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Khamis F, Al Awaidy S, Ba’Omar M, Osman W, Chhetri S, Ambusaid Z, Al Fahdi Z, Al Lawati J, Al Sulaimi K, Al Bulushi SA, Al Bahrani M, Al-Zakwani I. The Impact of Demographic, Clinical Characteristics and the Various COVID-19 Variant Types on All-Cause Mortality: A Case-Series Retrospective Study. Diseases 2022; 10:100. [PMID: 36412594 PMCID: PMC9680441 DOI: 10.3390/diseases10040100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
(1) Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into a pandemic affecting virtually every country in the world. We evaluated the demographic, clinical, laboratory, and all-cause mortality of moderate and severe COVID-19 patients admitted to a tertiary care hospital in Oman during the different COVID-19 waves and variant types. (2) Methods: A case-series retrospective study was carried out between 12 March 2020 and 30 June 2022. All adults over the age of 18 with laboratory-confirmed COVID-19 were enrolled. Analyses were performed using univariate and multivariate statistics. (3) Results: A total of 1462 confirmed cases enrolled with the mean age of the cohort was 55 ± 17 years with significant differences among the groups (p = 0.006). A total of 63% and 80% of the patients were males and citizens of Oman, respectively. Patients infected with the Alpha COVID-19 variant type were more likely to have acute respiratory distress syndrome (ARDS) (p < 0.001), stay longer in the hospital (p < 0.001), and get admitted to the intensive care unit (ICU) (p < 0.001). At the same time, those who had the Omicron COVID-19 type were more likely to have renal impairment (p < 0.001) and less likely to be associated with non-invasive ventilation (NIV) (p = 0.001) compared with other COVID-19 variant types. The Delta (adjusted odds ratio (aOR), 1.8; 95% confidence interval (CI): 1.22−2.66; p = 0.003) and Omicron (aOR, 1.88; 95% CI: 1.09−3.22; p = 0.022) COVID-19 variant types were associated with higher all-cause mortality when compared to the initial COVID-19 variant. Old age (aOR, 1.05; 95% CI: 1.04−1.06; p < 0.001), the presence of respiratory disease (aOR, 1.58; 95% CI: 1.02−2.44; p = 0.04), ICU admission (aOR, 3.41; 95% CI: 2.16−5.39; p < 0.001), lower eGFR (aOR, 1.61; 95% CI: 1.17−2.23; p = 0.004), and ARDS (aOR, 5.75; 95% CI: 3.69−8.98; p < 0.001) were also associated with higher mortality while NIV requirements were associated with lower odds of dying (aOR, 0.65; 95% CI: 0.46−0.91; p = 0.012). (4) Conclusions: Alpha and Delta variants were associated with a longer hospital stay, need for intensive care, mechanical ventilation, and increased mortality. Old age, cardiac renal dysfunction were commonly associated with Omicron variants. Large-scale national studies to further assess the risk factors for mortality related to COVID-19 waves are warranted.
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Affiliation(s)
- Faryal Khamis
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | | | - Muna Ba’Omar
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Wessam Osman
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Shabnam Chhetri
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Zaiyana Ambusaid
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Zakariya Al Fahdi
- Department of Medicine, Nizwa Hospital, Ministry of Health, Nizwa, PC 611, Oman
| | - Jaber Al Lawati
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Khalsa Al Sulaimi
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | | | - Maher Al Bahrani
- Department of Anaesthesia, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Ibrahim Al-Zakwani
- Department of Pharmacology & Clinical Pharmacy, College of Medicine & Health Sciences, Sultan Qaboos University, Al Khoudh, PC 123, Oman
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2
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Lueking R, Clark AE, Narasimhan M, Mahimainathan L, Muthukumar A, Larsen CP, SoRelle JA. SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis. Front Genet 2022; 13:942713. [PMID: 36226173 PMCID: PMC9549124 DOI: 10.3389/fgene.2022.942713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Immunocompromised patients can experience prolonged SARS-CoV-2 infections in the setting of a lack of protectivity immunity despite vaccination. As circulating SARS-CoV-2 strains become more heterogeneous, concomitant infection with multiple SARS-CoV-2 variants has become an increasing concern. Immunocompromised patient populations represent potential reservoirs for the emergence of novel SARS-CoV-2 variants through mutagenic change or coinfection followed by recombinatory events. Identification of SARS-CoV-2 coinfections is challenging using traditional next generation sequencing pipelines; however, targeted genotyping approaches can facilitate detection. Here we describe five COVID-19 cases caused by coinfection with different SARS-CoV-2 variants (Delta/Omicron BA.1 and Omicron BA.1/BA.2) as identified by multiplex fragment analysis.
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Affiliation(s)
- Richard Lueking
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Andrew E. Clark
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Madhusudhanan Narasimhan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Lenin Mahimainathan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Alagarraju Muthukumar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Christian P. Larsen
- Department of Internal Medicine, Division of Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jeffrey A. SoRelle
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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3
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Differentiation of SARS-CoV-2 Variants Using RT-qPCRs by Targeting Recurrent Mutation Sites: A Diagnostic Laboratory Experience from Multi-Center Regional Study, August 2020-December 2021, Poland. Int J Mol Sci 2022; 23:ijms23169416. [PMID: 36012683 PMCID: PMC9409138 DOI: 10.3390/ijms23169416] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 12/19/2022] Open
Abstract
Rapid identification of SARS-CoV-2 variants is essential for epidemiological surveillance. RT-qPCR-based variant differentiation tests can be used to quickly screen large sets of samples for relevant variants of concern/interest; this study was conducted on specimens collected at 11 centers located in Poland during routine SARS-CoV-2 diagnostics between August 2020 and December 2021. A total of 1096 samples (with CT < 30) were screened for Alpha, Beta, Delta, Kappa and Omicron variants using commercial assays targeting repeat mutation sites. Variants were assigned to 434 (39.6%) specimens; the remaining 662 (60.4%) samples were not classified (no tested mutations detected). Alpha (n = 289; 66.59%), Delta (n = 115; 26.5%), Kappa (n = 30; 6.91%) and Omicron (n = 2; 0.46%) variants were identified and their distribution changed over time. The first Alpha variant appeared in October 2020, and it began to gradually increase its proportion of the virus population by June 2021. In July 2021, it was replaced by the Delta variant, which already dominated by the end of the year. The first Kappa was detected in October 2021, while Omicron was found in December 2021. The screening of samples allowed the determination of epidemiological trends over a time interval reflecting the national COVID-19 waves.
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Bellamkonda N, Lambe UP, Sawant S, Nandi SS, Chakraborty C, Shukla D. Immune Response to SARS-CoV-2 Vaccines. Biomedicines 2022; 10:1464. [PMID: 35884770 PMCID: PMC9312515 DOI: 10.3390/biomedicines10071464] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
COVID-19 vaccines have been developed to confer immunity against the SARS-CoV-2 infection. Prior to the pandemic of COVID-19 which started in March 2020, there was a well-established understanding about the structure and pathogenesis of previously known Coronaviruses from the SARS and MERS outbreaks. In addition to this, vaccines for various Coronaviruses were available for veterinary use. This knowledge supported the creation of various vaccine platforms for SARS-CoV-2. Before COVID-19 there are no reports of a vaccine being developed in under a year and no vaccine for preventing coronavirus infection in humans had ever been developed. Approximately nine different technologies are being researched and developed at various levels in order to design an effective COVID-19 vaccine. As the spike protein of SARS-CoV-2 is responsible for generating substantial adaptive immune response, mostly all the vaccine candidates have been targeting the whole spike protein or epitopes of spike protein as a vaccine candidate. In this review, we have compiled the immune response to SARS-CoV-2 infection and followed by the mechanism of action of various vaccine platforms such as mRNA vaccines, Adenoviral vectored vaccine, inactivated virus vaccines and subunit vaccines in the market. In the end we have also summarized the various adjuvants used in the COVID-19 vaccine formulation.
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Affiliation(s)
- Navya Bellamkonda
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | | | - Sonali Sawant
- ICMR-NIV, Mumbai Unit, A. D. Road, Parel, Mumbai 400012, India; (U.P.L.); (S.S.)
| | - Shyam Sundar Nandi
- ICMR-NIV, Mumbai Unit, A. D. Road, Parel, Mumbai 400012, India; (U.P.L.); (S.S.)
| | | | - Deepak Shukla
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
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Abstract
Most of SARS-CoV-2 neutralizing antibodies (nAbs) targeted the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, mutations at RBD sequences found in the emerging SARS-CoV-2 variants greatly reduced the effectiveness of nAbs. Here we showed that four nAbs, S2-4D, S2-5D, S2-8D, and S2-4A, which recognized a conserved epitope in the S2 subunit of the S protein, can inhibit SARS-CoV-2 infection through blocking the S protein-mediated membrane fusion. Notably, these four nAbs exhibited broadly neutralizing activity against SARS-CoV-2 Alpha, Gamma, Delta, and Epsilon variants. Antisera collected from mice immunized with the identified epitope peptides of these four nAbs also exhibited potent virus neutralizing activity. Discovery of the S2-specific nAbs and their unique antigenic epitopes paves a new path for development of COVID-19 therapeutics and vaccines. IMPORTANCE The spike (S) protein on the surface of SARS-CoV-2 mediates receptor binding and virus-host cell membrane fusion during virus entry. Many neutralizing antibodies (nAbs), which targeted the receptor binding domain (RBD) of S protein, lost the neutralizing activity against the newly emerging SARS-CoV-2 variants with sequence mutations at the RBD. In contrast, the nAb against the highly conserved S2 subunit, which plays the key role in virus–host cell membrane fusion, was poorly discovered. We showed that four S2-specific nAbs, S2-4D, S2-5D, S2-8D, and S2-4A, inhibited SARS-CoV-2 infection through blocking the S protein-mediated membrane fusion. These nAbs exhibited broadly neutralizing activity against Alpha, Gamma, Delta, and Epsilon variants. Antisera induced by the identified epitope peptides also possessed potent neutralizing activity. This work not only unveiled the S2-specific nAbs but also discovered an immunodominant epitope in the S2 subunit that can be rationally designed as the broad-spectrum vaccine against the SARS-like coronaviruses.
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Lai GC, Chao TL, Lin SY, Kao HC, Tsai YM, Lu DC, Chiang YW, Chang SY, Chang SC. Neutralization or enhancement of SARS-CoV-2 infection by a monoclonal antibody targeting a specific epitope in the spike receptor-binding domain. Antiviral Res 2022; 200:105290. [PMID: 35296418 PMCID: PMC8918075 DOI: 10.1016/j.antiviral.2022.105290] [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: 12/09/2021] [Revised: 02/19/2022] [Accepted: 03/12/2022] [Indexed: 12/03/2022]
Abstract
Neutralizing antibodies (NAbs) are believed to be promising prophylactic and therapeutic treatment against the coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we reported two mouse monoclonal antibodies 7 Eb-4G and 1Ba–3H that specifically recognized the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein without exhibiting cross-reactivity with the S proteins of SARS-CoV and MERS-CoV. The binding epitopes of 7 Eb-4G and 1Ba–3H were respectively located in the regions of residues 457–476 and 477–496 in the S protein. Only 1Ba–3H exhibited the neutralizing activity for preventing the pseudotyped lentivirus from binding to the angiotensin-converting enzyme 2 (ACE2)-transfected HEK293T cells. The competitive ELISA further showed that 1Ba–3H interfered with the binding between RBD and ACE2. Epitope mapping experiments demonstrated that a single alanine replacement at residues 480, 482, 484, 485, and 488–491 in the RBD abrogated 1Ba–3H binding. 1Ba–3H exhibited the neutralizing activity against the wild-type, Alpha, Delta, and Epsilon variants of SARS-CoV-2, but lost the neutralizing activity against Gamma variant in the plaque reduction assay. On the contrary, 1Ba–3H enhanced the cellular infection of Gamma variant in a dose-dependent manner. Our findings suggest that the antibody-dependent enhancement of infection mediated by the RBD-specific antibody for different SARS-CoV-2 variants must be considered while developing the NAb.
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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8
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Lubinski B, Fernandes MH, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience 2022; 25:103589. [PMID: 34909610 PMCID: PMC8662955 DOI: 10.1016/j.isci.2021.103589] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern first identified in the United Kingdom in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7, or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that, although the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage, this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Maureen H.V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
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9
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de Souza GAP, Le Bideau M, Boschi C, Ferreira L, Wurtz N, Devaux C, Colson P, La Scola B. Emerging SARS-CoV-2 Genotypes Show Different Replication Patterns in Human Pulmonary and Intestinal Epithelial Cells. Viruses 2021; 14:v14010023. [PMID: 35062227 PMCID: PMC8777977 DOI: 10.3390/v14010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) quickly spread worldwide following its emergence in Wuhan, China, and hit pandemic levels. Its tremendous incidence favoured the emergence of viral variants. The current genome diversity of SARS-CoV-2 has a clear impact on epidemiology and clinical practice, especially regarding transmission rates and the effectiveness of vaccines. In this study, we evaluated the replication of different SARS-CoV-2 isolates representing different virus genotypes which have been isolated throughout the pandemic. We used three distinct cell lines, including Vero E6 cells originating from monkeys; Caco-2 cells, an intestinal epithelium cell line originating from humans; and Calu-3 cells, a pulmonary epithelium cell line also originating from humans. We used RT-qPCR to replicate different SARS-CoV-2 genotypes by quantifying the virus released in the culture supernatant of infected cells. We found that the different viral isolates replicate similarly in Caco-2 cells, but show very different replicative capacities in Calu-3 cells. This was especially highlighted for the lineages B.1.1.7, B.1.351 and P.1, which are considered to be variants of concern. These results underscore the importance of the evaluation and characterisation of each SARS-CoV-2 isolate in order to establish the replication patterns before performing tests, and of the consideration of the ideal SARS-CoV-2 genotype-cell type pair for each assay.
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Affiliation(s)
- Gabriel Augusto Pires de Souza
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marion Le Bideau
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Celine Boschi
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Lorène Ferreira
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Nathalie Wurtz
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Christian Devaux
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Unité de Recherche Microbe Phylogeny and Evoluition (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique—Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille, France; (G.A.P.d.S.); (M.L.B.); (C.B.); (L.F.); (N.W.); (C.D.); (P.C.)
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: ; Tel.: +33-0413-732-401
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10
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Lou F, Li M, Pang Z, Jiang L, Guan L, Tian L, Hu J, Fan J, Fan H. Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape. Front Immunol 2021; 12:744242. [PMID: 34804024 PMCID: PMC8602852 DOI: 10.3389/fimmu.2021.744242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
The global pandemic of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), places a heavy burden on global public health. Four SARS-CoV-2 variants of concern including B.1.1.7, B.1.351, B.1.617.2, and P.1, and two variants of interest including C.37 and B.1.621 have been reported to have potential immune escape, and one or more mutations endow them with worrisome epidemiologic, immunologic, or pathogenic characteristics. This review introduces the latest research progress on SARS-CoV-2 variants of interest and concern, key mutation sites, and their effects on virus infectivity, mortality, and immune escape. Moreover, we compared the effects of various clinical SARS-CoV-2 vaccines and convalescent sera on epidemic variants, and evaluated the neutralizing capability of several antibodies on epidemic variants. In the end, SARS-CoV-2 evolution strategies in different transmission stages, the impact of different vaccination strategies on SARS-CoV-2 immune escape, antibody therapy strategies and COVID-19 epidemic control prospects are discussed. This review will provide a systematic and comprehensive understanding of the secret of SARS-CoV-2 variants of interest/concern and immune escape.
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Affiliation(s)
- Fuxing Lou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Jiang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Guan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiaming Hu
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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11
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Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.06.438731. [PMID: 33851153 PMCID: PMC8043443 DOI: 10.1101/2021.04.06.438731] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern (VOC) first identified in the UK in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7 or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that while the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen H. V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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12
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Alleva DG, Delpero AR, Scully MM, Murikipudi S, Ragupathy R, Greaves EK, Sathiyaseelan T, Haworth JR, Shah NJ, Rao V, Nagre S, Lancaster TM, Webb SS, Jasa AI, Ronca SE, Green FM, Elyard HA, Yee J, Klein J, Karnes L, Sollie F, Zion TC. Development of an IgG-Fc fusion COVID-19 subunit vaccine, AKS-452. Vaccine 2021; 39:6601-6613. [PMID: 34642088 PMCID: PMC8491978 DOI: 10.1016/j.vaccine.2021.09.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022]
Abstract
AKS-452 is a biologically-engineered vaccine comprising an Fc fusion protein of the SARS-CoV-2 viral spike protein receptor binding domain antigen (Ag) and human IgG1 Fc (SP/RBD-Fc) in clinical development for the induction and augmentation of neutralizing IgG titers against SARS-CoV-2 viral infection to address the COVID-19 pandemic. The Fc moiety is designed to enhance immunogenicity by increasing uptake via Fc-receptors (FcγR) on Ag-presenting cells (APCs) and prolonging exposure due to neonatal Fc receptor (FcRn) recycling. AKS-452 induced approximately 20-fold greater neutralizing IgG titers in mice relative to those induced by SP/RBD without the Fc moiety and induced comparable long-term neutralizing titers with a single dose vs. two doses. To further enhance immunogenicity, AKS-452 was evaluated in formulations containing a panel of adjuvants in which the water-in-oil adjuvant, Montanide™ ISA 720, enhanced neutralizing IgG titers by approximately 7-fold after one and two doses in mice, including the neutralization of live SARS-CoV-2 virus infection of VERO-E6 cells. Furthermore, ISA 720-adjuvanted AKS-452 was immunogenic in rabbits and non-human primates (NHPs) and protected from infection and clinical symptoms with live SARS-CoV-2 virus in NHPs (USA-WA1/2020 viral strain) and the K18 human ACE2-trangenic (K18-huACE2-Tg) mouse (South African B.1.351 viral variant). These preclinical studies support the initiation of Phase I clinical studies with adjuvanted AKS-452 with the expectation that this room-temperature stable, Fc-fusion subunit vaccine can be rapidly and inexpensively manufactured to provide billions of doses per year especially in regions where the cold-chain is difficult to maintain.
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Affiliation(s)
- David G Alleva
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Andrea R Delpero
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Melanie M Scully
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Sylaja Murikipudi
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Ramya Ragupathy
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Emma K Greaves
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | | | - Jeffrey R Haworth
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Nishit J Shah
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Vidhya Rao
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Shashikant Nagre
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Thomas M Lancaster
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States
| | - Sarah S Webb
- Biomere Biomedical Research Models, 57 Union St., Worcester, MA 01608, United States
| | - Allison I Jasa
- Biomere Biomedical Research Models, 57 Union St., Worcester, MA 01608, United States
| | - Shannon E Ronca
- Feigin ABSL-3 Facility, Baylor, College of Medicine, 1102 Bates Ave, 300.15, Houston, TX 77030, United States
| | - Freedom M Green
- Feigin ABSL-3 Facility, Baylor, College of Medicine, 1102 Bates Ave, 300.15, Houston, TX 77030, United States
| | - Hanne Andersen Elyard
- BIOQUAL, Inc., 9600 Medical Center Drive, Suite 101, Rockville, MD 20850-3336, United States
| | - JoAnn Yee
- Primate Assay Laboratory, CA National Primate Research Center, University of California, Davis, CA 95616, United States
| | - Jeffrey Klein
- Sinclair Research Center, 562 State Road DD, Auxvasse, MO 65231, United States
| | - Larry Karnes
- Sinclair Research Center, 562 State Road DD, Auxvasse, MO 65231, United States
| | - Frans Sollie
- Pharmaceutical Research Associates Group B.V., Amerikaweg 18, 9407 TK Assen, Netherlands
| | - Todd C Zion
- Akston Biosciences Corporation., 100 Cummings Center, Suite 454C, Beverly, MA 01915, United States.
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13
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Chaintoutis SC, Chassalevris T, Tsiolas G, Balaska S, Vlatakis I, Mouchtaropoulou E, Siarkou VI, Tychala A, Koutsioulis D, Skoura L, Argiriou A, Dovas CI. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. J Virol Methods 2021; 296:114242. [PMID: 34274369 PMCID: PMC8282437 DOI: 10.1016/j.jviromet.2021.114242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
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Affiliation(s)
- Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece
| | - Victoria I Siarkou
- Laboratory of Microbiology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54134, Thessaloniki, Greece
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 Nikolaou Plastira str., Vassilika Vouton, 70013, Heraklion, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, 1 Stilponos Kyriakidi str., 54636, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloniki, Greece; Department of Food Science and Nutrition, University of the Aegean, 81400, Myrina, Lemnos, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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14
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Chaintoutis SC, Chassalevris T, Balaska S, Mouchtaropoulou E, Tsiolas G, Vlatakis I, Tychala A, Koutsioulis D, Argiriou A, Skoura L, Dovas CI. A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain. Life (Basel) 2021; 11:life11101015. [PMID: 34685386 PMCID: PMC8540511 DOI: 10.3390/life11101015] [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: 08/18/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination of other variants is thus of importance for public health interventions. For this reason, a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed, to target signature mutations associated with amino-acid substitutions at positions 478, 484 and 501 present in the receptor-binding motif (RBM) of the spike protein RBD. This region contains most contacting residues of SARS-CoV-2 that bind to ACE2. A novel strategy employing the use of non-extendable LNA oligonucleotide blockers that can reduce non-specific hybridization of probes increased the number of different mutated sites examined in a multiplex PCR. The combinatory analysis of the different fluorescence signals obtained enabled the preliminary differentiation of SARS-CoV-2 variants of concern. The assay is sensitive with a LOD of 263 copies/reaction for the Delta variant, 170 copies/reaction for the Beta variant, amplification efficiencies > 91% and a linear range of >5 log10 copies/reaction against all targets. Validation of the assay using known SARS-CoV-2-positive and negative samples from humans and animals revealed its ability to correctly identify the targeted mutations and preliminary characterize the SARS-CoV-2 variants. The novel approach for mutation typing using LNA oligonucleotide blockers can be modified to target signature mutations at four different sites in the RBM and further expand the range of variants detected.
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Affiliation(s)
- Serafeim C. Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
| | - Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
| | - Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
| | - George Tsiolas
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
| | - Ioannis Vlatakis
- EnzyQuest PC, Science and Technology Park of Crete, 100 N. Plastira Str., Vassilika Vouton, 70013 Heraklion, Greece; (I.V.); (D.K.)
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Dimitris Koutsioulis
- EnzyQuest PC, Science and Technology Park of Crete, 100 N. Plastira Str., Vassilika Vouton, 70013 Heraklion, Greece; (I.V.); (D.K.)
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece; (E.M.); (G.T.); (A.A.)
- Department of Food Science and Nutrition, University of the Aegean, 81400 Myrina, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Faculty of Health Sciences, Aristotle University of Thessaloniki, S. Kyriakidi Str., 54636 Thessaloniki, Greece; (S.B.); (A.T.); (L.S.)
| | - Chrysostomos I. Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 S. Voutyra Str., 54627 Thessaloniki, Greece; (S.C.C.); (T.C.)
- Correspondence: ; Tel.: +30-23-1099-9870
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15
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Li F, He P, Xiong D, Lou Y, Pu Q, Zhang H, Zhang H, Yu J. A Reverse Transcription Recombinase-Aided Amplification Method for Rapid and Point-of-Care Detection of SARS-CoV-2, including Variants. Viruses 2021; 13:1875. [PMID: 34578456 PMCID: PMC8472806 DOI: 10.3390/v13091875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/23/2022] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its emergence of variants needs rapid and point-of-care testing methods for a broad diagnosis. The regular RT-qPCR is time-consuming and limited in central laboratories, so a broad and large-scale screening requirement calls for rapid and in situ methods. In this regard, a reverse transcription recombinase-aided amplification (RT-RAA) is proposed here for the rapid and point-of-care detection of SARS-CoV-2. A set of highly conserved primers and probes targeting more than 98% of SARS-CoV-2 strains, including currently circulating variants (four variants of concerns (VOCs) and three variants of interest (VOIs)), was used in this study. With the preferred primers, the RT-RAA assay showed a 100% specificity to SARS-CoV-2 from eight other respiratory RNA viruses. Moreover, the assay here is of a high sensitivity and 0.48 copies/μL can be detected within 25 min at a constant temperature (42 °C), which can be realized on portable equipment. Furthermore, the RT-RAA assay demonstrated its high agreement for the detection of SARS-CoV-2 in clinical specimens compared with RT-qPCR. The rapid, simple and point-of-care RT-RAA method is expected to be an appealing detection tool to detect SARS-CoV-2, including variants, in clinical diagnostic applications.
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Affiliation(s)
- Fengyun Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yakun Lou
- Zhengzhou Zhongdao Biotechnology Co., Ltd., Zhengzhou 450000, China;
| | - Qiaosheng Pu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Haixia Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Giraldo-Ramirez S, Rendon-Marin S, Jaimes JA, Martinez-Gutierrez M, Ruiz-Saenz J. SARS-CoV-2 Clinical Outcome in Domestic and Wild Cats: A Systematic Review. Animals (Basel) 2021; 11:2056. [PMID: 34359182 PMCID: PMC8300124 DOI: 10.3390/ani11072056] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Recently, it has been proved that SARS-CoV-2 has the ability to infect multiple species. This work was aimed at identifying the clinical signs of SARS-CoV-2 infection in domestic and wild felids. A PRISMA-based systematic review was performed on case reports on domestic and wild cats, reports on experimental infections, case reports in databases, preprints and published press releases. Descriptive statistical analysis of the data was performed. A total of 256 articles, 63 detailed official reports and 2 press articles on SARS-CoV-2 infection in domestic and wild cats were analyzed, of which 19 articles and 65 reports were finally included. In domestic cats, most cats' infections are likely to be asymptomatic, and 46% of the reported infected animals were symptomatic and predominantly presented respiratory signs such as sneezing and coughing. In wild felines, respiratory clinical signs were most frequent, and up to 96.5% of the reported affected animals presented coughing. It is noteworthy that, to date, symptomatic animals with SARS-CoV-2 infection have been reported to belong to two different subfamilies (Phanterinae and Felinae), with up to five different felid species affected within the Felidae family. Reported results evince that the signs developed in felids show similar progression to those occurring in humans, suggesting a relationship between the viral cycle and target tissues of the virus in different species. While viral transmission to humans in contact with animal populations has not been reported, spill-back could result in the emergence of immune-escape mutants that might pose a risk to public health. Despite the clear results in the identification of the typical clinical picture of SARS-CoV-2 infection in felines, the number of detailed academic reports and papers on the subject is scarce. Therefore, further description of these cases will allow for more accurate and statistically robust clinical approaches in the future.
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Affiliation(s)
- Sebastian Giraldo-Ramirez
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia; (S.G.-R.); (S.R.-M.); (M.M.-G.)
| | - Santiago Rendon-Marin
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia; (S.G.-R.); (S.R.-M.); (M.M.-G.)
| | - Javier A. Jaimes
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA;
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia; (S.G.-R.); (S.R.-M.); (M.M.-G.)
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050012, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales—GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia; (S.G.-R.); (S.R.-M.); (M.M.-G.)
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17
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Serwin K, Ossowski A, Szargut M, Cytacka S, Urbańska A, Majchrzak A, Niedźwiedź A, Czerska E, Pawińska-Matecka A, Gołąb J, Parczewski M. Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Viruses 2021; 13:1295. [PMID: 34372500 PMCID: PMC8310356 DOI: 10.3390/v13071295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth-death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.
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Affiliation(s)
- Karol Serwin
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, 71-455 Szczecin, Poland; (K.S.); (A.U.)
| | - Andrzej Ossowski
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (A.O.); (M.S.); (S.C.)
| | - Maria Szargut
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (A.O.); (M.S.); (S.C.)
| | - Sandra Cytacka
- Department of Forensic Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland; (A.O.); (M.S.); (S.C.)
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, 71-455 Szczecin, Poland; (K.S.); (A.U.)
| | - Adam Majchrzak
- Independent Public Regional Hospital in Szczecin, 71-455 Szczecin, Poland; (A.M.); (A.N.); (E.C.); (A.P.-M.); (J.G.)
| | - Anna Niedźwiedź
- Independent Public Regional Hospital in Szczecin, 71-455 Szczecin, Poland; (A.M.); (A.N.); (E.C.); (A.P.-M.); (J.G.)
| | - Ewa Czerska
- Independent Public Regional Hospital in Szczecin, 71-455 Szczecin, Poland; (A.M.); (A.N.); (E.C.); (A.P.-M.); (J.G.)
| | - Anna Pawińska-Matecka
- Independent Public Regional Hospital in Szczecin, 71-455 Szczecin, Poland; (A.M.); (A.N.); (E.C.); (A.P.-M.); (J.G.)
| | - Joanna Gołąb
- Independent Public Regional Hospital in Szczecin, 71-455 Szczecin, Poland; (A.M.); (A.N.); (E.C.); (A.P.-M.); (J.G.)
| | - Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, 71-455 Szczecin, Poland; (K.S.); (A.U.)
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