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Purwono PB, Vacharathit V, Manopwisedjaroen S, Ludowyke N, Suksatu A, Thitithanyanont A. Infection kinetics, syncytia formation, and inflammatory biomarkers as predictive indicators for the pathogenicity of SARS-CoV-2 Variants of Concern in Calu-3 cells. PLoS One 2024; 19:e0301330. [PMID: 38568894 PMCID: PMC10990222 DOI: 10.1371/journal.pone.0301330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
The ongoing COVID-19 pandemic has led to the emergence of new SARS-CoV-2 variants as a result of continued host-virus interaction and viral genome mutations. These variants have been associated with varying levels of transmissibility and disease severity. We investigated the phenotypic profiles of six SARS-CoV-2 variants (WT, D614G, Alpha, Beta, Delta, and Omicron) in Calu-3 cells, a human lung epithelial cell line. In our model demonstrated that all variants, except for Omicron, had higher efficiency in virus entry compared to the wild-type. The Delta variant had the greatest phenotypic advantage in terms of early infection kinetics and marked syncytia formation, which could facilitate cell-to-cell spreading, while the Omicron variant displayed slower replication and fewer syncytia formation. We also identified the Delta variant as the strongest inducer of inflammatory biomarkers, including pro-inflammatory cytokines/chemokines (IP-10/CXCL10, TNF-α, and IL-6), anti-inflammatory cytokine (IL-1RA), and growth factors (FGF-2 and VEGF-A), while these inflammatory mediators were not significantly elevated with Omicron infection. These findings are consistent with the observations that there was a generally more pronounced inflammatory response and angiogenesis activity within the lungs of COVID-19 patients as well as more severe symptoms and higher mortality rate during the Delta wave, as compared to less severe symptoms and lower mortality observed during the current Omicron wave in Thailand. Our findings suggest that early infectivity kinetics, enhanced syncytia formation, and specific inflammatory mediator production may serve as predictive indicators for the virulence potential of future SARS-CoV-2 variants.
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Affiliation(s)
- Priyo Budi Purwono
- Faculty of Science, Department of Microbiology, Mahidol University, Bangkok, Thailand
- Faculty of Medicine, Department of Microbiology, Universitas Airlangga, Surabaya, Indonesia
| | - Vimvara Vacharathit
- Faculty of Science, Department of Microbiology, Mahidol University, Bangkok, Thailand
- Faculty of Science, Systems Biology of Diseases Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Natali Ludowyke
- Faculty of Science, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Ampa Suksatu
- Faculty of Science, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Arunee Thitithanyanont
- Faculty of Science, Department of Microbiology, Mahidol University, Bangkok, Thailand
- Faculty of Science, Department of Microbiology, Pornchai Matangkasombut Center for Microbial Genomics, Mahidol University, Bangkok, Thailand
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2
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Scovino AM, Dahab EC, Diniz-Lima I, de Senna Silveira E, Barroso SPC, Cardoso KM, Nico D, Makhoul GJ, da Silva-Junior EB, Freire-de-Lima CG, Freire-de-Lima L, da Fonseca LM, Valente N, Nacife V, Machado A, Araújo M, Vieira GF, Pauvolid-Corrêa A, Siqueira M, Morrot A. A Comparative Analysis of Innate Immune Responses and the Structural Characterization of Spike from SARS-CoV-2 Gamma Variants and Subvariants. Microorganisms 2024; 12:720. [PMID: 38674664 PMCID: PMC11052025 DOI: 10.3390/microorganisms12040720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 04/28/2024] Open
Abstract
The SARS-CoV-2 P.1 variant, responsible for an outbreak in Manaus, Brazil, is distinguished by 12 amino acid differences in the S protein, potentially increasing its ACE-2 affinity and immune evasion capability. We investigated the innate immune response of this variant compared to the original B.1 strain, particularly concerning cytokine production. Blood samples from three severe COVID-19 patients were analyzed post-infection with both strains. Results showed no significant difference in cytokine production of mononuclear cells and neutrophils for either variant. While B.1 had higher cytopathogenicity, neither showed viral replication in mononuclear cells. Structural analyses of the S protein highlighted physicochemical variations, which might be linked to the differences in infectivity between the strains. Our studies point to the increased infectivity of P.1 could stem from altered immunogenicity and receptor-binding affinity.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
| | - Israel Diniz-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Etiele de Senna Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
| | - Shana Priscila Coutinho Barroso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
- Biomanguinhos, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, Brazil
| | - Karina Martins Cardoso
- Laboratório de Biologia Molecular, Instituto de Pesquisa Biomédica, Hospital Naval Marcílio Dias, Marinha do Brazil, Rio de Janeiro 20725-090, Brazil; (S.P.C.B.); (K.M.C.)
| | - Dirlei Nico
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil (E.C.D.); (D.N.)
| | - Gustavo José Makhoul
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Elias Barbosa da Silva-Junior
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (I.D.-L.); (G.J.M.); (E.B.d.S.-J.); (C.G.F.-d.-L.); (L.F.-d.-L.)
- Curso de Medicina, Universidade Castelo Branco (UCB), Rio de Janeiro 21710-255, Brazil
| | - Natalia Valente
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Valeria Nacife
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Ana Machado
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Mia Araújo
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Gustavo Fioravanti Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil; (E.d.S.S.)
- PPGSDH—Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas 92010-000, Brazil
| | - Alex Pauvolid-Corrêa
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Laboratório de Virologia Veterinária de Viçosa, Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
| | - Marilda Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, COVID-19 National Reference Laboratory of Brazil and World Health Organization COVID-19 Reference Laboratory, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil; (N.V.); (V.N.); (A.M.); (A.P.-C.)
| | - Alexandre Morrot
- Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-360, Brazil
- Escola de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
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3
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Rodríguez-Artalejo FJ, Ruiz-Galiana J, Cantón R, De Lucas Ramos P, García-Botella A, García-Lledó A, Hernández-Sampelayo T, Gómez-Pavón J, González Del Castillo J, Martín-Delgado MC, Martín Sánchez FJ, Martínez-Sellés M, Molero García JM, Moreno Guillén S, García de Viedma D, Bouza E. COVID-19: On the threshold of the fifth year. The situation in Spain. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2024; 37:17-28. [PMID: 38009431 PMCID: PMC10874674 DOI: 10.37201/req/123.2023] [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: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023]
Abstract
Despite having emerged from pandemic status, the incidence of COVID-19 episodes has recently increased in Spain, including pediatric cases and admissions to Intensive Care Units. Several recombinant variants are circulating among us, particularly XBB arising from two Omicron BA.2 sublineages with mutations in the genes encoding the spicule proteins that could increase binding to the ACE2 receptor and be more prone to immune escape. Faced with these, 3 pharmaceutical companies have developed vaccines adapted to the XBB.1.5 sublineage that are already available for administration in our setting with risks that should not be different from those of previous mRNA vaccines and with clearly favorable benefit/risk ratios. They should be applied to patients with potential for poor COVID-19 evolution and to collectives that have a particular relationship of proximity with them. Their application should be understood not only from a perspective of individual convenience but also from that of collective responsibility. The most convenient seems to be a simultaneous immunization of COVID-19 and influenza in our environment. In the therapeutic aspect, there is little to expect right now from antisera, but the already known antiviral drugs are still available and indicated, although their efficacy will have to be reevaluated due to their impact on populations that are mostly immunized and with a better prognosis than in the past. In our opinion, it is necessary to continue to make a reasonable and timely use of masks and other non-pharmacological means of protection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - E Bouza
- Servicio de Microbiología Clínica y Enfermedades Infecciosas del Hospital General Universitario Gregorio Marañón, Universidad Complutense. CIBERES. Ciber de Enfermedades Respiratorias. Madrid, Spain.
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4
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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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5
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Lavrentieva A, Kaimakamis E, Voutsas V, Bitzani M. An observational study on factors associated with ICU mortality in Covid-19 patients and critical review of the literature. Sci Rep 2023; 13:7804. [PMID: 37179397 PMCID: PMC10182846 DOI: 10.1038/s41598-023-34613-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The novel pandemic caused by SARS-CoV-2 has been associated with increased burden on healthcare system. Recognizing the variables that independently predict death in COVID-19 is of great importance. The study was carried out prospectively in a single ICU in northern Greece. It was based on the collection of data during clinical practice in 375 adult patients who were tested positive for SARS-CoV-2 between April 2020 and February 2022. All patients were intubated due to acute respiratory insufficiency and received Invasive Mechanical Ventilation. The primary outcome was ICU mortality. Secondary outcomes were 28-day mortality and independent predictors of mortality at 28 days and during ICU hospitalization. For continuous variables with normal distribution, t-test was used for means comparison between two groups and one-way ANOVA for multiple comparisons. When the distribution was not normal, comparisons were performed using the Mann-Whitney test. Comparisons between discrete variables were made using the x2 test, whereas the binary logistic regression was employed for the definition of factors affecting survival inside the ICU and after 28 days. Of the total number of patients intubated due to COVID-19 during the study period, 239 (63.7%) were male. Overall, the ICU survival was 49.6%, whereas the 28-day survival reached 46.9%. The survival rates inside the ICU for the four main viral variants were 54.9%, 50.3%, 39.7% and 50% for the Alpha, Beta, Delta and Omicron variants, respectively. Logistic regressions for outcome revealed that the following parameters were independently associated with ICU survival: wave, SOFA @day1, Remdesivir use, AKI, Sepsis, Enteral Insufficiency, Duration of ICU stay and WBC. Similarly, the parameters affecting the 28-days survival were: duration of stay in ICU, SOFA @day1, WBC, Wave, AKI and Enteral Insufficiency. In this observational cohort study of critically ill COVID-19 patients we report an association between mortality and the wave sequence, SOFA score on admission, the use of Remdesivir, presence of AKI, presence of gastrointestinal failure, sepsis and WBC levels. Strengths of this study are the large number of critically ill COVID-19 patients included, and the comparison of the adjusted mortality rates between pandemic waves within a two year-study period.
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Affiliation(s)
- Athina Lavrentieva
- 1st Intensive Care Unit, "G. Papanikolaou" General Hospital, 57010, Thessaloniki, Greece
| | - Evangelos Kaimakamis
- 1st Intensive Care Unit, "G. Papanikolaou" General Hospital, 57010, Thessaloniki, Greece.
| | - Vassileios Voutsas
- 1st Intensive Care Unit, "G. Papanikolaou" General Hospital, 57010, Thessaloniki, Greece
| | - Militsa Bitzani
- 1st Intensive Care Unit, "G. Papanikolaou" General Hospital, 57010, Thessaloniki, Greece
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6
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Letafati A, Eyvazzadeh N, Gharehkhani A, Khorshidian A, Chalabiani S, Soufiani EK, Khakpoor N, Shamsodini B, Beheshti T, Bavili Olyaei RT, Soleimani A, Melyani F, Hossein GM. Comparison of AstraZeneca and sinopharm vaccines as boosters in protection against COVID-19 infection. Biologicals 2023; 82:101668. [PMID: 37004277 PMCID: PMC10008804 DOI: 10.1016/j.biologicals.2023.101668] [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: 05/30/2022] [Revised: 12/19/2022] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND As the global number of confirmed cases rises past 640 million, vaccination remains the most effective measure in controlling COVID-19. Studies have shown that two doses of vaccination can significantly reduce hospitalization and mortality rates among patients, but the effectiveness of booster doses is also important. We aimed to evaluate the role played by the type of the 3rd dose of vaccination by comparing the safety and efficacy of two common vaccination histories differing only in the 3rd received dose. METHODS We conducted a cross-sectional study on patients with respiratory symptoms suspected of having SARS-CoV-2 infection using Real-time PCR. We also collected information on the age, gender, and type of vaccine received for the third dose. RESULTS Out of 346 cases with respiratory symptoms, 120 cases tested positive for SARS-CoV-2 and had received two doses of Sinopharm and a different booster dose of either AZD1222 (AstraZeneca) or BIBP (Sinopharm). Among these 120 patients, vaccination with AZD1222 as a booster dose resulted in fewer symptoms compared to those vaccinated with three doses of BIBP. CONCLUSIONS Our study demonstrates that booster doses can help reduce hospitalization and the severity of infection, and it appears that a combination of different vaccines may be effective against severe COVID-19 infection.
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Affiliation(s)
- Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Nooshin Eyvazzadeh
- Department of Medical Bacteriology, Faculty of Medicine, Qazvin University of Medical Science, Qazvin, Iran
| | - Amirhossein Gharehkhani
- Department of Medical Laboratory Science, Faculty of Para Medicine, Islamic Azad University, Tehran Medical Branch, Tehran, Iran
| | - Ayeh Khorshidian
- Department of Biology, Faculty of Basic Sciences, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Siavash Chalabiani
- Department of Microbiology, Faculty of Biological Sciences, Islamic Azad University of Qom, Qom, Iran
| | - Elnaz Khodadoust Soufiani
- Department of Medical Laboratory Science, Faculty of Para Medicine, Islamic Azad University, Tehran Medical Branch, Tehran, Iran
| | - Niloofar Khakpoor
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Benyamin Shamsodini
- Department of Microbiology, Faculty of Basic Sciences, Islamic Azad University of Shahrekord, Shahrekord, Iran
| | - Taranom Beheshti
- Department of Genetics, Faculty of Advanced Sciences and Technology, Islamic Azad University of Tehran, Tehran, Iran
| | - Raha Taheri Bavili Olyaei
- Department of Medical Laboratory Science, Faculty of Medical Sciences, Islamic Azad University, Tabriz Medical Branch, Tabriz, Iran
| | - Anahita Soleimani
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Sarab University, Sarab, Iran
| | - Fatemeh Melyani
- Department of Medical Laboratory Sciences, Faculty of Para Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ghazal Mashhadi Hossein
- Department of Microbiology, Faculty of Basic Sciences, Islamic Azad University of Arak, Arak, Iran
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7
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Ismael N, van Wyk S, Tegally H, Giandhari J, San JE, Moir M, Pillay S, Utpatel C, Singh L, Naidoo Y, Ramphal U, Mabunda N, Abílio N, Arnaldo P, Xavier J, Amoako DG, Everatt J, Ramphal Y, Maharaj A, de Araujo L, Anyaneji UJ, Tshiabuila D, Viegas S, Lessells R, Engelbrecht S, Gudo E, Jani I, Niemann S, Wilkinson E, de Oliveira T. Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001593. [PMID: 36963096 PMCID: PMC10021167 DOI: 10.1371/journal.pgph.0001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
Abstract
Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.
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Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Lavanya Singh
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nuro Abílio
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Joicymara Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brasil
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ugochukwu J. Anyaneji
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sofia Viegas
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Richard Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Ilesh Jani
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
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8
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Carvajal-Barriga EJ, Fields RD. Sulfated polysaccharides as multi target molecules to fight COVID 19 and comorbidities. Heliyon 2023; 9:e13797. [PMID: 36811015 PMCID: PMC9936785 DOI: 10.1016/j.heliyon.2023.e13797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
The majority of research to combat SARS-CoV-2 infection exploits the adaptive immune system, but innate immunity, the first line of defense against pathogenic microbes, is equally important in understanding and controlling infectious diseases. Various cellular mechanisms provide physiochemical barriers to microbe infection in mucosal membranes and epithelia, with extracellular polysaccharides, particularly sulfated polysaccharides, being among the most widespread and potent extracellular and secreted molecules blocking and deactivating bacteria, fungi, and viruses. New research reveals that a range of polysaccharides effectively inhibits COV-2 infection of mammalian cells in culture. This review provides an overview of sulfated polysaccharides nomenclature, its significance as immunomodulators, antioxidants, antitumors, anticoagulants, antibacterial, and as potent antivirals. It summarizes current research on various interactions of sulfated polysaccharide with a range of viruses, including SARS-CoV-2, and their application for potential treatments for COVID-19. These molecules interact with biochemical signaling in immune cell responses, by actions in oxidative reactions, cytokine signaling, receptor binding, and through antiviral and antibacterial toxicity. These properties provide the potential for the development of novel therapeutic treatments for SARS-CoV-2 and other infectious diseases from modified polysaccharides.
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Affiliation(s)
- Enrique Javier Carvajal-Barriga
- Pontificia Universidad Católica Del Ecuador, Neotropical Center for the Biomass Research, Quito, Ecuador.,The Eunice Kennedy Shriver National Institutes of Health, National Institute of Children and Human Development, Bethesda, MD, USA
| | - R Douglas Fields
- The Eunice Kennedy Shriver National Institutes of Health, National Institute of Children and Human Development, Bethesda, MD, USA
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9
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Dong J, Chen R, Zhao H, Zhu Y. COVID-19 and ocular complications: A review of ocular manifestations, diagnostic tools, and prevention strategies. ADVANCES IN OPHTHALMOLOGY PRACTICE AND RESEARCH 2023; 3:33-38. [PMID: 36471811 PMCID: PMC9714126 DOI: 10.1016/j.aopr.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/18/2022] [Accepted: 11/13/2022] [Indexed: 12/02/2022]
Abstract
Background The novel severe acute respiratory syndrome coronavins 2 (SARS-CoV-2) led to the severe Corona Virus Disease 2019 (COVID-19) outbreak that started in December 2019 in China and caused enormous health and economic problems worldwide. Over time, SARS-CoV-2 has demonstrated the capacity for mutation. As the most prevalent new coronavirus variety worldwide, the Omicron variant has supplanted the Delta variant. The COVID-19 primarily damages the immune system and the lungs, but it can also harm other organs secondarily, depending on the patients' co-existing conditions. Main Text COVID-19 is associated with ophthalmic manifestations such as conjunctival congestion, tear overflow, and conjunctival edema, with the majority of eye complications occurring in patients with severe infection. The virus may make a patient more susceptible to thrombotic conditions that affect venous and arterial circulation. Meanwhile, it can lead to efferent complications and mucormycosis which is more common in patients with diabetes or who have critical or severe SARS-CoV-2 infection. Significantly, there are a number of ocular side effects following the COVID-19 vaccination, such as herpetic keratitis and facial nerve palsy, which have been reported. These side effects may be caused by the vaccinations' propensity to trigger autoimmune symptoms or thromboembolic events. At present, large-scale nucleic acid testing mainly relies on nasopharyngeal swabs and throat swabs. Tear samples and conjunctival swabs may be helpful samples for the diagnosis of ocular SARS-CoV-2 infection. The eye could be a new route of infection, and finding ways such as effective environmental disinfection, scientific administrative control management, qualified personal protection and other measures to protect the eyes could further reduce the risk of infection. Conclusions This review aims to sum up the ocular complications of COVID-19, the possible pathogenesis, and preventive strategies to protect ophthalmology practitioners and patients by reviewing the currently available literature on the topic.
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Affiliation(s)
- Jilian Dong
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ruida Chen
- Eye Department, Affiliated Dongyang Hospital, Wenzhou Medical University, Dongyang, China
- Eye Center, Affiliated Second Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hanhe Zhao
- Eye Center, Affiliated Second Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yirui Zhu
- Eye Center, Affiliated Second Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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10
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Mziray SR, van Zwetselaar M, Kayuki CC, Mbelele PM, Makubi AN, Magesa AS, Kisonga RM, Sonda TB, Kibiki GS, Githinji G, Heysell SK, Chilongola JO, Mpagama SG. Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania. Front Med (Lausanne) 2023; 9:1034682. [PMID: 36687433 PMCID: PMC9846855 DOI: 10.3389/fmed.2022.1034682] [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: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Background Coronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa. Methods This cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0. Results Twenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2. Conclusion We provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.
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Affiliation(s)
- Shabani Ramadhani Mziray
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kibong’oto Infectious Diseases Hospital, Sanya Juu, Tanzania
| | | | | | | | | | | | | | | | - Gibson S. Kibiki
- The Africa Research Excellence Fund (AREF), London, United Kingdom
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Jaffu O. Chilongola
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
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11
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COVID-19: Impact of Original, Gamma, Delta, and Omicron Variants of SARS-CoV-2 in Vaccinated and Unvaccinated Pregnant and Postpartum Women. Vaccines (Basel) 2022; 10:vaccines10122172. [PMID: 36560582 PMCID: PMC9786095 DOI: 10.3390/vaccines10122172] [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: 10/25/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
This study compares the clinical characteristics and disease progression among vaccinated and unvaccinated pregnant and postpartum women who tested positive for different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the Brazilian epidemiological data. Data of pregnant or postpartum patients testing positive for SARS-CoV-2 and presenting with coronavirus disease 2019 (COVID-19) from February 2020 to July 2022 were extracted from Brazilian national database. The patients were grouped based on vaccination status and viral variant (original, Gamma, Delta, and Omicron variants), and their demographics, clinical characteristics, comorbidities, symptoms, and outcomes were compared retrospectively. Data of 10,003 pregnant and 2361 postpartum women were extracted from the database. For unvaccinated postpartum women, intensive care unit (ICU) admission was more likely; invasive ventilation need was more probable if they tested positive for the original, Gamma, and Omicron variants; and chances of death were higher when infected with the original and Gamma variants than when infected with other variants. Vaccinated patients had reduced adverse outcome probability, including ICU admission, invasive ventilation requirement, and death. Postpartum women showed worse outcomes, particularly when unvaccinated, than pregnant women. Hence, vaccination of pregnant and postpartum women should be given top priority.
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12
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Zolfaghari MA, Ghadiri Moghaddam F, Rajput S, Karimi A, Naghi Vishteh M, Mahmoodpoor A, Dolati S, Yousefi M. SARS-CoV-2 vaccines: A double-edged sword throughout rapid evolution of COVID-19. Cell Biol Int 2022; 46:2009-2017. [PMID: 36047303 PMCID: PMC9539123 DOI: 10.1002/cbin.11903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 07/12/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022]
Abstract
After more than 2 years of the coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2, several questions have remained unanswered that affected our daily lives. Although substantial vaccine development could resist this challenge, emerging new variants in different countries could be considered as potent concerns regarding the adverse effects of reinfection or postvaccination. Precisely, these concerns address some significant and probable outcomes in vaccinated or reinfected models, followed by some virus challenges, such as antibody-dependent enhancement and cytokine storm. Therefore, the importance of evaluating the effectiveness of neutralizing antibodies (nAbs) elicited by vaccination and the rise of new variants must be addressed.
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Affiliation(s)
- Mohammad Ali Zolfaghari
- Student Research CommitteeTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
| | | | - Shabnam Rajput
- Department of Pediatrics, School of MedicineJahrom University of Medical SciencesJahromIran
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
- Biotechnology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohadeseh Naghi Vishteh
- Department of Genetics and Molecular Biology, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Ata Mahmoodpoor
- Department of AnesthesiologyTabriz University of Medical SciencesTabrizIran
| | - Sanam Dolati
- Physical Medicine and Rehabilitation Research Center, Aging Research InstituteTabriz University of Medical SciencesTabrizIran
| | - Mehdi Yousefi
- Stem Cell Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Immunology, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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13
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Huang RC, Chiu CH, Shang HS, Perng CL, Chiang TT, Tsai CC, Wang CH. Clinical characteristics analysis of COVID-19 patients from the first significant community outbreak by SARS-CoV-2 variant B.1.1.7 in Taiwan as experienced from a single northern medical center. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1036-1043. [PMID: 36057491 PMCID: PMC9381423 DOI: 10.1016/j.jmii.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/11/2022] [Accepted: 08/01/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND/PURPOSE Clinical characteristics of patients in the first community outbreak of coronavirus disease 2019 (COVID-19) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 in Taiwan have not been characterized. METHODS SARS-CoV-2 positive specimens from inpatients between May 7 and June 15 in 2021were screen for SARS-CoV-2 B.1.1.7 lineage by VirSNiP assay. Clinical characteristics were reviewed and compared with those from Feb 1 to April 30, 2020 and from Jan 1 to March 31, 2022. RESULTS One hundred forty-one inpatients from May 7 to June 15, 2021 infected with SARS-CoV-2 B.1.1.7 lineage were included. The major presenting symptoms were fever (88.7%) and cough (59.6%). Incidence of relevant complications including pulmonary embolism, simultaneous infections with bacteria, virus, and fungi were 0.7%, 12.8%, 13.5%, and 2.1%, respectively. Old age, high Charlson comorbidity index, short of breath, and initial critical illness were independently associated with 28-day mortality (all p < 0.05). In comparison to COVID-19 inpatients from Feb 1 to April 30, 2020, patients from the outbreak by SARS-CoV-2 B.1.1.7 lineage were older, more severe in disease condition, higher mortality but less obvious initial presenting symptoms. After implementation of nationwide vaccination campaign in the next half year of 2021, COVID-19 inpatients from Jan 1 to March 31 in 2022 indicated less severe diseases than those infected with SARS-CoV-2 B.1.1.7 lineage. CONCLUSION COVID-19 inpatients by SARS-CoV-2 variant B.1.1.7 with old age, multiple comorbidities, and more severe disease conditions were associated with increased mortality. Vaccination for this vulnerable populations may be helpful.
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Affiliation(s)
- Ruei-Chang Huang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Hsiang Chiu
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tsung-Ta Chiang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Chou Tsai
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ching-Hsun Wang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC,Corresponding author. Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Section 2, Cheng-Kung Road, Neihu 114, Taipei, Taiwan. Fax: +886-2-87927258
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14
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Salaikumaran MR, Kasamuthu PS, Aathmanathan VS, Burra VLSP. An in silico approach to study the role of epitope order in the multi-epitope-based peptide (MEBP) vaccine design. Sci Rep 2022; 12:12584. [PMID: 35869117 PMCID: PMC9307121 DOI: 10.1038/s41598-022-16445-3] [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] [Received: 10/23/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractWith different countries facing multiple waves, with some SARS-CoV-2 variants more deadly and virulent, the COVID-19 pandemic is becoming more dangerous by the day and the world is facing an even more dreadful extended pandemic with exponential positive cases and increasing death rates. There is an urgent need for more efficient and faster methods of vaccine development against SARS-CoV-2. Compared to experimental protocols, the opportunities to innovate are very high in immunoinformatics/in silico approaches, especially with the recent adoption of structural bioinformatics in peptide vaccine design. In recent times, multi-epitope-based peptide vaccine candidates (MEBPVCs) have shown extraordinarily high humoral and cellular responses to immunization. Most of the publications claim that respective reported MEBPVC(s) assembled using a set of in silico predicted epitopes, to be the computationally validated potent vaccine candidate(s) ready for experimental validation. However, in this article, for a given set of predicted epitopes, it is shown that the published MEBPVC is one among the many possible variants and there is high likelihood of finding more potent MEBPVCs than the published candidates. To test the same, a methodology is developed where novel MEBP variants are derived by changing the epitope order of the published MEBPVC. Further, to overcome the limitations of current qualitative methods of assessment of MEBPVC, to enable quantitative comparison and ranking for the discovery of more potent MEBPVCs, novel predictors, Percent Epitope Accessibility (PEA), Receptor specific MEBP vaccine potency (RMVP), MEBP vaccine potency (MVP) are introduced. The MEBP variants indeed showed varied MVP scores indicating varied immunogenicity. Further, the MEBP variants with IDs, SPVC_446 and SPVC_537, had the highest MVP scores indicating these variants to be more potent MEBPVCs than the published MEBPVC and hence should be preferred candidates for immediate experimental testing and validation. The method enables quicker selection and high throughput experimental validation of vaccine candidates. This study also opens the opportunity to develop new software tools for designing more potent MEBPVCs in less time.
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15
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Barnes JE, Lund-Andersen PK, Patel JS, Ytreberg FM. The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6. Sci Rep 2022; 12:18819. [PMID: 36335244 PMCID: PMC9637166 DOI: 10.1038/s41598-022-23482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2 is the pathogen responsible for COVID-19 that has claimed over six million lives as of July 2022. The severity of COVID-19 motivates a need to understand how it could evolve to escape potential treatments and to find ways to strengthen existing treatments. Here, we used the molecular modeling methods MD + FoldX and PyRosetta to study the SARS-CoV-2 spike receptor binding domain (S-RBD) bound to two neutralizing antibodies, B38 and CB6 and generated lists of antibody escape and antibody strengthening mutations. Our resulting watchlist contains potential antibody escape mutations against B38/CB6 and consists of 211/186 mutations across 35/22 S-RBD sites. Some of these mutations have been identified in previous studies as being significant in human populations (e.g., N501Y). The list of potential antibody strengthening mutations that are predicted to improve binding of B38/CB6 to S-RBD consists of 116/45 mutations across 29/13 sites. These mutations could be used to improve the therapeutic value of these antibodies.
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Affiliation(s)
- Jonathan E Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA
| | - Peik K Lund-Andersen
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83843, USA
| | - Jagdish Suresh Patel
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA.
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83843, USA.
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA.
- Department of Physics, University of Idaho, Moscow, ID, 83843, USA.
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16
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Alsaedi A, Alharbi M, Ossenkopp J, Farahat F, Taguas R, Algarni M, Alghamdi A, Okdah L, Alhayli S, Alswaji A, Doumith M, El-Saed A, Alzahrani M, Alshamrani M, Alghoribi MF. Epidemiological and molecular description of nosocomial outbreak of COVID-19 Alpha (B.1.1.7) variant in Saudi Arabia. J Infect Public Health 2022; 15:1279-1286. [PMID: 36274368 PMCID: PMC9557135 DOI: 10.1016/j.jiph.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Nosocomial outbreaks frequently occurred during the Coronavirus disease 2019 (COVID-19) pandemic; however, sharing experiences on outbreak containment is vital to reduce the related burden in different locations. OBJECTIVES This article aims at sharing a practical experience on COVID-19 outbreak containment, including contact tracing, screening of target population, testing including molecular analysis, and preventive modalities. It also provides an epidemiological and molecular analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‑CoV‑2) infection outbreak in a tertiary care hospital in Saudi Arabia. METHODS The outbreak occurred in a non-COVID medical ward at a tertiary care hospital in Jeddah, Saudi Arabia, from 22nd March and 15th April 2021. The multidisciplinary outbreak response team performed clinical and epidemiological investigations. Whole-Genome Sequencing (WGS) was implemented on selected isolates for further molecular characterization. RESULTS A total of eight nurses (20 % of the assigned ward nurses) and six patients (16.2 % of the ward admitted patients at the time of the outbreak) tested positive for the SARS-CoV-2 virus based on PCR testing. The outbreak investigation identified strong evidence of an epidemiologic link between the affected cases. WGS revealed a set of spike mutations and deletions specific to the Alpha variant (B.1.1.7 lineage). All the nurses had mild symptoms, and the fatality among the patients was 50 % (three out of the six patients). CONCLUSIONS The current nosocomial COVID-19 outbreak, caused by the Alpha variant, revealed multiple breaches in the adherence to the hospital infection control recommended measures. Containment strategies were successful in controlling the outbreak and limiting infection spread. Molecular analysis and genome sequencing are essential tools besides epidemiological investigation to inform appropriate actions, especially with emerging pathogens.
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Affiliation(s)
- Asim Alsaedi
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Maher Alharbi
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - John Ossenkopp
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia
| | - Fayssal Farahat
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Roxanne Taguas
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia
| | - Mousa Algarni
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia
| | - Ahmad Alghamdi
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Sadeem Alhayli
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Abdulrahman Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Michel Doumith
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Aiman El-Saed
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Mohammed Alzahrani
- King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia; Department of Surgery, King Abdulaziz Medical City, Saudi Arabia
| | - Majid Alshamrani
- Infection Prevention and Control Program, King Abdulaziz Medical City, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Majed F Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia.
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17
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Grobbelaar LM, Kruger A, Venter C, Burger EM, Laubscher GJ, Maponga TG, Kotze MJ, Kwaan HC, Miller JB, Fulkerson D, Huff W, Chang E, Wiarda G, Bunch CM, Walsh MM, Raza S, Zamlut M, Moore HB, Moore EE, Neal MD, Kell DB, Pretorius E. Relative Hypercoagulopathy of the SARS-CoV-2 Beta and Delta Variants when Compared to the Less Severe Omicron Variants Is Related to TEG Parameters, the Extent of Fibrin Amyloid Microclots, and the Severity of Clinical Illness. Semin Thromb Hemost 2022; 48:858-868. [PMID: 36174604 DOI: 10.1055/s-0042-1756306] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Earlier variants of SARS-CoV-2 have been associated with plasma hypercoagulability (as judged by thromboelastography) and an extensive formation of fibrin amyloid microclots, which are considered to contribute to the pathology of the coronavirus 2019 disease (COVID-19). The newer Omicron variants appear to be far more transmissible, but less virulent, even when taking immunity acquired from previous infections or vaccination into account. We here show that while the clotting parameters associated with Omicron variants are significantly raised over those of healthy, matched controls, they are only raised to levels significantly lower than those seen with more severe variants such as beta and delta. We also observed that individuals infected with omicron variants manifested less extensive microclot formation in platelet-poor plasma compared with those harboring the more virulent variants. The measurement of clotting effects between the different variants acts as a kind of "internal control" that demonstrates the relationship between the extent of coagulopathies and the virulence of the variant of interest. This adds to the evidence that microclots may play an important role in reflecting the severity of symptoms observed in COVID-19.
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Affiliation(s)
- Lize M Grobbelaar
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | - Arneaux Kruger
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | - Chantelle Venter
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa
| | | | | | - Tongai G Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Hau C Kwaan
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joseph B Miller
- Departments of Emergency Medicine and Internal Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Daniel Fulkerson
- Department of Neurosurgery, St. Joseph Regional Medical Center, Mishawaka, Indiana
| | - Wei Huff
- Department of Neurosurgery, St. Joseph Regional Medical Center, Mishawaka, Indiana
| | - Eric Chang
- Indiana University School of Medicine - South Bend, Notre Dame, Indiana
| | - Grant Wiarda
- Department of Internal Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Connor M Bunch
- Departments of Emergency Medicine and Internal Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Mark M Walsh
- Indiana University School of Medicine - South Bend, Notre Dame, Indiana.,Department of Internal Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana.,Department of Emergency Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Syed Raza
- Department of Critical Care Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Mahmud Zamlut
- Department of Critical Care Medicine, Saint Joseph Regional Medical Center, Mishawaka, Indiana
| | - Hunter B Moore
- Division of Transplant Surgery, Department of Surgery, Denver Health and University of Colorado Health Sciences Center, Denver, Colorado
| | - Ernest E Moore
- Department of Surgery, Ernest E. Moore Shock Trauma Center at Denver Health and University of Colorado Health Sciences Center, Denver, Colorado
| | - Matthew D Neal
- Pittsburgh Trauma Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Douglas B Kell
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa.,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, England, United Kingdom.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Matieland, South Africa.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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18
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Solanki K, Rajpoot S, Kumar A, J Zhang KY, Ohishi T, Hirani N, Wadhonkar K, Patidar P, Pan Q, Baig MS. Structural analysis of spike proteins from SARS-CoV-2 variants of concern highlighting their functional alterations. Future Virol 2022. [PMID: 35935449 PMCID: PMC9345306 DOI: 10.2217/fvl-2022-0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
Aim: Mutations in the SARS-CoV-2 spike (S) protein have dramatically changed the transmissibility and pathogenicity of the virus. Therefore, we studied the binding affinity of Omicron spike-receptor binding domain (S-RBD) with human ACE2 receptor. Materials & methods: We used pyDockWEB and HADDOCK 2.4 docking for our study. Results: Computational docking indicated higher binding affinity of Omicron S-RBD as compared with wild-type SARS-CoV-2 and Delta S-RBD with ACE2. Interface analysis suggested four mutated residues of Omicron S-RBD for its enhanced binding. We also showed decreased binding affinity of Omicron and Delta S-RBDs with monoclonal antibodies. Conclusion: Compared with wild-type SARS-CoV-2, Omicron S-RBD exhibit higher binding with ACE2 and lower affinity against monoclonal antibodies.
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Affiliation(s)
- Kundan Solanki
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomokazu Ohishi
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Numazu-Shi, Shizuoka, 410-0301, Japan
| | - Nik Hirani
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH164TJ, UK
| | - Khandu Wadhonkar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Pramod Patidar
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
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19
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Nasereddin A, Al-Jawabreh A, Dumaidi K, Al-Jawabreh A, Al-Jawabreh H, Ereqat S. Tracking of SARS-CoV-2 Alpha variant (B.1.1.7) in Palestine. INFECTION, GENETICS AND EVOLUTION 2022; 101:105279. [PMID: 35390503 PMCID: PMC8978447 DOI: 10.1016/j.meegid.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
Abstract
As surges of the COVID-19 pandemic continue globally, including in Palestine, several new SARS-CoV-2 variants have been introduced. This expansion has impacted transmission, disease severity, virulence, diagnosis, therapy, and natural and vaccine-induced immunity. Here, 183 whole genome sequences (WGS) were analyzed, of which 129 were from Palestinian cases, 62 of which were collected in 11 Palestinian districts between October 2020 and April 2021 and sequenced completely. A dramatic shift from the wild type to the Alpha variant (B 1.1.7) was observed within a short period of time. Cluster mapping revealed statistically significant clades in two main Palestinian cities, Al-Khalil (Monte Carlo hypothesis test-Poisson model, P = 0.00000000012) and Nablus (Monte Carlo hypothesis test-Poisson model, P = 0.014 and 0.015). The phylogenetic tree showed three main clusters of SARS-CoV-2 with high bootstrap values (>90). However, population genetics analysis showed a genetically homogenous population supported by low Wright's F-statistic values (Fst <0.25), high gene flow (Nm > 3), and statistically insignificant Tajima's D values (Tajima's test, neutrality model prediction, P = 0.02). The Alpha variant, rapidly replaced the wild type, causing a major surge that peaked in April 2021, with an increased COVID-19 mortality rate, especially, in the Al-Khalil and Nablus districts. The source of introduction remains uncertain, despite the minimal genetic variation. The study substantiates the use of WGS for SARS-CoV-2 surveillance as an early warning system to track down new variants requiring effective control.
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20
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Lino A, Cardoso MA, Martins‐Lopes P, Gonçalves HMR. Omicron - The new SARS-CoV-2 challenge? Rev Med Virol 2022; 32:e2358. [PMID: 35445774 PMCID: PMC9111063 DOI: 10.1002/rmv.2358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 virus has infected nearly 300 M people worldwide and has been associated with over 6 M deaths by March 2022. Since the virus emergence in December 2019 in Wuhan, several new mutations have been described. The World Health Organization has developed a working name for these emerging variants according to their impact on the worldwide population. In this context a high alert has been paid to variants of concern (VOC) due to their high infectiousness and transmissibility patterns. The most recent VOC, Omicron (B.1.1.529), has become dominant in the shortest time ever and has placed Europe under an overwhelming and unprecedented number of new cases. This variant has numerous mutations in regions that are associated with higher transmissibility, stronger viral binding, affinity and antibody escape. Moreover, the mutations and deletions present in the spike protein suggest that the SARS-CoV-2 specific attachment inhibitors may not be the best option for Omicron therapy. Omicron is the dominant variant circulating worldwide and, at the end of February 2022, it was responsible for nearly all sequences reported to GISAID. Omicron is made up of several sublineages, where the most common are BA.1 and BA.2 (or Nextstrain clade 21K and 21L, respectively). At a global level, it is possible to say that the proportion of BA.2 has been increasing relative to BA.1 and in some countries it has been replacing it at high rates. In order to better assess the Omicron effectiveness on antibody escape, spread and infectious ability it is of the highest relevance to maintain a worldwide tight surveillance. Even though this variant has been associated with a lower death rate, it is important to highlight that the number of people becoming infected is concerning and that further unpredictable mutations may emerge as the number of infected people rises.
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Affiliation(s)
- A. Lino
- BioISI ‐ Biosystems & Integrative Sciences InstituteFaculty of SciencesUniversity of LisbonLisbonPortugal
| | - M. A. Cardoso
- REQUIMTEInstituto Superior de Engenharia do PortoPortoPortugal
| | - P. Martins‐Lopes
- BioISI ‐ Biosystems & Integrative Sciences InstituteFaculty of SciencesUniversity of LisbonLisbonPortugal
- Department of Genetics and Biotechnology (DGB)University of Trás‐os‐Montes e Alto Douro (UTAD)Vila RealPortugal
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21
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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22
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Omicron: A highly transmissible SARS-CoV-2 variant. GENE REPORTS 2022; 27:101549. [PMID: 35165664 PMCID: PMC8828449 DOI: 10.1016/j.genrep.2022.101549] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
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23
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Gong W, Parkkila S, Wu X, Aspatwar A. SARS-CoV-2 variants and COVID-19 vaccines: Current challenges and future strategies. Int Rev Immunol 2022; 42:393-414. [PMID: 35635216 DOI: 10.1080/08830185.2022.2079642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/23/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022]
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite strict control measures implemented worldwide and immunization using novel vaccines, the pandemic continues to rage due to emergence of several variants of SARS-CoV-2 with increased transmission and immune escape. The rapid spread of variants of concern (VOC) in the recent past has created a massive challenge for the control of COVID-19 pandemic via the currently used vaccines. Vaccines that are safe and effective against the current and future variants of SARS-CoV-2 are essential in controlling the COVID-19 pandemic. Rapid production and massive rollout of next-generation vaccines against the variants are key steps to control the COVID-19 pandemic and to help us return to normality. Coordinated surveillance of SARS-CoV-2, rapid redesign of new vaccines and extensive vaccination are needed to counter the current SARS-CoV-2 variants and prevent the emergence of new variants. In this article, we review the latest information on the VOCs and variants of interest (VOIs) and present the information on the clinical trials that are underway on evaluating the effectiveness of COVID-19 vaccines on VOCs. We also discuss the current challenges posed by the VOCs in controlling the COVID-19 pandemic and future strategies to overcome the threat posed by the highly virulent and rapidly transmissible variants of SARS-CoV2.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Ltd, Tampere University Hospital, Tampere, Finland
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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24
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Professional practice for COVID-19 risk reduction among health care workers: A cross-sectional study with matched case-control comparison. PLoS One 2022; 17:e0264232. [PMID: 35313328 PMCID: PMC8936447 DOI: 10.1371/journal.pone.0264232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/04/2022] [Indexed: 11/19/2022] Open
Abstract
Background Health care workers (HCWs) are particularly exposed to COVID-19 and therefore it is important to study preventive measures in this population. Aim To investigate socio-demographic factors and professional practice associated with the risk of COVID-19 among HCWs in health establishments in Normandy, France. Methods A cross-sectional and 3 case-control studies using bootstrap methods were conducted in order to explore the possible risk factors that lead to SARS-CoV2 transmission within HCWs. Case-control studies focused on risk factors associated with (a) care of COVID-19 patients, (b) care of non COVID-19 patients and (c) contacts between colleagues. Participants 2,058 respondents, respectively 1,363 (66.2%) and 695 (33.8%) in medical and medico-social establishments, including HCW with and without contact with patients. Results 301 participants (14.6%) reported having been infected by SARS-CoV2. When caring for COVID-19 patients, HCWs who declared wearing respirators, either for all patient care (ORa 0.39; 95% CI: 0.29–0.51) or only when exposed to aerosol-generating procedures (ORa 0.56; 95% CI: 0.43–0.70), had a lower risk of infection compared with HCWs who declared wearing mainly surgical masks. During care of non COVID-19 patients, wearing mainly a respirator was associated with a higher risk of infection (ORa 1.84; 95% CI: 1.06–3.37). An increased risk was also found for HCWs who changed uniform in workplace changing rooms (ORa 1.93; 95% CI: 1.63–2.29). Conclusion Correct use of PPE adapted to the situation and risk level is essential in protecting HCWs against infection.
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25
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Nasimiyu C, Matoke-Muhia D, Rono GK, Osoro E, Obado DO, Mwangi JM, Mwikwabe N, Thiong’o K, Dawa J, Ngere I, Gachohi J, Kariuki S, Amukoye E, Mureithi M, Ngere P, Amoth P, Were I, Makayotto L, Nene V, Abworo EO, Njenga MK, Seifert SN, Oyola SO. Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.28.22271467. [PMID: 35262086 PMCID: PMC8902869 DOI: 10.1101/2022.02.28.22271467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Results Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. Conclusions The emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.
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Affiliation(s)
- Carolyne Nasimiyu
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University, Pullman, USA
| | | | | | - Eric Osoro
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University, Pullman, USA
| | | | | | | | | | - Jeanette Dawa
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
| | - Isaac Ngere
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
| | - John Gachohi
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
| | | | | | - Marianne Mureithi
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | | | | | - Ian Were
- Kenya Ministry of Health, Nairobi, Kenya
| | | | | | | | - M. Kariuki Njenga
- Washington State Global Health Program-Kenya, Washington State University, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University, Pullman, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, USA
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26
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Mohsen MO, Balke I, Zinkhan S, Zeltina V, Liu X, Chang X, Krenger PS, Plattner K, Gharailoo Z, Vogt AS, Augusto G, Zwicker M, Roongta S, Rothen DA, Josi R, da Costa JJ, Sobczak JM, Nonic A, Brand L, Nuss K, Martina B, Speiser DE, Kündig T, Jennings GT, Walton SM, Vogel M, Zeltins A, Bachmann MF. A scalable and highly immunogenic virus-like particle-based vaccine against SARS-CoV-2. Allergy 2022; 77:243-257. [PMID: 34496033 PMCID: PMC8653185 DOI: 10.1111/all.15080] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND SARS-CoV-2 caused one of the most devastating pandemics in the recent history of mankind. Due to various countermeasures, including lock-downs, wearing masks, and increased hygiene, the virus has been controlled in some parts of the world. More recently, the availability of vaccines, based on RNA or adenoviruses, has greatly added to our ability to keep the virus at bay; again, however, in some parts of the world only. While available vaccines are effective, it would be desirable to also have more classical vaccines at hand for the future. Key feature of vaccines for long-term control of SARS-CoV-2 would be inexpensive production at large scale, ability to make multiple booster injections, and long-term stability at 4℃. METHODS Here, we describe such a vaccine candidate, consisting of the SARS-CoV-2 receptor-binding motif (RBM) grafted genetically onto the surface of the immunologically optimized cucumber mosaic virus, called CuMVTT -RBM. RESULTS Using bacterial fermentation and continuous flow centrifugation for purification, the yield of the production process is estimated to be >2.5 million doses per 1000-litre fermenter run. We demonstrate that the candidate vaccine is highly immunogenic in mice and rabbits and induces more high avidity antibodies compared to convalescent human sera. The induced antibodies are more cross-reactive to mutant RBDs of variants of concern (VoC). Furthermore, antibody responses are neutralizing and long-lived. In addition, the vaccine candidate was stable for at least 14 months at 4℃. CONCLUSION Thus, the here presented VLP-based vaccine may be a good candidate for use as conventional vaccine in the long term.
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27
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Islam S, Islam T, Islam MR. New Coronavirus Variants are Creating More Challenges to Global Healthcare System: A Brief Report on the Current Knowledge. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2022; 15:2632010X221075584. [PMID: 35141522 PMCID: PMC8819824 DOI: 10.1177/2632010x221075584] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022]
Abstract
The coronavirus is naturally mutating over time and producing new variants. Some of them are more contagious and destructive than previous strains. Also, some variants are capable of therapeutic escaping. Earlier SARS-CoV-2 variants proved that some are supercritical, and newly mutated strains are creating new challenges to the global healthcare systems. Here we aimed to evaluate different coronavirus variants and associated challenges for healthcare systems. We searched for information online and on the PubMed, Scopus, and Embase databases. We found the wild-type virus is more sensitive for neutralization and more controllable than newer variants. The Delta and Omicron variants are more highly transmissible than Alpha, Beta, and Gamma variants. Also, few strains are resistant to neutralization. Therefore, there is a chance of reinfection among the vaccinated population. The transmissibility and resistance of the recently identified Omicron variant is still unclear. The Delta variant is the most dangerous among all variants due to its high transmissibility, disease severity, and mortality rate. For poor and developing countries, oxygen supply, medication, vaccination, and device supply are challenging during epidemic waves. Slowing down the transmission, mass vaccination, vaccine redesign, re-compiling action plans, and following safety guidelines can be effective solutions to the new challenges.
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Affiliation(s)
- Salsabil Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Towhidul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
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28
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Swai J, Gui M, Long M, Wei Z, Hu Z, Liu S. Humoral and cellular immune response to severe acute respiratory syndrome coronavirus-2 vaccination in haemodialysis and kidney transplant patients. Nephrology (Carlton) 2022; 27:7-24. [PMID: 34510645 PMCID: PMC8646800 DOI: 10.1111/nep.13974] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/22/2021] [Accepted: 09/07/2021] [Indexed: 12/26/2022]
Abstract
End-stage renal disease (ESRD) patients are amongst the vulnerable groups and thus prioritized in the Coronavirus disease-2019 vaccination programmes. However, this cohort was excluded from vaccine-trials and yet shares the same vaccination scheme with the general population. Here, we explore trends of immune response-proportions amongst ESRD patients on renal replacement therapy for up to 4 weeks post-vaccination completion with Pfizer/Moderna vaccines. From inception to 10 July 2021, we searched six online-databases for articles reporting humoral and cellular immune response proportions for up to 4 weeks post booster-vaccination. We pooled the responders' proportions by meta-analysis and conducted a meta-regression stratifying outcomes by significant confounders. Twenty-seven eligible studies reported 2789 ESRD patients. 1337, 1452 and 477 were on haemodialysis, received kidney transplantation, and healthy controls, respectively. Haemodialysis patients' proportions of humoral and cellular immune responses varied from 87.29% (80.77-93.81)-88.78% (86.76-90.80) and 62.86% (56.56, 69.17)-85.78% (78.99, 92.57), respectively, between first- and fourth-weeks. Kidney transplant patients' proportions of humoral and cellular immune responses ranged from 2.6% (0.06-13.48)-29.87% (27.68, 32.07) and 5.13% (0.63-17.3)-59.84% (54.57-65.10), respectively, between first- and fourth-weeks. All healthy controls maintained ≥93% proportions of both responses throughout the follow-up. Study design and country of study influenced the pooled response proportions. Conclusively, haemodialysis and kidney transplant patients have lower proportions of humoral and cellular immune responses than healthy controls. However, haemodialysis patients' response proportions improve, reaching near healthy-control levels by the fourth week. Kidney transplant patients' lower responses' proportions also improve but remain significantly lower than healthy controls throughout four-weeks. The "one-size-fits-all" vaccination scheme might be inadequate for kidney transplant patients.
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Affiliation(s)
- Joel Swai
- Division of Nephrology and ImmunologyUniversity of AlbertaEdmontonCanada
- Department of NephrologyBenjamin Mkapa HospitalDodoma CityTanzania
| | - Ming Gui
- Department of Nephrology and RheumatologyThird Xiangya Hospital of Central South UniversityChangshaChina
| | - Mao Long
- Department of Nephrology and RheumatologyThird Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhu Wei
- Department of Infectious DiseasesThird Xiangya Hospital of Central South UniversityChangshaChina
| | - Zixuan Hu
- Department of Internal MedicineThird Xiangya Hospital of Central South UniversityChangshaChina
| | - Shaojun Liu
- Department of Internal MedicineThird Xiangya Hospital of Central South UniversityChangshaChina
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29
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Islam S, Islam T, Islam MR. New Coronavirus Variants are Creating More Challenges to Global Healthcare System: A Brief Report on the Current Knowledge. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2022. [PMID: 35141522 DOI: 10.1177/2632010x2210755846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The coronavirus is naturally mutating over time and producing new variants. Some of them are more contagious and destructive than previous strains. Also, some variants are capable of therapeutic escaping. Earlier SARS-CoV-2 variants proved that some are supercritical, and newly mutated strains are creating new challenges to the global healthcare systems. Here we aimed to evaluate different coronavirus variants and associated challenges for healthcare systems. We searched for information online and on the PubMed, Scopus, and Embase databases. We found the wild-type virus is more sensitive for neutralization and more controllable than newer variants. The Delta and Omicron variants are more highly transmissible than Alpha, Beta, and Gamma variants. Also, few strains are resistant to neutralization. Therefore, there is a chance of reinfection among the vaccinated population. The transmissibility and resistance of the recently identified Omicron variant is still unclear. The Delta variant is the most dangerous among all variants due to its high transmissibility, disease severity, and mortality rate. For poor and developing countries, oxygen supply, medication, vaccination, and device supply are challenging during epidemic waves. Slowing down the transmission, mass vaccination, vaccine redesign, re-compiling action plans, and following safety guidelines can be effective solutions to the new challenges.
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Affiliation(s)
- Salsabil Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Towhidul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md Rabiul Islam
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
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30
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Fan S, Xiao K, Li D, Zhao H, Zhang J, Yu L, Chang P, Zhu S, Xu X, Liao Y, Ji T, Jiang G, Yan D, Zeng F, Duan S, Xia B, Wang L, Yang F, He Z, Song Y, Cui P, Li X, Zhang Y, Zheng B, Zhang Y, Xu W, Li Q. Preclinical immunological evaluation of an intradermal heterologous vaccine against SARS-CoV-2 variants. Emerg Microbes Infect 2021; 11:212-226. [PMID: 34931939 PMCID: PMC8745378 DOI: 10.1080/22221751.2021.2021807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent emergence of COVID-19 variants has necessitated the development of new vaccines that stimulate the formation of high levels of neutralizing antibodies against S antigen variants. A new strategy involves the intradermal administration of heterologous vaccines composed of one or two doses of inactivated vaccine and a booster dose with the mutated S1 protein (K-S). Such vaccines improve the immune efficacy by increasing the neutralizing antibody titers and promoting specific T cell responses against five variants of the RBD protein. A viral challenge test with the B.1.617.2 (Delta) variant confirmed that both administration schedules (i.e. “1 + 1” and “2 + 1”) ensured protection against this strain. These results suggest that the aforementioned strategy is effective for protecting against new variants and enhances the anamnestic immune response in the immunized population.
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Affiliation(s)
- Shengtao Fan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Kang Xiao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Dandan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Heng Zhao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Jingjing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Li Yu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Penglan Chang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Shuangli Zhu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Xingli Xu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yun Liao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Tianjiao Ji
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Guorun Jiang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Dongmei Yan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Fengyuan Zeng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Suqin Duan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Baicheng Xia
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Lichun Wang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yang Song
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Pingfang Cui
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Xiaolei Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Yaxing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Bangyi Zheng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Ying Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Qihan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
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31
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He X, He C, Hong W, Zhang K, Wei X. The challenges of COVID-19 Delta variant: Prevention and vaccine development. MedComm (Beijing) 2021; 2:846-854. [PMID: 34909755 PMCID: PMC8661803 DOI: 10.1002/mco2.95] [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: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 02/05/2023] Open
Abstract
Several SARS-CoV-2 variants have emerged since the pandemic, bringing about a renewed threat to the public. Delta variant (B.1.617.2) was first detected in October 2020 in India and was characterized as variants of concern (VOC) by WHO on May 11, 2021. Delta variant rapidly outcompeted other variants to become the dominant circulating lineages due to its clear competitive advantage. There is emerging evidence of enhanced transmissibility and reduced vaccine effectiveness (VE) against Delta variant. Therefore, it is crucial to understand the features and phenotypic effects of this variant. Herein, we comprehensively described the evaluation and features of Delta variant, summarized the effects of mutations in spike on the infectivity, transmission ability, immune evasion, and provided a perspective on efficient approaches for preventing and overcoming COVID-19.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanP. R. China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanP. R. China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanP. R. China
| | - Kang Zhang
- Center for Biomedicine and InnovationsFaculty of MedicineMacau University of Science and TechnologyTaipaMacauP. R. China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanP. R. China
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32
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Lin L, Liu Y, Tang X, He D. The Disease Severity and Clinical Outcomes of the SARS-CoV-2 Variants of Concern. Front Public Health 2021; 9:775224. [PMID: 34917580 PMCID: PMC8669511 DOI: 10.3389/fpubh.2021.775224] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023] Open
Abstract
With the continuation of the pandemic, many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have appeared around the world. Owing to a possible risk of increasing the transmissibility of the virus, severity of the infected individuals, and the ability to escape the antibody produced by the vaccines, the four SARS-CoV-2 variants of Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) have attracted the most widespread attention. At present, there is a unified conclusion that these four variants have increased the transmissibility of SARS-CoV-2, but the severity of the disease caused by them has not yet been determined. Studies from June 1, 2020 to October 15, 2021 were considered, and a meta-analysis was carried out to process the data. Alpha, Beta, Gamma, and Delta variants are all more serious than the wild-type virus in terms of hospitalization, ICU admission, and mortality, and the Beta and Delta variants have a higher risk than the Alpha and Gamma variants. Notably, the random effects of Beta variant to the wild-type virus with respect to hospitalization rate, severe illness rate, and mortality rate are 2.16 (95% CI: 1.19-3.14), 2.23 (95% CI: 1.31-3.15), and 1.50 (95% CI: 1.26-1.74), respectively, and the random effects of Delta variant to the wild-type virus are 2.08 (95% CI: 1.77-2.39), 3.35 (95% CI: 2.5-4.2), and 2.33 (95% CI: 1.45-3.21), respectively. Although, the emergence of vaccines may reduce the threat posed by SARS-CoV-2 variants, these are still very important, especially the Beta and Delta variants.
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Affiliation(s)
- Lixin Lin
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Ying Liu
- School of International Business, Xiamen University Tan Kah Kee College, Zhangzhou, China
| | - Xiujuan Tang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Daihai He
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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33
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Murdaca G, Paladin F, Tonacci A, Isola S, Allegra A, Gangemi S. The Potential Role of Cytokine Storm Pathway in the Clinical Course of Viral Respiratory Pandemic. Biomedicines 2021; 9:biomedicines9111688. [PMID: 34829918 PMCID: PMC8615478 DOI: 10.3390/biomedicines9111688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/13/2021] [Indexed: 01/01/2023] Open
Abstract
The "cytokine storm" (CS) consists of a spectrum of different immune dysregulation disorders characterized by constitutional symptoms, systemic inflammation and multiorgan dysfunction triggered by an uncontrolled immune response. Particularly in respiratory virus infections, the cytokine storm plays a primary role in the pathogenesis of respiratory disease and the clinical outcome of respiratory diseases, leading to complications such as alveolar edema and hypoxia. In this review, we wanted to analyze the different pathogenetic mechanisms involved in the various respiratory viral pandemics (COVID-19; SARS; MERS; H1N1 influenza A and Spanish flu) which have affected humans in this and last century, with particular attention to the phenomenon of the "cytokine storm" which determines the clinical severity of the respiratory disease and consequently its lethality.
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Affiliation(s)
- Giuseppe Murdaca
- Clinical Immunology Unit, Department of Internal Medicine, University of Genoa and Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-0103537924; Fax: +39-0105556950
| | - Francesca Paladin
- Department of Internal Medicine, University of Genoa and Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Alessandro Tonacci
- Clinical Physiology Institute, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy;
| | - Stefania Isola
- School and Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (S.I.); (S.G.)
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy;
| | - Sebastiano Gangemi
- School and Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (S.I.); (S.G.)
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34
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Ong SJ, Anil G, Chia KL, Khoo D, Lee JK, Chen PX, Nares TM, Koh CJ, Su P, Yang C, Singh P, Rajendran PC, Fotheringham T, Quek ST, Renfrew I. The effectiveness of the Safety in Interventional Radiology (SIR) Shield in reducing droplet transmission and its effect on image quality and radiation dose. Br J Radiol 2021; 95:20210835. [PMID: 34672690 PMCID: PMC8722246 DOI: 10.1259/bjr.20210835] [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] [Indexed: 01/25/2023] Open
Abstract
Objective: To evaluate the efficacy of a barrier shield in reducing droplet transmission and its effect on image quality and radiation dose in an interventional suite. Methods: A human cough droplet visualisation model in a supine position was developed to assess efficacy of barrier shield in reducing environmental contamination. Its effect on image quality (resolution and contrast) was evaluated via image quality test phantom. Changes in the radiation dose to patient post-shield utilisation was measured. Results: Use of the shield prevented escape of visible fluorescent cough droplets from the containment area. No subjective change in line-pair resolution was observed. No significant difference in contrast-to-noise ratio was measured. Radiation dosage to patient was increased; this is predominantly attributed to the increased air gap and not the physical properties of the shield. Conclusion: Use of the barrier shield provided an effective added layer of personal protection in the interventional radiology theatre for aerosol generating procedures. Advances in knowledge: This is the first time a human supine cough droplet visualisation has been developed. While multiple types of barrier shields have been described, this is the first systematic practical evaluation of a barrier shield designed for use in the interventional radiology theatre.
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Affiliation(s)
- Shao Jin Ong
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Gopinathan Anil
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore.,Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Koon Liang Chia
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Deborah Khoo
- Department of Anaesthesia, National University Hospital Singapore, Singapore, Singapore
| | - Joseph Kt Lee
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore.,Department of Radiology, The University of North Carolina, Chapel Hill, North Carolina, USA
| | - Priscilla Xh Chen
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Teddy M Nares
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Calvin J Koh
- Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Hospital Singapore, Singapore, Singapore
| | - Peijing Su
- Department of Medicine, National University Hospital Singapore, Singapore, Singapore
| | - Cunli Yang
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Pavel Singh
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Prapul C Rajendran
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Timothy Fotheringham
- Department of Radiology, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Swee T Quek
- Department of Diagnostic Imaging, National University Hospital Singapore, Singapore, Singapore
| | - Ian Renfrew
- Department of Radiology, Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
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35
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Ramesh S, Govindarajulu M, Parise RS, Neel L, Shankar T, Patel S, Lowery P, Smith F, Dhanasekaran M, Moore T. Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy. Vaccines (Basel) 2021; 9:1195. [PMID: 34696303 PMCID: PMC8537675 DOI: 10.3390/vaccines9101195] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.
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Affiliation(s)
- Sindhu Ramesh
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Rachel S. Parise
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Logan Neel
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Tharanath Shankar
- Department of Internal Medicine, Ramaiah Medical College and Hospital, Bengaluru 560054, Karnataka, India;
| | - Shriya Patel
- Department of Neuroscience, Middlebury College, Middlebury, VT 05753, USA;
| | - Payton Lowery
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Forrest Smith
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Muralikrishnan Dhanasekaran
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Timothy Moore
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
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36
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Immune Responses against SARS-CoV-2-Questions and Experiences. Biomedicines 2021; 9:biomedicines9101342. [PMID: 34680460 PMCID: PMC8533170 DOI: 10.3390/biomedicines9101342] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/07/2023] Open
Abstract
Understanding immune reactivity against SARS-CoV-2 is essential for coping with the COVID-19 pandemic. Herein, we discuss experiences and open questions about the complex immune responses to SARS-CoV-2. Some people react excellently without experiencing any clinical symptoms, they do not get sick, and they do not pass the virus on to anyone else ("sterilizing" immunity). Others produce antibodies and do not get COVID-19 but transmit the virus to others ("protective" immunity). Some people get sick but recover. A varying percentage develops respiratory failure, systemic symptoms, clotting disorders, cytokine storms, or multi-organ failure; they subsequently decease. Some develop long COVID, a new pathologic entity similar to fatigue syndrome or autoimmunity. In reality, COVID-19 is considered more of a systemic immune-vascular disease than a pulmonic disease, involving many tissues and the central nervous system. To fully comprehend the complex clinical manifestations, a profound understanding of the immune responses to SARS-CoV-2 is a good way to improve clinical management of COVID-19. Although neutralizing antibodies are an established approach to recognize an immune status, cellular immunity plays at least an equivalent or an even more important role. However, reliable methods to estimate the SARS-CoV-2-specific T cell capacity are not available for clinical routines. This deficit is important because an unknown percentage of people may exist with good memory T cell responsibility but a low number of or completely lacking peripheral antibodies against SARS-CoV-2. Apart from natural immune responses, vaccination against SARS-CoV-2 turned out to be very effective and much safer than naturally acquired immunity. Nevertheless, besides unwanted side effects of the currently available vector and mRNA preparations, concerns remain whether these vaccines will be strong enough to defeat the pandemic. Altogether, herein we discuss important questions, and try to give answers based on the current knowledge and preliminary data from our laboratories.
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37
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Angius F, Pala G, Manzin A. SARS-CoV-2 and Its Variants: The Pandemic of Unvaccinated. Front Microbiol 2021; 12:749634. [PMID: 34630373 PMCID: PMC8497702 DOI: 10.3389/fmicb.2021.749634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabrizio Angius
- Microbiology and Virology Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Cagliari, Italy
| | - Giuseppe Pala
- Microbiology and Virology Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Cagliari, Italy
| | - Aldo Manzin
- Microbiology and Virology Unit, Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Cagliari, Italy
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Benítez-Cardoza CG, Vique-Sánchez JL. Identifying compounds that prevent the binding of the SARS-CoV-2 S-protein to ACE2. Comput Biol Med 2021; 136:104719. [PMID: 34358993 PMCID: PMC8325380 DOI: 10.1016/j.compbiomed.2021.104719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
We investigated compounds selected by molecular docking to identify a specific treatment for COVID-19 that decreases the interaction between angiotensin-converting enzyme 2 (ACE2) and the receptor-binding domain (RBD) of SARS-CoV-2. Five compounds that interact with ACE2 amino acids Gln24, Asp30, His34, Tyr41, Gln42, Met82, Lys353, and Arg357 were evaluated using specific binding assays for their effects on the interaction between ACE2 with RBD. The compound labeled ED demonstrated favorable ACE2-binding, with an IC50 of 31.95 μM. ED cytotoxicity, evaluated using PC3 cells in an MTT assay, was consistent with the low theoretical toxicity previously reported. We propose that ED mainly interacts with His34, Glu37, and Lys353 in ACE2 and that it has an inhibitory effect on the interaction of ACE2 with the RBD of the S-protein. We recommend further investigation to develop ED into a potential drug or adjuvant in COVID-19 treatment.
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Affiliation(s)
| | - José Luis Vique-Sánchez
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, BC, Mexico; Ciencias de La Salud Mexicali, Universidad Autónoma de Baja California, Mexicali, BC, Mexico.
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Li G, Zhou Z, Du P, Yu M, Li N, Xiong X, Huang H, Liu Z, Dai Q, Zhu J, Guo C, Wu S, Baptista-Hon DT, Miao M, Ming LW, Wu Y, Zeng F, Zhang CL, Zhang ED, Song H, Liu J, Lau JYN, Xiang AP, Zhang K. The SARS-CoV-2 spike L452R-E484Q variant in the Indian B.1.617 strain showed significant reduction in the neutralization activity of immune sera. PRECISION CLINICAL MEDICINE 2021; 4:149-154. [PMID: 35693215 PMCID: PMC8385834 DOI: 10.1093/pcmedi/pbab016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/11/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
To assess the impact of the key non-synonymous amino acid substitutions in the RBD of the spike protein of SARS-CoV-2 variant B.1.617.1 (dominant variant identified in the current India outbreak) on the infectivity and neutralization activities of the immune sera, L452R and E484Q (L452R-E484Q variant), pseudotyped virus was constructed (with the D614G background). The impact on binding with the neutralizing antibodies was also assessed with an ELISA assay. Pseudotyped virus carrying a L452R-E484Q variant showed a comparable infectivity compared with D614G. However, there was a significant reduction in the neutralization activity of the immune sera from non-human primates vaccinated with a recombinant receptor binding domain (RBD) protein, convalescent patients, and healthy vaccinees vaccinated with an mRNA vaccine. In addition, there was a reduction in binding of L452R-E484Q-D614G protein to the antibodies of the immune sera from vaccinated non-human primates. These results highlight the interplay between infectivity and other biologic factors involved in the natural evolution of SARS-CoV-2. Reduced neutralization activities against the L452R-E484Q variant will have an impact on health authority planning and implications for the vaccination strategy/new vaccine development.
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Affiliation(s)
- Gen Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Zhongcheng Zhou
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Peng Du
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Meixing Yu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Ning Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Xinxin Xiong
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Hong Huang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Zhihai Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Qinjin Dai
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Jie Zhu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Chengbin Guo
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Shanyun Wu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Daniel T Baptista-Hon
- University Hospital and Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau 030027, China
| | - Man Miao
- University Hospital and Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau 030027, China
| | - Lam Wai Ming
- University Hospital and Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau 030027, China
| | - Yong Wu
- Jinan University First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou 635099, China
| | - Charlotte L Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Edward D Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Haifeng Song
- Department of Bioinformatics and AI, Bioland Laboratory, Guangzhou 510000, China
| | | | - Johnson Yiu-Nam Lau
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong 610051, China
| | - Andy P Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510000, China
| | - Kang Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510620, China
- University Hospital and Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau 030027, China
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40
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Tashkandi N, Aljuaid M, McKerry T, Alchin J, Taylor L, Catangui EJ, Mulla R, Sinnappan S, Nammour G, El-Saed A, Alshamrani MM. Nursing strategic pillars to enhance nursing preparedness and response to COVID-19 pandemic at a tertiary care hospital in Saudi Arabia. J Infect Public Health 2021; 14:1155-1160. [PMID: 34371365 PMCID: PMC8252703 DOI: 10.1016/j.jiph.2021.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/17/2021] [Accepted: 06/27/2021] [Indexed: 11/24/2022] Open
Abstract
Background COVID-19 pandemic caused enormous implications on the frontline staff. The objective was to share our nursing experience in responding to COVID-19 pandemic at a large hospital and its impact on nursing safety and healthcare services. Methods Six nursing strategic pillars were implemented. Pillar 1: establishing corona command centre. Pillar 2: limiting exposure by virtual care model, strict infection control measures, altered patient flow, active surveillance, and contact tracing. Pillar 3: maintaining sufficient supplies of personal protective equipment. Pillar 4: creating surge capacity by establishing dedicated COVID-19 units and increasing critical care beds. Pillar 5: training and redeployment of nurses and implementing alternate staffing models. Pillar 6: monitoring staff wellbeing, establishing mental health support hotline and clinic, providing hotel self-quarantine, and financial incentives. Results Out of 5483 nurses, 543 (10%) were trained for redeployment, mainly at acute and intensive care units. After serving 11,623 infected patient including 1646 hospitalizations during the first 9 months of the pandemic, only 385 (7.0%) nurses were infected with COVID-19. Out of them, only 10 (2.6%) required hospitalization, one (0.3%) required ICU admission, and none died. Although the number of patients hospitalized at our hospital during the current pandemic was 17 folds higher than the 2015 outbreak of middle East respiratory syndrome coronavirus, the hospital administration did not have to close the hospital as they did in 2015. Conclusions Proactive nursing leadership and implementation of multiple nursing pillars enabled the facility to maintain the safety of nursing workforce while serving large influx of COVID-19 patients.
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Affiliation(s)
- Nabeeha Tashkandi
- Nursing Services, King Abdualziz Medical City (KAMC), Riyadh, Saudi Arabia.
| | - Maha Aljuaid
- Clinical Nursing, Ambulatory and Haemodialysis Care, KAMC, Riyadh, Saudi Arabia
| | | | - John Alchin
- Clinical Nursing, Critical Care, KAMC, Riyadh, Saudi Arabia
| | - Laura Taylor
- Clinical Nursing, Surgical Care, KAMC, Riyadh, Saudi Arabia
| | | | - Rana Mulla
- Nursing Education and Clinical Practice, KAMC, Riyadh, Saudi Arabia
| | - Suwarnnah Sinnappan
- Clinical Nursing, Obstetrical, Gynecological and Neonatal Care, KAMC, Riyadh, Saudi Arabia
| | - Georges Nammour
- Clinical Nursing, Emergency Care, KAMC, Riyadh, Saudi Arabia
| | - Aiman El-Saed
- Infection Prevention and Control, KAMC, Riyadh, Saudi Arabia
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41
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Novelli G, Colona VL, Pandolfi PP. A focus on the spread of the delta variant of SARS-CoV-2 in India. Indian J Med Res 2021; 153:537-541. [PMID: 34259195 PMCID: PMC8555585 DOI: 10.4103/ijmr.ijmr_1353_21] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome (RM), Italy
- IRCCS Neuromed, Pozzilli (IS), Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno (NV), USA
| | - Vito Luigi Colona
- Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome (RM), Italy
| | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology & Health Sciences, MBC, University of Turin, Turin (TO), Italy
- Renown Institute for Cancer, Nevada System of Higher Education, Reno (NV), USA
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