1
|
Xu YL, Li XJ, Cai W, Yu WY, Chen J, Lee Q, Choi YJ, Wu F, Lou YJ, Ying HZ, Yu CH, Wu QF. Diosmetin-7-O-β-D-glucopyranoside from Pogostemonis Herba alleviated SARS-CoV-2-induced pneumonia by reshaping macrophage polarization and limiting viral replication. JOURNAL OF ETHNOPHARMACOLOGY 2025; 336:118704. [PMID: 39182703 DOI: 10.1016/j.jep.2024.118704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Viral pneumonia is the leading cause of death after SARS-CoV-2 infection. Despite effective at early stage, long-term treatment with glucocorticoids can lead to a variety of adverse effects and limited benefits. The Chinese traditional herb Pogostemonis Herba is the aerial part of Pogostemon Cablin (Blanco) Benth., which has potent antiviral, antibacterial, anti-inflammatory, and anticancer effects. It was used widely for treating various throat and respiratory diseases, including COVID-19, viral infection, cough, allergic asthma, acute lung injury and lung cancer. AIM OF THE STUDY To investigate the antiviral and anti-inflammatory effects of chemical compounds from Pogostemonis Herba in SARS-CoV-2-infected hACE2-overexpressing mouse macrophage RAW264.7 cells and hACE2 transgenic mice. MATERIALS AND METHODS The hACE2-overexpressing RAW264.7 cells were exposed with SARS-CoV-2. The cell viability was detected by CCK8 assay and cell apoptotic rate was by flow cytometric assay. The expressions of macrophage M1 phenotype markers (TNF-α and IL-6) and M2 markers (IL-10 and Arg-1) as well as the viral loads were detected by qPCR. The mice were inoculated intranasally with SARS-CoV-2 omicron variant to induce viral pneumonia. The levels of macrophages, neutrophils, and T cells in the lung tissues of infected mice were analyzed by full spectrum flow cytometry. The expressions of key proteins were detected by Western blot assay. RESULTS Diosmetin-7-O-β-D-glucopyranoside (DG) presented the strongest anti-SARS-CoV-2 activity. Intervention with DG at the concentrations of 0.625-2.5 μM not only reduced the viral replication, cell apoptosis, and the productions of inflammatory cytokines (IL-6 and TNF-α) in SARS-CoV-2-infected RAW264.7 cells, but also reversed macrophage polarity from M1 to M2 phenotype. Furthermore, treatment with DG (25-100 mg/kg) alleviated acute lung injury, and reduced macrophage infiltration in SARS-COV-2-infected mice. Mechanistically, DG inhibited SARS-COV-2 gene expression and HK3 translation via targeting YTHDF1, resulting in the inactivation of glycolysis-mediated NF-κB pathway. CONCLUSIONS DG exerted the potent antiviral and anti-inflammatory activities. It reduced pneumonia in SARS-COV-2-infected mice via inhibiting the viral replication and accelerating M2 macrophage polarization via targeting YTHDF1, indicating its potential for COVID-19 treatment.
Collapse
Affiliation(s)
- Yun-Lu Xu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xue-Jian Li
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Wei Cai
- College of Chinese Medicine, Zhejiang Pharmaceutical University, Ningbo, 315500, China
| | - Wen-Ying Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Jing Chen
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qin Lee
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China; Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea
| | - Yong-Jun Choi
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea
| | - Fang Wu
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ying-Jun Lou
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Hua-Zhong Ying
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Chen-Huan Yu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China.
| | - Qiao-Feng Wu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| |
Collapse
|
2
|
Wang S, Li W, Wang Z, Yang W, Li E, Xia X, Yan F, Chiu S. Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduct Target Ther 2024; 9:223. [PMID: 39256346 PMCID: PMC11412324 DOI: 10.1038/s41392-024-01917-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/13/2024] [Accepted: 07/05/2024] [Indexed: 09/12/2024] Open
Abstract
To adequately prepare for potential hazards caused by emerging and reemerging infectious diseases, the WHO has issued a list of high-priority pathogens that are likely to cause future outbreaks and for which research and development (R&D) efforts are dedicated, known as paramount R&D blueprints. Within R&D efforts, the goal is to obtain effective prophylactic and therapeutic approaches, which depends on a comprehensive knowledge of the etiology, epidemiology, and pathogenesis of these diseases. In this process, the accessibility of animal models is a priority bottleneck because it plays a key role in bridging the gap between in-depth understanding and control efforts for infectious diseases. Here, we reviewed preclinical animal models for high priority disease in terms of their ability to simulate human infections, including both natural susceptibility models, artificially engineered models, and surrogate models. In addition, we have thoroughly reviewed the current landscape of vaccines, antibodies, and small molecule drugs, particularly hopeful candidates in the advanced stages of these infectious diseases. More importantly, focusing on global trends and novel technologies, several aspects of the prevention and control of infectious disease were discussed in detail, including but not limited to gaps in currently available animal models and medical responses, better immune correlates of protection established in animal models and humans, further understanding of disease mechanisms, and the role of artificial intelligence in guiding or supplementing the development of animal models, vaccines, and drugs. Overall, this review described pioneering approaches and sophisticated techniques involved in the study of the epidemiology, pathogenesis, prevention, and clinical theatment of WHO high-priority pathogens and proposed potential directions. Technological advances in these aspects would consolidate the line of defense, thus ensuring a timely response to WHO high priority pathogens.
Collapse
Affiliation(s)
- Shen Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Wujian Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhenshan Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin, China
| | - Wanying Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, 230027, Anhui, China.
- Department of Laboratory Medicine, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| |
Collapse
|
3
|
Carvajal JJ, García-Castillo V, Cuellar SV, Campillay-Véliz CP, Salazar-Ardiles C, Avellaneda AM, Muñoz CA, Retamal-Díaz A, Bueno SM, González PA, Kalergis AM, Lay MK. New insights into the pathogenesis of SARS-CoV-2 during and after the COVID-19 pandemic. Front Immunol 2024; 15:1363572. [PMID: 38911850 PMCID: PMC11190347 DOI: 10.3389/fimmu.2024.1363572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the respiratory distress condition known as COVID-19. This disease broadly affects several physiological systems, including the gastrointestinal, renal, and central nervous (CNS) systems, significantly influencing the patient's overall quality of life. Additionally, numerous risk factors have been suggested, including gender, body weight, age, metabolic status, renal health, preexisting cardiomyopathies, and inflammatory conditions. Despite advances in understanding the genome and pathophysiological ramifications of COVID-19, its precise origins remain elusive. SARS-CoV-2 interacts with a receptor-binding domain within angiotensin-converting enzyme 2 (ACE2). This receptor is expressed in various organs of different species, including humans, with different abundance. Although COVID-19 has multiorgan manifestations, the main pathologies occur in the lung, including pulmonary fibrosis, respiratory failure, pulmonary embolism, and secondary bacterial pneumonia. In the post-COVID-19 period, different sequelae may occur, which may have various causes, including the direct action of the virus, alteration of the immune response, and metabolic alterations during infection, among others. Recognizing the serious adverse health effects associated with COVID-19, it becomes imperative to comprehensively elucidate and discuss the existing evidence surrounding this viral infection, including those related to the pathophysiological effects of the disease and the subsequent consequences. This review aims to contribute to a comprehensive understanding of the impact of COVID-19 and its long-term effects on human health.
Collapse
Affiliation(s)
- Jonatan J. Carvajal
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Valeria García-Castillo
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | - Shelsy V. Cuellar
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
| | | | - Camila Salazar-Ardiles
- Center for Research in Physiology and Altitude Medicine (FIMEDALT), Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Andrea M. Avellaneda
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Antofagasta, Chile
| | - Christian A. Muñoz
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Angello Retamal-Díaz
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Margarita K. Lay
- Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, University of Antofagasta, Antofagasta, Chile
- Research Center in Immunology and Biomedical Biotechnology of Antofagasta (CIIBBA), University of Antofagasta, Antofagasta, Chile
- Millennium Institute on Immunology and Immunotherapy, Department of Biotechnology, Faculty of Marine Sciences and Biological Resources, Department of Medical Technology, Faculty of Health Sciences, University of Antofagasta, Antofagasta, Chile
| |
Collapse
|
4
|
Choi H, Hwang M, Cornelius L, Navarathna DH, Chatterjee P, Jinadatha C. Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak. Viruses 2024; 16:337. [PMID: 38543703 PMCID: PMC10974601 DOI: 10.3390/v16030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 05/23/2024] Open
Abstract
The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10-3 subs/site/year. This study provides more insight into an ever-evolving virus.
Collapse
Affiliation(s)
- Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Lisa Cornelius
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (L.C.); (C.J.)
| | - Dhammika H. Navarathna
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX 76504, USA;
| | - Piyali Chatterjee
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Chetan Jinadatha
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (L.C.); (C.J.)
- School of Medicine, Texas A&M University, Bryan, TX 77807, USA
| |
Collapse
|
5
|
Ciccozzi A, Fiori PL, Casu M, Sanna D, Ciccozzi M, Scarpa F. The mutation point of view of the SARS-CoV-2 HV.1 lineage. J Med Virol 2024; 96:e29359. [PMID: 38164631 DOI: 10.1002/jmv.29359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Affiliation(s)
- Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Azienza Ospedaliera Universitaria (AOU) Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| |
Collapse
|
6
|
Alrehaily A, Elfiky AA, Ibrahim IM, Ibrahim MN, Sonousi A. Novel sofosbuvir derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective. Sci Rep 2023; 13:23080. [PMID: 38155165 PMCID: PMC10754943 DOI: 10.1038/s41598-023-49712-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023] Open
Abstract
The human coronavirus, SARS-CoV-2, had a negative impact on both the economy and human health, and the emerging resistant variants are an ongoing threat. One essential protein to target to prevent virus replication is the viral RNA-dependent RNA polymerase (RdRp). Sofosbuvir, a uridine nucleotide analog that potently inhibits viral polymerase, has been found to help treat SARS-CoV-2 patients. This work combines molecular docking and dynamics simulation (MDS) to test 14 sofosbuvir-based modifications against SARS-CoV-2 RdRp. The results reveal comparable (slightly better) average binding affinity of five modifications (compounds 3, 4, 11, 12, and 14) to the parent molecule, sofosbuvir. Compounds 3 and 4 show the best average binding affinities against SARS-CoV-2 RdRp (- 16.28 ± 5.69 and - 16.25 ± 5.78 kcal/mol average binding energy compared to - 16.20 ± 6.35 kcal/mol for sofosbuvir) calculated by Molecular Mechanics Generalized Born Surface Area (MM-GBSA) after MDS. The present study proposes compounds 3 and 4 as potential SARS-CoV-2 RdRp blockers, although this has yet to be proven experimentally.
Collapse
Affiliation(s)
- Abdulwahed Alrehaily
- Biology Department, Faculty of Science, Islamic University of Madinah, 42351, Madinah, Saudi Arabia
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed N Ibrahim
- Clinical Laboratories Department, College of Applied Medical Sciences, Jouf University, Qurrayat, Saudi Arabia
| | - Amr Sonousi
- Pharmaceutical Organic Department, Faculty of Pharmacy, Cairo University, Giza, Egypt
- University of Hertfordshire Hosted By Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| |
Collapse
|
7
|
Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Gregoriou I, Ioannides M, Ioannou C, Kalakouta O, Karagiannis C, Marcou M, Masia C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Shammas C, Stylianou DC, Zinieri B, Lemey P, Network TCOMESSAR, Kostrikis LG. Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacton Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021-Oct 2022). Viruses 2023; 15:1933. [PMID: 37766339 PMCID: PMC10535466 DOI: 10.3390/v15091933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021-January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed "Deltacron", was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation-a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus's local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus's epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic's dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.
Collapse
Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, 6301 Larnaca, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Costakis Ioannou
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, 1148 Nicosia, Cyprus
| | | | - Markella Marcou
- Department of Microbiology, Archbishop Makarios III Hospital, 2012 Nicosia, Cyprus
| | - Christina Masia
- Medical Laboratory of Ammochostos General Hospital, Ammochostos General Hospital, 5310 Paralimni, Cyprus
| | - Michail Mendris
- Microbiology Department, Limassol General Hospital, 4131 Limassol, Cyprus
| | | | - Philippos C. Patsalis
- Medicover Genetics, 2409 Nicosia, Cyprus
- Medical School, University of Nicosia, 2417 Nicosia, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, 2029 Nicosia, Cyprus
| | - Christos Shammas
- S.C.I.N.A. Bioanalysis Sciomedical Centre Ltd., 4040 Limassol, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Barbara Zinieri
- Microbiology Department, Paphos General Hospital, Achepans, 8026 Paphos, Cyprus
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | | | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
| |
Collapse
|
8
|
He P, Xia K, Song Y, Tandon R, Channappanavar R, Zhang F, Linhardt RJ. Synthesis of multivalent sialyllactose-conjugated PAMAM dendrimers: Binding to SARS-CoV-2 spike protein and influenza hemagglutinin. Int J Biol Macromol 2023; 246:125714. [PMID: 37423440 PMCID: PMC10528195 DOI: 10.1016/j.ijbiomac.2023.125714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) and influenza viruses have spread around the world at an unprecedented rate. Despite multiple vaccines, new variants of SARS-CoV-2 and influenza have caused a remarkable level of pathogenesis. The development of effective antiviral drugs to treat SARS-CoV-2 and influenza remains a high priority. Inhibiting viral cell surface attachment represents an early and efficient means to block virus infection. Sialyl glycoconjugates, on the surface of human cell membranes, play an important role as host cell receptors for influenza A virus and 9-O-acetyl-sialylated glycoconjugates are receptors for MERS, HKU1 and bovine coronaviruses. We designed and synthesized multivalent 6'-sialyllactose-counjugated polyamidoamine dendrimers through click chemistry at room temperature concisely. These dendrimer derivatives have good solubility and stability in aqueous solutions. SPR, a real-time analysis quantitative method for of biomolecular interactions, was used to study the binding affinities of our dendrimer derivatives by utilizing only 200 micrograms of each dendrimer. Three SARS-CoV-2 S-protein receptor binding domain (wild type and two Omicron mutants) bound to multivalent 9-O-acetyl-6'-sialyllactose-counjugated and 6'-sialyllactose-counjugated dendrimers bound to a single H3N2 influenza A virus's HA protein (A/Hong Kong/1/1968), the SPR study results suggest their potential anti-viral activities.
Collapse
Affiliation(s)
- Peng He
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yuefan Song
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ritesh Tandon
- Center for Immunology and Microbial Research, Department of Cell Biology, Medicine and BioMolecular Sciences, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rudra Channappanavar
- Department of Veterinary Pathobiology, Oklahoma Center for Respiratory and Infectious Diseases (OCRID), Oklahoma State University, Stillwater, OK, USA
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| |
Collapse
|
9
|
Almalki SSR, Izhari MA, Alyahyawi HE, Alatawi SK, Klufah F, Ahmed WAM, Alharbi R. Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia. J Multidiscip Healthc 2023; 16:2117-2136. [PMID: 37529147 PMCID: PMC10389082 DOI: 10.2147/jmdh.s419859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
Purpose Omicron (B.1.1.529) is one of the highly mutated variants of concern of SARS-CoV-2. Lineages of Omicron bear a remarkable degree of mutations leading to enhanced pathogenicity and upward transmission trajectory. Mutating Omicron lineages may trigger a fresh COVID-19 wave at any time in any region. We aimed at the whole-genome sequencing of SARS-CoV-2 to determine variants/subvariants and significant mutations which can foster virus evolution, monitoring of disease spread, and outbreak management. Methods We used Illumina-NovaSeq 6000 for SARS-CoV-2 genome sequencing, MEGA 10.2 and nextstrain tools for phylogeny; CD-HIT program (version 4.8.1) and MUSCLE program for clustering and alignment. At the same time, UCSF Chimera was employed for protein visualization. Results Predominant Omicron pango lineages in Al-Baha were BA.5.2/B22 (n=4, 57%), and other lineages were BA.2.12/21L (n=1, 14.28%), BV.1/22B (n=1, 14.28%) and BA.5.2.18/22B (n=1, 14.28%). 22B nextstrain clade was predominant, while only one lineage showed 21L. BA.5.2/22B, BA.5.2/22B harbored a maximum of n=24 mutations in the spike region. Twelve crucial RBD mutations: D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, and Y505H were identified except the lineage BA.5.2/22B in which F486V mutation was not observed. Critical deletions S106 in membrane protein NSP6, E31in nucleocapsid, and L24 in spike region were observed in all the lineages. Furthermore, we identified common mutations of Omicron variants of SARS-CoV-2 in therapeutic hot spot spike region: T19I, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, A653V, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1146D, L452R, F486V, N679K and D796Y. The effect of RBD-targeted mutations on neutralizing (NAbs) binding was considerable. Conclusion The outcome of this first report on SARS-CoV-2 variants identification and mutation in the Al-Baha region could be used to lay down the policies to manage and impede the regional outbreak of COVID-19 effectively.
Collapse
Affiliation(s)
- Shaia S R Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohammad Asrar Izhari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Saleha Keder Alatawi
- Department of Optometry, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Faisal Klufah
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Waled A M Ahmed
- Department of Nursing, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Raed Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| |
Collapse
|
10
|
Mahalingam G, Arjunan P, Periyasami Y, Dhyani AK, Devaraju N, Rajendiran V, Christopher AC, Kt RD, Dhanasingh I, Thangavel S, Murugesan M, Moorthy M, Srivastava A, Marepally S. Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor. Sci Rep 2023; 13:8743. [PMID: 37253762 DOI: 10.1038/s41598-023-35070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Spike glycoprotein of SARS-CoV-2 variants plays a critical role in infection and transmission through its interaction with human angiotensin converting enzyme 2 (hACE2) receptors. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with the hACE2 receptors. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike glycoproteins of SARS-CoV-2 variants including Wuhan Hu-1(Wild), Delta, C.1.2 and Omicron. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptors expressing HEK-293T cell line, evaluated their binding efficiencies and competitive binding of spike variants with D614G spike pseudotyped virus. In line with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2 receptors. Our study using the cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors.
Collapse
Affiliation(s)
- Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Porkizhi Arjunan
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Ajay Kumar Dhyani
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Nivedita Devaraju
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Abisha Crystal Christopher
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Ramya Devi Kt
- Department of Biotechnology, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Immanuel Dhanasingh
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Mohankumar Murugesan
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Alok Srivastava
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a Unit of inStem, Bengaluru), CMC Campus, Vellore, Tamil Nadu, 632002, India.
| |
Collapse
|
11
|
Mahalingam G, Periyasami Y, Arjunan P, Subaschandrabose RK, Mathivanan TV, Mathew RS, Devi RKT, Premkumar PS, Muliyil J, Srivastava A, Moorthy M, Marepally S. Omicron infection increases IgG binding to spike protein of predecessor variants. J Med Virol 2023; 95:e28419. [PMID: 36546401 PMCID: PMC9880675 DOI: 10.1002/jmv.28419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in India in 2020-2022 was driven predominantly by Wild (Wuhan-Hu-1 and D614G), Delta, and Omicron variants. The aim of this study was to examine the effect of infections on the humoral immune response and cross-reactivity to spike proteins of Wuhan-Hu-1, Delta, C.1.2., and Omicron. Residual archival sera (N = 81) received between January 2020 and March 2022 were included. Infection status was inferred by a positive SARS-CoV-2 RT-PCR and/or serology (anti-N and anti-S antibodies) and sequencing of contemporaneous samples (N = 18) to infer lineage. We estimated the levels and cross-reactivity of infection-induced sera including Wild, Delta, Omicron as well as vaccine breakthrough infections (Delta and Omicron). We found an approximately two-fold increase in spike-specific IgG antibody binding in post-Omicron infection compared with the pre-Omicron period, whilst the change in pre- and post-Delta infections were similar. Further investigation of Omicron-specific humoral responses revealed primary Omicron infection as an inducer of cross-reactive antibodies against predecessor variants, in spite of the weaker degree of humoral response compared to Wuhan-Hu-1 and Delta infection. Intriguingly, Omicron vaccine-breakthrough infections when compared with primary infections, exhibited increased humoral responses against RBD (7.7-fold) and Trimeric S (Trimeric form of spike protein) (34.6-fold) in addition to increased binding of IgGs towards previously circulating variants (4.2 - 6.5-fold). Despite Delta breakthrough infections showing a higher level of humoral response against RBD (2.9-fold) and Trimeric S (5.7-fold) compared to primary Delta sera, a demonstrably reduced binding (36%-49%) was observed to Omicron spike protein. Omicron vaccine breakthrough infection results in increased intensity of humoral response and wider breadth of IgG binding to spike proteins of antigenically-distinct, predecessor variants.
Collapse
Affiliation(s)
- Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Porkizhi Arjunan
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | | | - Tamil V. Mathivanan
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Roshlin S. Mathew
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Ramya K. T. Devi
- Department of BiotechnologySRM Institute of Science and TechnologyTamil NaduIndia
| | | | | | - Alok Srivastava
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| | - Mahesh Moorthy
- Department of Clinical VirologyChristian Medical CollegeVelloreTamil NaduIndia
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a unit of inStem, Bengaluru)Christian Medical CollegeVelloreTamil NaduIndia
| |
Collapse
|
12
|
Kumar A, Asghar A, Singh HN, Faiq MA, Kumar S, Narayan RK, Kumar G, Dwivedi P, Sahni C, Jha RK, Kulandhasamy M, Prasoon P, Sesham K, Kant K, Pandey SN. SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e42700. [PMID: 36688013 PMCID: PMC9843602 DOI: 10.2196/42700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Background Emergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named "Omicron." Following Omicron's emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa. Objective The aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants. Methods We performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa. Results Compared with the current list of global VOCs/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=-0.99, P<.001; 95% CI -0.99 to -0.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=-0.04, P>.05; 95% CI -0.52 to 0.58). Conclusions In silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs/VOIs, including Delta, but reduced virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.
Collapse
Affiliation(s)
- Ashutosh Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Adil Asghar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Systems Biology Columbia University Irving Medical Center New York, NY United States
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network New Delhi India
- New York University Langone Health Center Robert I Grossman School of Medicine New York University New York, NY United States
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network New Delhi India
- Center for Proteomics and Drug Discovery Amity Institute of Biotechnology Amity University, Maharashtra Mumbai India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network New Delhi India
- Dr BC Roy Multi-speciality Medical Research Centre Indian Institute of Technology Kharagpur India
| | - Gopichand Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Prakhar Dwivedi
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Chetan Sahni
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy Institute of Medical Sciences Banaras Hindu University Varanasi India
| | - Rakesh K Jha
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Biochemistry Maulana Azad Medical College New Delhi India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network New Delhi India
- School of Medicine University of Pittsburgh Pittsburgh, PA United States
| | - Kishore Sesham
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy All India Institute of Medical Sciences-Mangalagiri Mangalagiri India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Microbiology All India Institute of Medical Sciences-Bathinda Bathinda India
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Zoology Banaras Hindu University Varanasi India
| |
Collapse
|
13
|
Bellinati L, Campalto M, Mazzotta E, Ceglie L, Cavicchio L, Mion M, Lucchese L, Salomoni A, Bortolami A, Quaranta E, Magarotto J, Favarato M, Squarzon L, Natale A. One-Year Surveillance of SARS-CoV-2 Exposure in Stray Cats and Kennel Dogs from Northeastern Italy. Microorganisms 2022; 11:microorganisms11010110. [PMID: 36677401 PMCID: PMC9866628 DOI: 10.3390/microorganisms11010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Dogs and cats are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During the pandemic, several studies have been performed on owned cats and dogs, whereas limited data are available on the exposure to stray animals. The objective of this study was to investigate the exposure to SARS-CoV-2 of feral cats and kennel dogs in northeastern Italy, through serological and molecular methods. From May 2021 to September 2022, public health veterinary services collected serum, oropharyngeal, and rectal swab samples from 257 free-roaming dogs newly introduced to shelters, and from 389 feral cats examined during the routinely trap-neutered-return programs. The swabs were analyzed for viral RNA through a real-time reverse transcriptase PCR (rRT-PCR), and sera were tested for the presence of the specific antibody against SARS-CoV-2 (enzyme-linked immunosorbent assay). Serology was positive in nine dogs (9/257) and three cats (3/389), while two asymptomatic cats tested positive to rRT-PCR. One cat turned out to be positive both for serology and molecular analysis. In addition, this study described the case of a possible human-to-animal SARS-CoV-2 transmission in a cat that travelled in close contact to a COVID-19-positive refugee from Ukraine. This study shows that SARS-CoV-2 can infect, in natural conditions, stray cats and kennel dogs in northeastern Italy, although with a low prevalence.
Collapse
Affiliation(s)
- Laura Bellinati
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Mery Campalto
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
- Correspondence:
| | - Elisa Mazzotta
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Lara Cavicchio
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Monica Mion
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Laura Lucchese
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Angela Salomoni
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Alessio Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | - Erika Quaranta
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| | | | - Mosè Favarato
- UOSD Genetica e Citogenetica e Diagnostica Molecolare-Azienda ULSS 3 Serenissima, 30174 Venice, Italy
| | - Laura Squarzon
- UOSD Genetica e Citogenetica e Diagnostica Molecolare-Azienda ULSS 3 Serenissima, 30174 Venice, Italy
| | - Alda Natale
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy
| |
Collapse
|
14
|
Noor R. How do the severe acute respiratory coronavirus 2 (SARS-CoV-2) and its variants escape the host protective immunity and mediate pathogenesis? BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:255. [PMID: 36254244 PMCID: PMC9556142 DOI: 10.1186/s42269-022-00945-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/06/2022] [Indexed: 05/10/2023]
Abstract
Background To protect the global population from the ongoing COVID-19 pandemic caused by the severe acute respiratory β-coronavirus 2 (SARS-CoV-2), a number of vaccines are currently being used in three dosages (i.e., along with the booster dose) to induce the immunity required to combat the SARS-CoV-2 and its variants. So far, several antivirals and the commercial vaccines have been found to evoke the required humoral and cellular immunity within a huge population around world. However, an important aspect to consider is the avoidance mechanism of the host protective immunity by SARS-CoV-2 variants. Main body of the abstract Indeed, such an immune escape strategy has been noticed previously in case of SARS-CoV-1 and the Middle East Respiratory Syndrome coronavirus (MERS-CoV). Regarding the SARS-CoV-2 variants, the most important aspect on vaccine development is to determine whether the vaccine is actually capable to elicit the immune response or not, especially the viral spike (S) protein. Short conclusion Present review thus focused on such elicitation of immunity as well as pondered to the avoidance of host immunity by the SARS-CoV-2 Wuhan strain and its variants.
Collapse
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
| |
Collapse
|
15
|
Jalal K, Khan K, Basharat Z, Abbas MN, Uddin R, Ali F, Khan SA, Hassan SSU. Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60035-60053. [PMID: 35414157 PMCID: PMC9005162 DOI: 10.1007/s11356-022-19979-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.
Collapse
Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Sciences, HEJ Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Fawad Ali
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Saeed Ahmad Khan
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| |
Collapse
|
16
|
Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, Tan JW, Li L. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J 2022; 19:103. [PMID: 35710544 PMCID: PMC9202327 DOI: 10.1186/s12985-022-01830-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. METHODS For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID's EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. RESULTS As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia's daily infections during the period of March-May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. CONCLUSIONS SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential.
Collapse
Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | - Holie Frendy
- Faculty of Medicine and Health Sciences, Krida Wacana Christian University, Jakarta, Indonesia
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
17
|
Van Goethem N, Chung PYJ, Meurisse M, Vandromme M, De Mot L, Brondeel R, Stouten V, Klamer S, Cuypers L, Braeye T, Catteau L, Nevejan L, van Loenhout JAF, Blot K. Clinical Severity of SARS-CoV-2 Omicron Variant Compared with Delta among Hospitalized COVID-19 Patients in Belgium during Autumn and Winter Season 2021-2022. Viruses 2022; 14:1297. [PMID: 35746768 PMCID: PMC9227815 DOI: 10.3390/v14061297] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/08/2023] Open
Abstract
This retrospective multi-center matched cohort study assessed the risk for severe COVID-19 (combination of severity indicators), intensive care unit (ICU) admission, and in-hospital mortality in hospitalized patients when infected with the Omicron variant compared to when infected with the Delta variant. The study is based on a causal framework using individually-linked data from national COVID-19 registries. The study population consisted of 954 COVID-19 patients (of which, 445 were infected with Omicron) above 18 years old admitted to a Belgian hospital during the autumn and winter season 2021-2022, and with available viral genomic data. Patients were matched based on the hospital, whereas other possible confounders (demographics, comorbidities, vaccination status, socio-economic status, and ICU occupancy) were adjusted for by using a multivariable logistic regression analysis. The estimated standardized risk for severe COVID-19 and ICU admission in hospitalized patients was significantly lower (RR = 0.63; 95% CI (0.30; 0.97) and RR = 0.56; 95% CI (0.14; 0.99), respectively) when infected with the Omicron variant, whereas in-hospital mortality was not significantly different according to the SARS-CoV-2 variant (RR = 0.78, 95% CI (0.28-1.29)). This study demonstrates the added value of integrated genomic and clinical surveillance to recognize the multifactorial nature of COVID-19 pathogenesis.
Collapse
Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Pui Yan Jenny Chung
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Marjan Meurisse
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Mathil Vandromme
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Laurane De Mot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Ruben Brondeel
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Veerle Stouten
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Sofieke Klamer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Lize Cuypers
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium; (L.C.); (L.N.)
| | - Toon Braeye
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Lucy Catteau
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Louis Nevejan
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium; (L.C.); (L.N.)
| | - Joris A. F. van Loenhout
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Koen Blot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| |
Collapse
|
18
|
Bohlin J, Page CM, Lee Y, Pettersson JHO, Jugessur A, Magnus P, Håberg SE. Age and sex effects on DNA methylation sites linked to genes implicated in severe COVID-19 and SARS-CoV-2 host cell entry. PLoS One 2022; 17:e0269105. [PMID: 35679253 PMCID: PMC9182232 DOI: 10.1371/journal.pone.0269105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Male sex and advanced age are associated with severe symptoms of COVID-19. Sex and age also exhibit substantial associations with genome-wide DNA methylation (DNAm) differences in humans. Using a random sample of Illumina EPIC-based genome-wide methylomes from peripheral whole blood of 1,976 parents, participating in The Norwegian Mother, Father and Child Cohort Study (MoBa), we explored whether DNAm in genes linked to SARS-CoV-2 host cell entry and to severe COVID-19 were associated with sex and age. This was carried out by testing 1,572 DNAm sites (CpGs) located near 45 genes for associations with age and sex. We found that DNAm in 281 and 231 of 1,572 CpGs were associated (pFDR<0.01) with sex and aging, respectively. CpGs linked to SARS-CoV-2 host cell entry genes were all associated with age and sex, except for the ACE2 receptor gene (located on the X-chromosome), which was only associated with sex (pFDR<0.01). Furthermore, we examined whether 1,487 autosomal CpGs associated with host-cell entry and severe COVID-19 were more or less associated with sex and age than what would be expected from the same number of randomly sampled genome-wide CpGs. We found that the CpGs associated with host-cell entry and severe COVID-19 were not more or less associated with sex (R2 = 0.77, p = 0.09) than the CpGs sampled from random genomic regions; age was actually found to be significantly less so (R2 = 0.36, p = 0.04). Hence, while we found wide-spread associations between sex and age at CpGs linked to genes implicated with SARS-CoV-2 host cell entry and severe COVID-19, the effect from the sum of these CpGs was not stronger than that from randomly sampled CpGs; for age it was significantly less so. These findings could suggest that advanced age and male sex may not be unsurmountable barriers for the SARS-CoV-2 virus to evolve increased infectiousness.
Collapse
Affiliation(s)
- Jon Bohlin
- Department of Method Development and analytics, Norwegian Institute of Public Health, Oslo, Norway
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- * E-mail:
| | - Christian M. Page
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, University of Oslo, Oslo, Norway
| | - Yunsung Lee
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - John H.-O. Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, the University of Sydney, Sydney, New South Wales, Australia
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Per Magnus
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E. Håberg
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
19
|
Vashishtha C, Bhardwaj A, Diwaker A, Sharma S, Sharma MK, Sarin S. Collateral Impact on Patients of Liver Diseases in the Second COVID-19 Wave: A Retrospective Cohort Study. Cureus 2022; 14:e25542. [PMID: 35800810 PMCID: PMC9246352 DOI: 10.7759/cureus.25542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 11/27/2022] Open
Abstract
Background The second wave of the COVID-19 pandemic in India started in April 2021. This necessitated a change in focus from chronic ailments. This wave lasted till May 2021. Its impact on liver disease patients without COVID-19 infection has not been analyzed. Methods Records of liver disease patients from the Institute database admitted from April to May 2021 were compared with that from April to May 2019 i.e., prior to the pandemic. The primary outcome was a comparison of in-hospital mortality rates. Secondary outcomes were a comparison of 30 and 90-day readmission rates and liver transplantation rates. Results Seven hundred and seventy-one patients in April-May 2019 (group 1) and 545 patients in April-May 2021 (group 2) were analyzed. Patients in group 2 were sicker with higher PT (INR), urea, creatinine, CTP, and MELD score and low serum sodium, albumin, and platelet count with a higher prevalence of variceal bleed, hepatic encephalopathy, and acute kidney injury. There was higher mortality in group 2 (128/545; 23.5%) than group 1 (124/ 771;16.1%), OR 1.6, 95% CI 1.2 - 2.1, p<0.01. 30 day readmission rate was numerically higher in group1; 18.3% vs 16.9%, p=0.5. The 31-90 day readmission rate was higher in group 1; 29.4% vs 16.9%, p<0.01. There was no significant difference in the number of patients undergoing liver transplantation in two groups, 19 in group 1 and 14 in group 2 (p=0.90). Conclusion The second wave of the COVID-19 pandemic had a significant collateral impact on liver disease patients even without causing infection in them. Patients were sicker at the time of admission with higher mortality.
Collapse
|
20
|
Martínez-González B, Vázquez-Sirvent L, Soria ME, Mínguez P, Salar-Vidal L, García-Crespo C, Gallego I, de Ávila AI, Llorens C, Soriano B, Ramos-Ruiz R, Esteban J, Fernandez-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Pérez-Jorge C, Domingo E, Perales C. Vaccine breakthrough infections with SARS-CoV-2 Alpha mirror mutations in Delta Plus, Iota, and Omicron. J Clin Invest 2022; 132:e157700. [PMID: 35259127 PMCID: PMC9057617 DOI: 10.1172/jci157700] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
Replication of SARS-CoV-2 in the human population is defined by distributions of mutants that are present at different frequencies within the infected host and can be detected by ultra-deep sequencing techniques. In this study, we examined the SARS-CoV-2 mutant spectra of amplicons from the spike-coding (S-coding) region of 5 nasopharyngeal isolates derived from patients with vaccine breakthrough. Interestingly, all patients became infected with the Alpha variant, but amino acid substitutions that correspond to the Delta Plus, Iota, and Omicron variants were present in the mutant spectra of the resident virus. Deep sequencing analysis of SARS-CoV-2 from patients with vaccine breakthrough revealed a rich reservoir of mutant types and may also identify tolerated substitutions that can be represented in epidemiologically dominant variants.
Collapse
Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María E. Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics and Genomics, IIS-FJD, UAM, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, IIS-FJD, UAM, Madrid, Spain
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana I. de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park,” Universidad de Valencia, Valencia, Spain
| | - Beatriz Soriano
- Biotechvana, “Scientific Park,” Universidad de Valencia, Valencia, Spain
| | - Ricardo Ramos-Ruiz
- Unidad de Genómica, “Scientific Park of Madrid,” Campus de Cantoblanco, Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ricardo Fernandez-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics and Genomics, IIS-FJD, UAM, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, Madrid, Spain
- IIS-FJD, UAM, Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Concepción Pérez-Jorge
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB), CSIC, Campus de Cantoblanco, Madrid, Spain
| |
Collapse
|
21
|
Varret M, Martin FX, Varret F. A tentative tracking of the SARS-Cov2 pandemic in France, based on a corrected SIR model including vaccination effects. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202226301002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed successive extensions of the SIR model in order to track the dynamics of the SARS-Cov2 disease. The analysis of health system available data is published in a chronicle accessible on the net: https://corona-circule.github.io/lettres/. This chronicle was initiated on late march 2020 and up to now contains 50 issues. A constant concern was the reliability of the data: for instance, we very soon evidenced that the number of confirmed cases, because of the asymptomatic carriers and the erratic testing policy, was hugely underestimated. By the end of 2020 we made a basic change in the model which consisted in accounting for a constant contagiousness time (SIR-tcc) instead of the probabilistic evolution of the end of the infection assumed so far. Recently we completed this SIR-tcc model for the vaccination effects in order to properly track the evolution of the group immunity threshold. Calculations were performed using the Excel facility (Microsoft), allowing a manual fitting of the model parameters. The results have dealt with a large number of countries, but we focus here on the data regarding France. Further pieces of information are also presented, in order to help elucidating some the factors responsible for the complex history of the pandemic dynamics. (submitted dec 14th 2021)
Collapse
|
22
|
Kumar A, Asghar A, Dwivedi P, Kumar G, Narayan RK, Jha RK, Parashar R, Sahni C, Pandey SN. A Bioinformatics Tool for Predicting Future COVID-19 Waves Based on a Retrospective Analysis of the Second Wave in India: Model Development Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e36860. [PMID: 36193192 PMCID: PMC9516867 DOI: 10.2196/36860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022]
Abstract
Background Since the start of the COVID-19 pandemic, health policymakers globally have been attempting to predict an impending wave of COVID-19. India experienced a devastating second wave of COVID-19 in the late first week of May 2021. We retrospectively analyzed the viral genomic sequences and epidemiological data reflecting the emergence and spread of the second wave of COVID-19 in India to construct a prediction model. Objective We aimed to develop a bioinformatics tool that can predict an impending COVID-19 wave. Methods We analyzed the time series distribution of genomic sequence data for SARS-CoV-2 and correlated it with epidemiological data for new cases and deaths for the corresponding period of the second wave. In addition, we analyzed the phylodynamics of circulating SARS-CoV-2 variants in the Indian population during the study period. Results Our prediction analysis showed that the first signs of the arrival of the second wave could be seen by the end of January 2021, about 2 months before its peak in May 2021. By the end of March 2021, it was distinct. B.1.617 lineage variants powered the wave, most notably B.1.617.2 (Delta variant). Conclusions Based on the observations of this study, we propose that genomic surveillance of SARS-CoV-2 variants, complemented with epidemiological data, can be a promising tool to predict impending COVID-19 waves.
Collapse
Affiliation(s)
- Ashutosh Kumar
- Department of Anatomy All India Institute of Medical Sciences - Patna Patna India
| | - Adil Asghar
- Department of Anatomy All India Institute of Medical Sciences - Patna Patna India
| | - Prakhar Dwivedi
- Department of Anatomy All India Institute of Medical Sciences - Patna Patna India
| | - Gopichand Kumar
- Department of Anatomy All India Institute of Medical Sciences - Patna Patna India
| | - Ravi K Narayan
- Department of Anatomy Dr B C Roy Multispeciality Medical Research Center Indian Institute of Technology-Kharagpur Kharagpur India
| | - Rakesh K Jha
- Department of Anatomy All India Institute of Medical Sciences - Patna Patna India
| | - Rakesh Parashar
- India Health Lead Oxford Policy Management Limited Oxford United Kingdom
| | - Chetan Sahni
- Department of Anatomy Institute of Medical Sciences Banaras Hindu University Varanasi India
| | - Sada N Pandey
- Department of Zoology Banaras Hindu University Varanasi India
| |
Collapse
|
23
|
Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis. Pathogens 2021; 11:pathogens11010045. [PMID: 35055993 PMCID: PMC8779645 DOI: 10.3390/pathogens11010045] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the SARS-CoV-2 Omicron variant and whether these changes modulate the interactions with the angiotensin-converting enzyme 2 (ACE2) host receptor. The mutations associated with the Omicron variant were retrieved from the GISAID and covariants.org databases, and a structural model was built using the SWISS-Model server. The interaction between the spike and the human ACE2 was evaluated using two different docking software, Zdock and Haddock. We found that the binding free energy was lower for the Omicron variant as compared to the WT spike. In addition, the Omicron spike protein showed an increased number of electrostatic interactions with ACE2 than the WT spike, especially the interactions related to charged residues. This study contributes to a better understanding of the changes in the interaction between the Omicron spike and the human host ACE2 receptor.
Collapse
|