 218 control subjects and 250 patients. Genotyping of the MKK4 variants was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) procedure. RESULTS Individuals with A/T and T/T genotypes for the rs3809728 (-1044 A>T) variant showed a significantly increased risk for CRC (P=0.012 and 0.007, respectively); while individuals with the G/G genotype for the rs3826392 (-1304 T>G) variant showed a decreased risk for CRC (P=0.012). Genotypes of the MKK4 rs3809728 variant were also significantly related to colon localization and advanced TNM stage in CRC patients. T-T haplotype (rs3826392 and rs3809728) of the MKK4 gene was associated with risk in patients with CRC. CONCLUSION The rs3826392 variant in the MKK4 gene could be a cancer protective factor, while the rs3809728 variant could be a risk factor. These variants play a significant role in CRC risk.
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Affiliation(s)
| | - Anilú Margarita Saucedo-Sariñana
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - Patricio Barros-Núñez
- Unidad de Investigación Seguimiento Enfermedades Metabólicas, Unidad Médica de Alta Especialidad Pediatría, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco. México
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - Tomás Daniel Pineda-Razo
- Servicio de Oncología Médica, Hospital de Especialidades, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - María Eugenia Marín-Contreras
- Servicio de Gastroenterología, Hospital de Especialidades, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - Silvia Esperanza Flores-Martínez
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - Mónica Alejandra Rosales-Reynoso
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México,Corresponding author: Mónica Alejandra Rosales-Reynoso. División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México. Tel/ Fax: +52-3336683000;
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