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Ceylan AC, Çavdarlı B, Ceylan GG, Topçu V, Satılmış SBA, Bektaş ŞG, Kalem AK, Kayaaslan B, Eser F, Kalkan EA, İnan O, Hasanoğlu İ, Yüksel S, Ateş İ, İzdeş S, Güner R, Gündüz CNS. Impact of Inflammation-Related Genes on COVID-19: Prospective Study at Turkish Cohort. TOHOKU J EXP MED 2023; 261:179-185. [PMID: 37635061 DOI: 10.1620/tjem.2023.j071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
The pandemic coronavirus disease 2019 (COVID-19) has caused a high mortality rate and poses a significant threat to the population. The disease may progress with mild symptoms or may cause the need for intensive care, depending on many factors. In this study, it was aimed to determine if there is a tendency due to genetic factors in COVID-19 patients. Ninety-four of 188 patients with mild clinical and 94 with severe clinical symptoms were included in the study. The targeted panel including coagulopathy (F2, F5), viral invasion (ACE2), and inflammation (CXCL8, IFNAR2, IFNL4, IL10, IL2, IL6, IRF7, TLR3, TLR7, TNF) related genes was performed sequenced by the next generation sequencing (NGS). The variants found were classified and univariate analyses were performed to select candidate variables for logistic model. Risk factors and variants were compared. It was revealed that the presence of 2 or more risk factors caused the disease to progress severely (p < 0.001). Heterozygous IRF7:c.1357-23dup variant had a 2.5 times higher risk for mild disease compared to severe disease. Other variants were found to be more significant in mild disease. Since polymorphic variants were not evaluated in the literature, the findings of our study could not be compared with the literature. However, as variants that may be effective in the severity of infections may differ according to ethnicity. This study has the feature of being a guide for subsequent studies to be carried out especially in Turkish population. Clinical course of the COVID-19 is likely to depend on a variety of risk factors, including age, sex, clinical status, immunology and genetic factors.
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Affiliation(s)
- Ahmet Cevdet Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
| | | | - Gülay Güleç Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
| | - Vehap Topçu
- Department of Medical Genetics, Ankara City Hospital
| | | | | | - Ayşe K Kalem
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Bircan Kayaaslan
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Fatma Eser
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | | | - Osman İnan
- Department of Internal Medicine, Ankara City Hospital
| | - İmran Hasanoğlu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Selcen Yüksel
- Department of Biostatistics, Ankara Yıldırım Beyazıt University
| | - İhsan Ateş
- Department of Internal Medicine, Ankara City Hospital, Health Science University
| | - Seval İzdeş
- Department of Anesthesiology and Reanimation-Critical Care, Ankara City Hospital
- Department of Anesthesiology and Reanimation-Critical Care, Faculty of Medicine, Ankara Yıldırım Beyazıt University
| | - Rahmet Güner
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - C Nur Semerci Gündüz
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
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Islam MA, Kaifa FH, Chandran D, Bhattacharya M, Chakraborty C, Bhattacharya P, Dhama K. XBB.1.5: A new threatening SARS-CoV-2 Omicron subvariant. Front Microbiol 2023; 14:1154296. [PMID: 37143546 PMCID: PMC10152970 DOI: 10.3389/fmicb.2023.1154296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Md. Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Kishoreganj, Bangladesh
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Fatema Hasan Kaifa
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Deepak Chandran
- Department of Veterinary Sciences and Animal Husbandry, Amrita School of Agricultural Sciences, Amrita Vishwa Vidyapeetham University, Coimbatore, Tamil Nadu, India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, VyasaVihar, Balasore, Odisha, India
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | - Prosun Bhattacharya
- COVID-19 Research @KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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3
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Gimenes Lima G, Portilho AI, De Gaspari E. Animal Models to Test SARS-CoV-2 Vaccines: Which Ones Are in Use and Future Expectations. Pathogens 2022; 12. [PMID: 36678369 DOI: 10.3390/pathogens12010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Since late 2019 and early 2020, with the emergence of the COVID-19 pandemic, scientists are rushing to develop treatment and prevention methods to combat SARS-CoV-2. Among these are vaccines. In view of this, the use of animals as experimental models, both to investigate the immunopathology of the disease and to evaluate the efficacy and safety of vaccines, is mandatory. This work aims to describe, through recent scientific articles found in reliable databases, the animal models used for the in vivo testing of COVID-19 vaccines, demonstrating some possibilities of more advantageous/gold-standard models for SARS-CoV-2 vaccines. The majority of the studies use rodents and primates. Meanwhile, the most adequate model to be used as the gold standard for in vivo tests of COVID-19 vaccines is not yet conclusive. Promising options are being discussed as new tests are being carried out and new SARS-CoV-2 variants are emerging.
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Lee J, Lee DG, Jung J, Ryu JH, Shin S, Cho SY, Lee R, Oh EJ. Comprehensive assessment of SARS-CoV-2 antibodies against various antigenic epitopes after naive COVID-19 infection and vaccination (BNT162b2 or ChAdOx1 nCoV-19). Front Immunol 2022; 13:1038712. [PMID: 36578491 PMCID: PMC9791030 DOI: 10.3389/fimmu.2022.1038712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Comprehensive assessment of SARS-CoV-2 antibodies against antigenic epitopes and cross-neutralization on variants is essential to monitor after infection or vaccination. From 32 COVID-19 patients and 40 vaccinated individuals [20 Oxford-AstraZeneca (AZ) and 20 Pfizer-BioNTech (BNT)], 348 serial sera are collected until 40 days after infection and 3 months after homologous booster vaccination. Antibody levels were monitored using a multiplex-bead assay including variant spike antigens, Roche (S1/RBD total) and a surrogate virus neutralization test (GenScript). Anti-S/S1/RBD levels were higher than anti-S2/N levels from 2 weeks after infection and were higher in severe infection (P < 0.05). Vaccination showed highest antibody levels after 1-month booster and had consistently high levels in the order of anti-full S, anti-RBD, anti-S1 and anti-S2. Infection induced higher anti-S2/N levels than prime vaccination (P < 0.05). Three months after BNT/BNT vaccination, antibody levels against S1/RBD and 23 variant antigens were higher than post-infection or AZ groups (P < 0.05). Regarding intraindividual changes from post-prime to post-boost vaccination, boost induced a 1.1- to 3.9-fold increase on multiplex-bead assay, 22.8- to 24.2-fold on Roche assay and 22.8- to 24.2-fold on GenScript assay. Post-prime levels by multiplex-bead assay predicted post-boost levels, but Roche and GenScript results were not predictive in the AZ group. The kinetics of SARS-CoV-2 antibody levels vary depending on the antigenic epitopes, assay kit, disease severity or vaccine type. Assessing seroconversion using multiplex-bead assays may contribute to monitoring the disease course, adjusting vaccination strategies, and accelerating vaccination efficacy.
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Affiliation(s)
- Jihyun Lee
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dong-Gun Lee
- Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Jung
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Resesarch and Development Institute for In Vitro Diagnostic Medical Devices of Catholic University of Korea, Seoul, Republic of Korea
| | - Ji Hyeong Ryu
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soyoung Shin
- Resesarch and Development Institute for In Vitro Diagnostic Medical Devices of Catholic University of Korea, Seoul, Republic of Korea,Department of Laboratory Medicine, Daejeon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung-Yeon Cho
- Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Raeseok Lee
- Division of Infectious Diseases, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eun-Jee Oh
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Resesarch and Development Institute for In Vitro Diagnostic Medical Devices of Catholic University of Korea, Seoul, Republic of Korea,*Correspondence: Eun-Jee Oh,
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Alba JMG, Pérez-Martínez Z, Boga JA, Rojo-Alba S, de Oña JG, Alvarez-Argüelles ME, Rodríguez GM, Gonzalez IC, González IH, Coto E, García SM. Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy. Microorganisms 2022; 10:1954. [PMID: 36296230 PMCID: PMC9610377 DOI: 10.3390/microorganisms10101954] [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: 08/19/2022] [Revised: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. METHODS From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. RESULTS The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. CONCLUSIONS The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.
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Affiliation(s)
- José María González Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Zulema Pérez-Martínez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - José A. Boga
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Susana Rojo-Alba
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Juan Gómez de Oña
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Marta E. Alvarez-Argüelles
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Garbriel Martín Rodríguez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Isabel Costales Gonzalez
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | | | - Eliecer Coto
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Genetic Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Santiago Melón García
- Unit of Virology, Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitario del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Pedini P, Filosa L, Bichel N, Picard C, Silvy M, Chiaroni J, Izard C, Laget L, Mazières S. Five-Years Review of RHCE Alleles Detected after Weak and/or Discrepant C Results in Southern France. Genes (Basel) 2022; 13:1058. [PMID: 35741820 DOI: 10.3390/genes13061058] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
Immunohematology laboratories are regularly facing transfusion issues due to serological weaknesses. Altered (partial) RH antigens account for most of them. In some situations, RHCE variant alleles are involved. Herein we present our three-step molecular exploration, with allele frequencies, that has efficiently untangled RH2 phenotype weaknesses and discrepancies in our 2017–2021 cohort. In the last 5 years, the PACA Corse EFS molecular platform received 265 samples from healthy blood donors or patients with C and C/e typing difficulties. The first-intention technique (DNA array and real time PCR for RHCE*CeRN research) detected RHCE variant alleles in 143 cases (54%). The RHCE alleles classically found in African populations were the most frequent, with RHCE*CeRN allele in 40 cases (15%) and (C)ces haplotype type 1 and 2 in 26 cases (10%). A “CE” effect haplotype was suspected in 56 cases, due to the uncommon DCE haplotype that may explain the low C expression. When there were no RHCE*Ce or RHCE*CE alleles, we then searched for RHD polymorphisms by DNA array. We detected the RHD*DAU5 and RHD*DIVa in 18 and 7 cases respectively, suggesting that C ambiguity is related to the presence of these alleles which has never been described with DAU5. If no variant RHCE and RHD alleles were detected, we finally sequenced the 10 exons of both RHCE and RHD genes according to the clinical context and found seven new RHCE alleles. Thus, this molecular strategy would improve the knowledge of RHCE variants’ expression and, thus, optimize the transfusion management.
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Sant' Ana I, Torrini R, Alves Coelho MC, Cantoni J, Madeira M, Ribeiro M. X-linked hypophosphatemic rickets: Description of seven new variants in patients followed up in reference hospitals in Rio de Janeiro. Mol Genet Genomic Med 2022; 10:e1941. [PMID: 35384411 PMCID: PMC9184672 DOI: 10.1002/mgg3.1941] [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: 08/05/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background X‐linked hypophosphatemic rickets (XLHR) is a rare genetic disease, often delayed in diagnosis due to the low degree of suspicion and limited access to sophisticated diagnostic tools that confirm the diagnosis, such as genetic testing. Methods Through a cross‐sectional and observational study, 26 patients with a previously presumptive diagnosis of X‐linked hypophosphatemic rickets (based on clinical history, laboratory findings, and physical examination), were followed for approximately 12 months. During 12 months of follow‐up, only 16 patients underwent genetic testing and enrolled in the study. Previous data were analyzed, such as clinical history (e.g., gender, current age, age of clinical diagnosis, age of admission to hospital, family history, and previous orthopedic surgery), physical exam, imaging tests (e.g., radiological changes) and laboratory tests (e.g., tubular maximum reabsorption rate of phosphate to glomerular filtration rate, alkaline phosphatase, and phosphate levels) at the time of the patient’s admission to IEDE and UFRJ, to corroborate and substantiate our research. These data were extracted from the medical records of the patients. Results Among the 16 patients analyzed by molecular biology techniques, the new generation sequencing (NGS), using DNA samples from oral swabs, we obtained seven variants never previously described, which were verified by Sanger sequencing. Among the seven variants never previously described, the most common coding impact was the nonsense mutation. We found two frameshift, one intronic splicing variant, three nonsense, and one deletion splice junction loss. Among patients with new mutations who presented data in the medical record, 100% showed a reduction in TmP/GFR (average of 1.98 mg/dl), the most sensitive laboratory parameter at the time of diagnosis, as well as serum phosphorus (100% had hypophosphatemia on arrival at the referral hospitals––average of 2.4 mg/dl and median 2.3 mg/dl). We also performed NGS on three mothers of the patients with identified mutations. Among these mothers, only one tested negative for the mutation and no family history was reported as well. This mother had serum phosphate of 3.5 mg/dl (normal range: 2.5–4.5 mg/dl) at the time of genetic test collection. The others had a positive test, low serum phosphorus at the time of the molecular test, in addition to a positive family history. Conclusion This study describes seven new variants in the PHEX gene and aims to increase the knowledge of the scientific community about the types of mutations involving this gene, increasing information on the genetic basis of this condition, enabling future considerations about genotype–phenotype correlation, in addition to diagnosis accurate and early.
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Affiliation(s)
- Iara Sant' Ana
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil.,Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Renato Torrini
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | | | - Joyce Cantoni
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | - Miguel Madeira
- Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Márcia Ribeiro
- Medical Genetic Service, Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Mukherjee S, Ray SK. Third waves of the COVID-19 pandemic: Prominence of initial public health Interference. Infect Disord Drug Targets 2022; 22:e080222200919. [PMID: 35135456 DOI: 10.2174/1871526522666220208115101] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/06/2021] [Accepted: 12/02/2021] [Indexed: 11/22/2022]
Abstract
Since the first news of a coronavirus-related pneumonia outbreak in December 2019, the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which causes COVID-19, has spread worldwide, with more than 100 million people infected in over 210 countries and two million people dying as of today. In the UK (B.1.1.7), South Africa (B.1.351), Brazil (P.1), and India (B.1.617), independent SARS-CoV-2 lineages have recently been established. The virus will access these variants via the angiotensin-converting enzyme-2 (ACE2) receptor due to several mutations in the immune-dominant spike protein. SARS-CoV-2 has caused substantial morbidity and mortality, as well as significant strain on public health systems and the global economy, due to the severity and intensity at which it has spread. COVID-19 vaccines have shown to be highly successful in clinical trials and can be used to fight the pandemic. The COVID-19 pandemic's environmental trends change at breakneck speed, making predictions based on traditional epidemiological knowledge particularly speculative. Following the first outbreak, the second wave of COVID-19 swept across the globe, infecting various countries. A third wave of coronavirus infection has already been experienced in a few countries. Many of us have said, "When this is over," but what exactly does that mean? Since the virus's first-, second-, and third-order effects manifest over various time periods, the pandemic will not be considered 'over' until the 'third phase' of the COVID-19 pandemic has passed. It is the best time to take preventative steps and immunize ourselves with vaccines in order to prepare for the predicted third wave of COVID-19 in some countries. To effectively suppress and monitor the COVID-19 pandemic, early and timely measures with improved social distancing policies should be enforced. We must continue critical public health efforts to suppress transmission and reduce mortality while working toward the rollout of a safe and efficient vaccine, and we must have the patience to listen, learn, improve, innovate, and evolve.
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Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020. India
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Alhudiri IM, Ramadan AM, Ibrahim KM, Abdalla A, Eljilani M, Salem MA, Elgheriani HM, El Meshri SE, Elzagheid A. Whole-genome sequencing of SARS-COV-2 showed wide spread of B.1.525 in February 2021 in Libya. Libyan J Med 2021; 16:2001210. [PMID: 34757863 PMCID: PMC8583741 DOI: 10.1080/19932820.2021.2001210] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alpha (B.1.1.7) SARS-COV-2 variant was detected in September 2020 in minks and humans in Denmark and UK. This variant has several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The National Center for Disease Control (NCDC) announced on 24 February 2021 a 25% frequency of B.1.1.7 strain in Libya using a reverse-transcriptase quantitative PCR assay. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes its failure of amplification (SGTF). This deletion is not specific for B.1.1.7, but is also characteristic of two other SARS-COV-2 variants. This study aimed to estimate the frequency of B.1.1.7 and identify other variants circulating in Libya in February 2021. We performed whole genome sequencing of 67 positive SARS-COV-2 samples collected on 25 February 2021 in Libya which were also tested by RT-qPCR for SGTF. Our results showed that 55% of samples had mutations specific to B.1.525 strain and only ~3% of samples belonged to B.1.1.7. These findings suggested that B.1.525 was spreading widely in Libya. The use of such RT-qPCR assay, although useful to track some variants, cannot discriminate between variants with H69-V70 deletion. RT-qPCR assays could be multiplexed to identify multiple variants and screen samples prior to sequencing. We emphasize on the need for providing whole-genome sequencing to the main COVID-19 diagnostic laboratories in Libya as well as establishing international collaboration for building capacity and advancing research in this time of the pandemic.
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Affiliation(s)
- Inas M Alhudiri
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
| | - Ahmad M Ramadan
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
| | - Khaled M Ibrahim
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
| | - Adel Abdalla
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
| | - Mouna Eljilani
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
| | - Mohamed Ali Salem
- Microbiology Department, Biotechnology Research Center, Tripoli, Libya
| | | | | | - Adam Elzagheid
- Genetic Engineering Department, Biotechnology Research Center, Tripoli, Libya
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Khan A, Mohammad A, Haq I, Nasar M, Ahmad W, Yousafi Q, Suleman M, Ahmad S, Albutti A, Khan T, Marafie SK, Alshawaf E, Ali SS, Abubaker J, Wei DQ. Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity. Microorganisms 2021; 9:2331. [PMID: 34835456 PMCID: PMC8619099 DOI: 10.3390/microorganisms9112331] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 01/21/2023] Open
Abstract
Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Inamul Haq
- Department of Animal Sciences, Jeonbuk National University, 567 Baekji-Daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Jeonju 54896, Korea;
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea
| | - Mohammad Nasar
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Waqar Ahmad
- Department of Microbiology, Abdul Wali Khan University (AWKUM), Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25120, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Sulaiman K. Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
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11
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Januszewski M, Ziuzia-Januszewska L, Santor-Zaczynska M, Jakimiuk AA, Oleksik T, Pokulniewicz M, Pluta K, Wierzba W, Jakimiuk AJ. COVID-19 in Pregnancy-Perinatal Outcomes and Vertical Transmission Preventative Strategies, When Considering More Transmissible SARS-CoV-2 Variants. J Clin Med 2021; 10:3724. [PMID: 34442020 DOI: 10.3390/jcm10163724] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic affected the physical and mental health of people around the world and left unprepared health care systems struggling to mount an adequate response. Understanding the impact of COVID-19 on pregnancy in terms of perinatal and fetal outcomes is essential to propose strategies for mminimising viral transmission. Overall, 91 pregnant women in labour, or with indication for induction of labour, with COVID-19 were admitted to hospital. On the day of admission, each pregnant woman underwent a nasopharyngeal swab to validate SARS-CoV-2 infection. Whenever delivery was by caesarean section, an amniotic fluid sample was collected after uterus incision. Neonates were tested twice: first by nasopharyngeal swab at birth and secondly either at 24 h after (when babies were isolated) or at discharge (when rooming-in). All samples underwent rRT-PCR testing for SARS-CoV-2. The SARS-CoV-2 RNA tests by nasopharyngeal swab of the pregnant women produced positive results in 47 patients. This cohort gave birth to 48 infants who were double tested by nasopharyngeal swab and included in the prospective observational study. Moreover, in this same cohort, 39 amniotic fluid samples were taken during caesarean section. All samples underwent rRT-PCR testing for SARS-CoV-2 and came back negative. The study results suggest a low risk of vertical transmission of COVID-19 and favourable perinatal outcomes due to adequate preventative strategies. This approach may prove to be more beneficial in the new SARS-CoV-2 variants era.
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12
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Khan A, Zia T, Suleman M, Khan T, Ali SS, Abbasi AA, Mohammad A, Wei DQ. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. J Cell Physiol 2021; 236:7045-7057. [PMID: 33755190 PMCID: PMC8251074 DOI: 10.1002/jcp.30367] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The evolution of the SARS‐CoV‐2 new variants reported to be 70% more contagious than the earlier one is now spreading fast worldwide. There is an instant need to discover how the new variants interact with the host receptor (ACE2). Among the reported mutations in the Spike glycoprotein of the new variants, three are specific to the receptor‐binding domain (RBD) and required insightful scrutiny for new therapeutic options. These structural evolutions in the RBD domain may impart a critical role to the unique pathogenicity of the SARS‐CoV‐2 new variants. Herein, using structural and biophysical approaches, we explored that the specific mutations in the UK (N501Y), South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y), and hypothetical (N501Y‐E484K) variants alter the binding affinity, create new inter‐protein contacts and changes the internal structural dynamics thereby increases the binding and eventually the infectivity. Our investigation highlighted that the South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y) variants are more lethal than the UK variant (N501Y). The behavior of the wild type and N501Y is comparable. Free energy calculations further confirmed that increased binding of the spike RBD to the ACE2 is mainly due to the electrostatic contribution. Further, we find that the unusual virulence of this virus is potentially the consequence of Darwinian selection‐driven epistasis in protein evolution. The triple mutants (South African and Brazilian) may pose a serious threat to the efficacy of the already developed vaccine. Our analysis would help to understand the binding and structural dynamics of the new mutations in the RBD domain of the Spike protein and demand further investigation in in vitro and in vivo models to design potential therapeutics against the new variants.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Tauqir Zia
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber-Pakhtunkhwa, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber-Pakhtunkhwa, Pakistan
| | - Aamir Ali Abbasi
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Guangdong, Shenzhen, P.R. China
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13
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Hernández-Zavala A, Cortés-Camacho F, Palma-Lara I, Godínez-Aguilar R, Espinosa AM, Pérez-Durán J, Villanueva-Ocampo P, Ugarte-Briones C, Serrano-Bello CA, Sánchez-Santiago PJ, Bonilla-Delgado J, Yáñez-López MA, Victoria-Acosta G, López-Ornelas A, García Alonso-Themann P, Moreno J, Palacios-Reyes C. Two Novel FAM20C Variants in A Family with Raine Syndrome. Genes (Basel) 2020; 11:genes11020222. [PMID: 32093234 PMCID: PMC7073523 DOI: 10.3390/genes11020222] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 11/29/2019] [Revised: 01/30/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
Two siblings from a Mexican family who carried lethal Raine syndrome are presented. A newborn term male (case 1) and his 21 gestational week brother (case 2), with a similar osteosclerotic pattern: generalized osteosclerosis, which is more evident in facial bones and cranial base. Prenatal findings at 21 weeks and histopathological features for case 2 are described. A novel combination of biallelic FAM20C pathogenic variants were detected, a maternal cytosine duplication at position 456 and a paternal deletion of a cytosine in position 474 in exon 1, which change the reading frame with a premature termination at codon 207 and 185 respectively. These changes are in concordance with a negative detection of the protein in liver and kidney as shown in case 2. Necropsy showed absence of pancreatic Langerhans Islets, which are reported here for the first time. Corpus callosum absence is added to the few reported cases of brain defects in Raine syndrome. This report shows two new FAM20C variants not described previously, and negative protein detection in the liver and the kidney. We highlight that lethal Raine syndrome is well defined as early as 21 weeks, including mineralization defects and craniofacial features. Pancreas and brain defects found here in FAM20C deficiency extend the functional spectrum of this protein to previously unknown organs.
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Affiliation(s)
- Araceli Hernández-Zavala
- Laboratory of Cellular and Molecular Morphology, Section of Postgraduate Studies and Research, Escuela Superior de Medicina, Instituto Politécnico Nacional, Salvador Díaz Mirón esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Mexico City 11340, Mexico; (A.H.-Z.); (F.C.-C.); (I.P.-L.)
| | - Fernando Cortés-Camacho
- Laboratory of Cellular and Molecular Morphology, Section of Postgraduate Studies and Research, Escuela Superior de Medicina, Instituto Politécnico Nacional, Salvador Díaz Mirón esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Mexico City 11340, Mexico; (A.H.-Z.); (F.C.-C.); (I.P.-L.)
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Icela Palma-Lara
- Laboratory of Cellular and Molecular Morphology, Section of Postgraduate Studies and Research, Escuela Superior de Medicina, Instituto Politécnico Nacional, Salvador Díaz Mirón esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Mexico City 11340, Mexico; (A.H.-Z.); (F.C.-C.); (I.P.-L.)
| | - Ricardo Godínez-Aguilar
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Ana María Espinosa
- Service of Clinical Pharmacology, Hospital General de México, Dr. Balmis 148, Doctores, Cuauhtémoc, Mexico City 06720, Mexico;
| | - Javier Pérez-Durán
- National Institute of Perinatology, Calle Montes Urales 800, Lomas - Virreyes, Lomas de Chapultepec IV Section, Miguel Hidalgo, Mexico City 11000, Mexico; (J.P.-D.); (P.G.A.-T.)
| | - Patricia Villanueva-Ocampo
- Deparment of Ginecology, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico;
| | - Carlos Ugarte-Briones
- Department of Pathology, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (C.U.-B.); (C.A.S.-B.); (P.J.S.-S.)
| | - Carlos Alberto Serrano-Bello
- Department of Pathology, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (C.U.-B.); (C.A.S.-B.); (P.J.S.-S.)
| | - Paula Jesús Sánchez-Santiago
- Department of Pathology, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (C.U.-B.); (C.A.S.-B.); (P.J.S.-S.)
| | - José Bonilla-Delgado
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Marco Antonio Yáñez-López
- Department of Radiology & Imagenology, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico;
| | - Georgina Victoria-Acosta
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Adolfo López-Ornelas
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Patricia García Alonso-Themann
- National Institute of Perinatology, Calle Montes Urales 800, Lomas - Virreyes, Lomas de Chapultepec IV Section, Miguel Hidalgo, Mexico City 11000, Mexico; (J.P.-D.); (P.G.A.-T.)
| | - José Moreno
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
| | - Carmen Palacios-Reyes
- Direction and Division of Research, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Mexico City 07760, Mexico; (R.G.-A.); (J.B.-D.); (G.V.-A.); (A.L.-O.); (J.M.)
- Correspondence:
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