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Lista MJ, Winstone H, Wilson HD, Dyer A, Pickering S, Galao RP, De Lorenzo G, Cowton VM, Furnon W, Suarez N, Orton R, Palmarini M, Patel AH, Snell L, Nebbia G, Swanson C, Neil SJD. The P681H Mutation in the Spike Glycoprotein of the Alpha Variant of SARS-CoV-2 Escapes IFITM Restriction and Is Necessary for Type I Interferon Resistance. J Virol 2022; 96:e0125022. [PMID: 36350154 PMCID: PMC9749455 DOI: 10.1128/jvi.01250-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
The appearance of new dominant variants of concern (VOC) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the coronavirus disease 2019 (COVID-19) pandemic. Of these, the alpha variant (also known as B.1.1.7), which appeared initially in the United Kingdom, became the dominant variant in much of Europe and North America in the first half of 2021. The spike (S) glycoprotein of alpha acquired seven mutations and two deletions compared to the ancestral virus, including the P681H mutation adjacent to the polybasic cleavage site, which has been suggested to enhance S cleavage. Here, we show that the alpha spike protein confers a level of resistance to beta interferon (IFN-β) in human lung epithelial cells. This correlates with resistance to an entry restriction mediated by interferon-induced transmembrane protein 2 (IFITM2) and a pronounced infection enhancement by IFITM3. Furthermore, the P681H mutation is essential for resistance to IFN-β and context-dependent resistance to IFITMs in the alpha S. P681H reduces dependence on endosomal cathepsins, consistent with enhanced cell surface entry. However, reversion of H681 does not reduce cleaved spike incorporation into particles, indicating that it exerts its effect on entry and IFN-β downstream of furin cleavage. Overall, we suggest that, in addition to adaptive immune escape, mutations associated with VOC may well also confer a replication and/or transmission advantage through adaptation to resist innate immune mechanisms. IMPORTANCE Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission. Here, we show that the alpha (B.1.1.7) VOC of SARS-CoV-2 is substantially more resistant to type I interferons than the parental Wuhan-like virus. This correlates with resistance to the antiviral protein IFITM2 and enhancement by its paralogue IFITM3. The key determinant of this is a proline-to-histidine change at position 681 in S adjacent to the furin cleavage site, which in the context of the alpha spike modulates cell entry pathways of SARS-CoV-2. Reversion of the mutation is sufficient to restore interferon and IFITM2 sensitivity, highlighting the dynamic nature of the SARS CoV-2 as it adapts to both innate and adaptive immunity in the humans.
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Affiliation(s)
- Maria Jose Lista
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Helena Winstone
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Harry D. Wilson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Adam Dyer
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Suzanne Pickering
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Rui Pedro Galao
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa M. Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
| | - Luke Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Chad Swanson
- Department of Infectious Diseases, King’s College London, London, United Kingdom
| | - Stuart J. D. Neil
- Department of Infectious Diseases, King’s College London, London, United Kingdom
- UKRI Genotype-2-Phenotype Consortium, London, United Kingdom
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2
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Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far. Vaccines (Basel) 2022; 10:1926. [PMID: 36423021 PMCID: PMC9698608 DOI: 10.3390/vaccines10111926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Kangkan Deka
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Tutumoni Kalita
- Girijananda Chowdhury Institute of Pharmaceutical Science, Azara, Guwahati 781017, Assam, India
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3
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Tandel D, Sah V, Singh NK, Potharaju PS, Gupta D, Shrivastava S, Sowpati DT, Harshan KH. SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses in Human Colon Epithelial Cells. Microbiol Spectr 2022; 10:e0160422. [PMID: 36073824 PMCID: PMC9602719 DOI: 10.1128/spectrum.01604-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/17/2022] [Indexed: 12/31/2022] Open
Abstract
The Delta variant of SARS-CoV-2 has caused more severe infections than its previous variants. We studied the host innate immune response to Delta, Alpha, and two earlier variants to map the evolution of the recent ones. Our biochemical and transcriptomic studies in human colon epithelial cell line Caco2 reveal that Alpha and Delta have progressively evolved over the ancestral variants by silencing the innate immune response, thereby limiting cytokine and chemokine production. Though Alpha silenced the retinoic acid-inducible gene (RIG)-I-like receptor (RLR) pathway just like Delta did, it failed to persistently silence the innate immune response, unlike Delta. Both Alpha and Delta have evolved to resist interferon (IFN) treatment, while they are still susceptible to RLR activation, further highlighting the importance of RLR-mediated, IFN-independent mechanisms in restricting SARS-CoV-2. Our studies reveal that SARS-CoV-2 Delta has integrated multiple mechanisms to silence the host innate immune response and evade the IFN response. We speculate that Delta's silent replication and sustained suppression of the host innate immune response, thereby resulting in delayed or reduced intervention by the adaptive immune response, could have potentially contributed to the severe symptoms and poor recovery index associated with it. It is likely that this altered association with the host would play an important role in the coevolution of SARS-CoV-2 with humans. IMPORTANCE Viruses generally learn to coexist with the host during the process of evolution. It is expected that SARS-CoV-2 would also evolve to coexist in humans by trading off its virulence for longer persistence, causing milder disease. Clinically, the fatality associated with COVID-19 has been declining due to vaccination and preinfections, but the Delta variant caused the most severe disease and fatality across several parts of the world. Our study identified an evolving trend of SARS-CoV-2 variants where the variants that emerged during early parts of the pandemic caused a more robust innate immune response, while the later emerging variant Delta showed features of suppression of the response. The features that Delta has acquired could have strongly influenced the distinct pathophysiology associated with its infection. How these changed associations with the host influence the long-term evolution of the virus and the disease outcome should be closely studied to understand the process of viral evolution.
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Affiliation(s)
- Dixit Tandel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy for Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vishal Sah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy for Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nitesh Kumar Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Poojitha Sai Potharaju
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy for Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Divya Gupta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | | | - Divya Tej Sowpati
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy for Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Krishnan H. Harshan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy for Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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4
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Cantoni D, Murray MJ, Kalemera MD, Dicken SJ, Stejskal L, Brown G, Lytras S, Coey JD, McKenna J, Bridgett S, Simpson D, Fairley D, Thorne LG, Reuschl A, Forrest C, Ganeshalingham M, Muir L, Palor M, Jarvis L, Willett B, Power UF, McCoy LE, Jolly C, Towers GJ, Doores KJ, Robertson DL, Shepherd AJ, Reeves MB, Bamford CGG, Grove J. Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Rep 2022; 23:e54322. [PMID: 35999696 PMCID: PMC9535765 DOI: 10.15252/embr.202154322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
The emergence of SARS-CoV-2 variants has exacerbated the COVID-19 global health crisis. Thus far, all variants carry mutations in the spike glycoprotein, which is a critical determinant of viral transmission being responsible for attachment, receptor engagement and membrane fusion, and an important target of immunity. Variants frequently bear truncations of flexible loops in the N-terminal domain (NTD) of spike; the functional importance of these modifications has remained poorly characterised. We demonstrate that NTD deletions are important for efficient entry by the Alpha and Omicron variants and that this correlates with spike stability. Phylogenetic analysis reveals extensive NTD loop length polymorphisms across the sarbecoviruses, setting an evolutionary precedent for loop remodelling. Guided by these analyses, we demonstrate that variations in NTD loop length, alone, are sufficient to modulate virus entry. We propose that variations in NTD loop length act to fine-tune spike; this may provide a mechanism for SARS-CoV-2 to navigate a complex selection landscape encompassing optimisation of essential functionality, immune-driven antigenic variation and ongoing adaptation to a new host.
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Affiliation(s)
- Diego Cantoni
- MRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
| | - Matthew J Murray
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | | | - Samuel J Dicken
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Lenka Stejskal
- Division of Evolution, Infection and GenomicsUniversity of ManchesterManchesterUK
| | - Georgina Brown
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Spyros Lytras
- MRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
| | - Jonathon D Coey
- Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | | | | | - David Simpson
- Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | | | - Lucy G Thorne
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | | | - Calum Forrest
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | | | - Luke Muir
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Machaela Palor
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Lisa Jarvis
- Scottish National Blood Transfusion ServiceGlasgowUK
| | - Brian Willett
- MRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
| | - Ultan F Power
- Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Laura E McCoy
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Clare Jolly
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Greg J Towers
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Katie J Doores
- Department of Infectious DiseasesKing's College LondonLondonUK
| | - David L Robertson
- MRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
| | | | - Matthew B Reeves
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Connor G G Bamford
- Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Joe Grove
- MRC‐University of Glasgow Centre for Virus ResearchUniversity of GlasgowGlasgowUK
- Division of Infection and ImmunityUniversity College LondonLondonUK
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5
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Gao X, Tian H, Zhu K, Li Q, Hao W, Wang L, Qin B, Deng H, Cui S. Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport. Nat Commun 2022; 13:4782. [PMID: 35970938 PMCID: PMC9376891 DOI: 10.1038/s41467-022-32489-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
The emergence of heavily mutated SARS-CoV-2 variants of concern (VOCs) place the international community on high alert. In addition to numerous mutations that map in the spike protein of VOCs, expression of the viral accessory proteins ORF6 and ORF9b also elevate; both are potent interferon antagonists. Here, we present the crystal structures of Rae1-Nup98 in complex with the C-terminal tails (CTT) of SARS-CoV-2 and SARS-CoV ORF6 to 2.85 Å and 2.39 Å resolution, respectively. An invariant methionine (M) 58 residue of ORF6 CTT extends its side chain into a hydrophobic cavity in the Rae1 mRNA binding groove, resembling a bolt-fitting-hole; acidic residues flanking M58 form salt-bridges with Rae1. Our mutagenesis studies identify key residues of ORF6 important for its interaction with Rae1-Nup98 in vitro and in cells, of which M58 is irreplaceable. Furthermore, we show that ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport correlate with the binding affinity between ORF6 and Rae1-Nup98. Finally, binding of ORF6 to Rae1-Nup98 is linked to ORF6-induced interferon antagonism. Taken together, this study reveals the molecular basis for the antagonistic function of Sarbecovirus ORF6, and implies a strategy of using ORF6 CTT-derived peptides for immunosuppressive drug development. Sarbecovirus ORF6 binds to the Rae1-Nup98 complex, a component of the cytoplasmic face of the nuclear pore complex, and has been shown to suppress interferon responses. Here, the authors provide structures of Rae1-Nup98 in complex with the C-terminal tails of SARS-CoV-2 and SARS-CoV ORF6 and provide insights into ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Qing Li
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Hao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China. .,Sanming Project of Medicine in Shenzhen, National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
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6
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Shivshankar P, Karmouty-Quintana H, Mills T, Doursout MF, Wang Y, Czopik AK, Evans SE, Eltzschig HK, Yuan X. SARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets. Inflammation 2022; 45:1430-1449. [PMID: 35320469 PMCID: PMC8940980 DOI: 10.1007/s10753-022-01656-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 02/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in a global pandemic with severe socioeconomic effects. Immunopathogenesis of COVID-19 leads to acute respiratory distress syndrome (ARDS) and organ failure. Binding of SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2 (hACE2) on bronchiolar and alveolar epithelial cells triggers host inflammatory pathways that lead to pathophysiological changes. Proinflammatory cytokines and type I interferon (IFN) signaling in alveolar epithelial cells counter barrier disruption, modulate host innate immune response to induce chemotaxis, and initiate the resolution of inflammation. Here, we discuss experimental models to study SARS-CoV-2 infection, molecular pathways involved in SARS-CoV-2-induced inflammation, and viral hijacking of anti-inflammatory pathways, such as delayed type-I IFN response. Mechanisms of alveolar adaptation to hypoxia, adenosinergic signaling, and regulatory microRNAs are discussed as potential therapeutic targets for COVID-19.
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Affiliation(s)
- Pooja Shivshankar
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Internal Medicine, Divisions of Critical Care, Pulmonary and Sleep Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Tingting Mills
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Marie-Francoise Doursout
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Yanyu Wang
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Agnieszka K Czopik
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Holger K Eltzschig
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA
| | - Xiaoyi Yuan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
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7
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Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, Jones B, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Hughes GL, Anderson ER, Patterson EI, Druce J, Screaton G, Carroll MW, Stewart JP, Hiscox JA. Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. mSphere 2022; 7:e0091321. [PMID: 35491827 PMCID: PMC9241508 DOI: 10.1128/msphere.00913-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/18/2022] [Indexed: 01/02/2023] Open
Abstract
New variants of SARS-CoV-2 are continuing to emerge and dominate the global sequence landscapes. Several variants have been labeled variants of concern (VOCs) because they may have a transmission advantage, increased risk of morbidity and/or mortality, or immune evasion upon a background of prior infection or vaccination. Placing the VOCs in context with the underlying variability of SARS-CoV-2 is essential in understanding virus evolution and selection pressures. Dominant genome sequences and the population genetics of SARS-CoV-2 in nasopharyngeal swabs from hospitalized patients were characterized. Nonsynonymous changes at a minor variant level were identified. These populations were generally preserved when isolates were amplified in cell culture. To place the Alpha, Beta, Delta, and Omicron VOCs in context, their growth was compared to clinical isolates of different lineages from earlier in the pandemic. The data indicated that the growth in cell culture of the Beta variant was more than that of the other variants in Vero E6 cells but not in hACE2-A549 cells. Looking at each time point, Beta grew more than the other VOCs in hACE2-A549 cells at 24 to 48 h postinfection. At 72 h postinfection there was no difference in the growth of any of the variants in either cell line. Overall, this work suggested that exploring the biology of SARS-CoV-2 is complicated by population dynamics and that these need to be considered with new variants. In the context of variation seen in other coronaviruses, the variants currently observed for SARS-CoV-2 are very similar in terms of their clinical spectrum of disease. IMPORTANCE SARS-CoV-2 is the causative agent of COVID-19. The virus has spread across the planet, causing a global pandemic. In common with other coronaviruses, SARS-CoV-2 genomes can become quite diverse as a consequence of replicating inside cells. This has given rise to multiple variants from the original virus that infected humans. These variants may have different properties and in the context of a widespread vaccination program may render vaccines less effective. Our research confirms the degree of genetic diversity of SARS-CoV-2 in patients. By comparing the growth of previous variants to the pattern seen with four variants of concern (VOCs) (Alpha, Beta, Delta, and Omicron), we show that, at least in cells, Beta variant growth exceeds that of Alpha, Delta, and Omicron VOCs at 24 to 48 h in both Vero E6 and hACE2-A549 cells, but by 72 h postinfection, the amount of virus is not different from that of the other VOCs.
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Affiliation(s)
- Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Benjamin Jones
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm G. Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Department of Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - J. Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Grant L. Hughes
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Enyia R. Anderson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edward I. Patterson
- Departments of Vector Biology and Tropical Disease Biology, Center for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julian Druce
- Virus Identification Laboratory, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Public Health England, Salisbury, United Kingdom
| | - James P. Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Infectious Disease, University of Georgia, Georgia, USA
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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8
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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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9
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Nchioua R, Schundner A, Kmiec D, Prelli Bozzo C, Zech F, Koepke L, Graf A, Krebs S, Blum H, Frick M, Sparrer KMJ, Kirchhoff F. SARS-CoV-2 Variants of Concern Hijack IFITM2 for Efficient Replication in Human Lung Cells. J Virol 2022; 96:e0059422. [PMID: 35543509 PMCID: PMC9175628 DOI: 10.1128/jvi.00594-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 12/17/2022] Open
Abstract
It has recently been shown that an early SARS-CoV-2 isolate (NL-02-2020) hijacks interferon-induced transmembrane proteins (IFITMs) for efficient replication in human lung cells, cardiomyocytes, and gut organoids. To date, several "variants of concern" (VOCs) showing increased infectivity and resistance to neutralization have emerged and globally replaced the early viral strains. Here, we determined whether the five current SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, and Omicron) maintained the dependency on IFITM proteins for efficient replication. We found that depletion of IFITM2 strongly reduces viral RNA production by all VOCs in the human epithelial lung cancer cell line Calu-3. Silencing of IFITM1 had modest effects, while knockdown of IFITM3 resulted in an intermediate phenotype. Strikingly, depletion of IFITM2 generally reduced infectious virus production by more than 4 orders of magnitude. In addition, an antibody directed against the N terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in induced pluripotent stem cell (iPSC)-derived alveolar epithelial type II cells, thought to represent major viral target cells in the lung. In conclusion, endogenously expressed IFITM proteins (especially IFITM2) are critical cofactors for efficient replication of genuine SARS-CoV-2 VOCs, including the currently dominant Omicron variant. IMPORTANCE Recent data indicate that SARS-CoV-2 requires endogenously expressed IFITM proteins for efficient infection. However, the results were obtained with an early SARS-CoV-2 isolate. Thus, it remained to be determined whether IFITMs are also important cofactors for infection of emerging SARS-CoV-2 VOCs that outcompeted the original strains in the meantime. This includes the Omicron VOC, which currently dominates the pandemic. Here, we show that depletion of endogenous IFITM2 expression almost entirely prevents productive infection of Alpha, Beta, Gamma, Delta, and Omicron SARS-CoV-2 VOCs in human lung cells. In addition, an antibody targeting the N terminus of IFITM2 inhibited SARS-CoV-2 VOC replication in iPSC-derived alveolar epithelial type II cells. Our results show that SARS-CoV-2 VOCs, including the currently dominant Omicron variant, are strongly dependent on IFITM2 for efficient replication, suggesting a key proviral role of IFITMs in viral transmission and pathogenicity.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Annika Schundner
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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10
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Lekana-Douki SE, N'dilimabaka N, Levasseur A, Colson P, Andeko JC, Zong Minko O, Banga Mve-Ella O, Fournier PE, Devaux C, Ondo BM, Akombi FL, Yacka Mouele Bolo L, Ngonga Dikongo AM, Diané A, Mabika Mabika A, Mathouet JF, Dzembo C, Atiga NC, Mouity Matoumba A, Ndjangangoye NK, Bréchard L, Bedotto-Buffet M, Mangombi Pambou JB, Kandet Yattara M, Mbongo Nkama EA, Mintsa Ndong A, Adegnika AA, Raoult D, Fenollar F, Lekana-Douki JB. Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon. Front Med (Lausanne) 2022; 9:877391. [PMID: 35655849 PMCID: PMC9152426 DOI: 10.3389/fmed.2022.877391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.
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Affiliation(s)
| | - Nadine N'dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Julia Cyrielle Andeko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Ornella Zong Minko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Octavie Banga Mve-Ella
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Christian Devaux
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | | | | | | | | | - Abdoulaye Diané
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Arsène Mabika Mabika
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Jenny Francine Mathouet
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Cresh Dzembo
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Nick Chenis Atiga
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Anicet Mouity Matoumba
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | | | | | | | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institute of Tropical Medecine, University of Tübingen and German Center for Infectious Research (DZIF), Tübingen, Germany
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jean-Bernard Lekana-Douki
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Sante, Libreville, Gabon
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11
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Thakur N, Gallo G, Newman J, Peacock TP, Biasetti L, Hall CN, Wright E, Barclay W, Bailey D. SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges. J Gen Virol 2022; 103. [PMID: 35377298 DOI: 10.1099/jgv.0.001735] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in PR China in late 2019 a number of variants have emerged, with two of these - alpha and delta - subsequently growing to global prevalence. One characteristic of these variants are changes within the spike protein, in particular the receptor-binding domain (RBD). From a public health perspective, these changes have important implications for increased transmissibility and immune escape; however, their presence could also modify the intrinsic host range of the virus. Using viral pseudotyping, we examined whether the variants of concern (VOCs) alpha, beta, gamma and delta have differing host angiotensin-converting enzyme 2 (ACE2) receptor usage patterns, focusing on a range of relevant mammalian ACE2 proteins. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes that we subsequently attributed to N501Y and E484K substitutions within the spike RBD.
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Affiliation(s)
- Nazia Thakur
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK.,Nuffield Department of Medicine, The Jenner Institute, Oxford, OX3 7DQ, UK
| | - Giulia Gallo
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Joseph Newman
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College - London, W2 1PG, UK
| | - Luca Biasetti
- School of Psychology and Neuroscience, University of Sussex, Falmer, BN1 9QH, UK
| | - Catherine N Hall
- School of Psychology and Neuroscience, University of Sussex, Falmer, BN1 9QH, UK
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Falmer, BN1 9QG, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College - London, W2 1PG, UK
| | - Dalan Bailey
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
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12
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Jung C, Kmiec D, Koepke L, Zech F, Jacob T, Sparrer KMJ, Kirchhoff F. Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? J Virol 2022; 96:e0207721. [PMID: 35225672 PMCID: PMC8941872 DOI: 10.1128/jvi.02077-21] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Emerging strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, that show increased transmission fitness and/or immune evasion are classified as "variants of concern" (VOCs). Recently, a SARS-CoV-2 variant first identified in November 2021 in South Africa has been recognized as a fifth VOC, termed "Omicron." What makes this VOC so alarming is the high number of changes, especially in the viral Spike protein, and accumulating evidence for increased transmission efficiency and escape from neutralizing antibodies. In an amazingly short time, the Omicron VOC has outcompeted the previously dominating Delta VOC. However, it seems that the Omicron VOC is overall less pathogenic than other SARS-CoV-2 VOCs. Here, we provide an overview of the mutations in the Omicron genome and the resulting changes in viral proteins compared to other SARS-CoV-2 strains and discuss their potential functional consequences.
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Affiliation(s)
- Christoph Jung
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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13
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Riou C, Keeton R, Moyo-Gwete T, Hermanus T, Kgagudi P, Baguma R, Valley-Omar Z, Smith M, Tegally H, Doolabh D, Iranzadeh A, Tyers L, Mutavhatsindi H, Tincho MB, Benede N, Marais G, Chinhoyi LR, Mennen M, Skelem S, du Bruyn E, Stek C, de Oliveira T, Williamson C, Moore PL, Wilkinson RJ, Ntusi NAB, Burgers WA. Escape from recognition of SARS-CoV-2 variant spike epitopes but overall preservation of T cell immunity. Sci Transl Med 2022; 14:eabj6824. [PMID: 34931886 PMCID: PMC9434381 DOI: 10.1126/scitranslmed.abj6824] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 variants that escape neutralization and potentially affect vaccine efficacy have emerged. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is incompletely understood. We assessed neutralizing antibody and T cell responses in 44 South African COVID-19 patients either infected with the Beta variant (dominant from November 2020 to May 2021) or infected before its emergence (first wave, Wuhan strain) to provide an overall measure of immune evasion. We show that robust spike-specific CD4 and CD8 T cell responses were detectable in Beta-infected patients, similar to first-wave patients. Using peptides spanning the Beta-mutated regions, we identified CD4 T cell responses targeting the wild-type peptides in 12 of 22 first-wave patients, all of whom failed to recognize corresponding Beta-mutated peptides. However, responses to mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3 of 44) mounted CD8 responses that targeted the mutated regions. Among the spike epitopes tested, we identified three epitopes containing the D215, L18, or D80 residues that were specifically recognized by CD4 T cells, and their mutated versions were associated with a loss of response. This study shows that despite loss of recognition of immunogenic CD4 epitopes, CD4 and CD8 T cell responses to Beta are preserved overall. These observations may explain why several vaccines have retained the ability to protect against severe COVID-19 even with substantial loss of neutralizing antibody activity against Beta.
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Affiliation(s)
- Catherine Riou
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Roanne Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa.,MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tandile Hermanus
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa.,MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa.,MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Mikhail Smith
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Lynn Tyers
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Hygon Mutavhatsindi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Marius B Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Ntombi Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Gert Marais
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa.,Groote Schuur Hospital Medical Virology Laboratory of the National Health Laboratory Service, Observatory 7925, South Africa
| | - Lionel R Chinhoyi
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Elsa du Bruyn
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa
| | - Cari Stek
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Department of Infectious Diseases, Imperial College London, London W12 0NN, UK
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Carolyn Williamson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa.,MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Department of Infectious Diseases, Imperial College London, London W12 0NN, UK.,The Francis Crick Institute, London NW1 1AT, UK
| | - Ntobeko A B Ntusi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory 7925, South Africa.,Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Wendy A Burgers
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory 7925, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa.,Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
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14
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Despres HW, Mills MG, Shirley DJ, Schmidt MM, Huang ML, Roychoudhury P, Jerome KR, Greninger AL, Bruce EA. Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants. Proc Natl Acad Sci U S A 2022; 119:e2116518119. [PMID: 35058348 PMCID: PMC8812544 DOI: 10.1073/pnas.2116518119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between levels of viral RNA and infectious virus for individual variants is unknown. We measured infectious viral titer (using a microfocus-forming assay) and total and subgenomic viral RNA levels (using RT-PCR) in a set of 162 clinical samples containing SARS-CoV-2 Alpha, Delta, and Epsilon variants that were collected in identical swab kits from outpatient test sites and processed soon after collection. We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite this, the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (5.9- and 3.0-fold increase; P < 0.0001, P = 0.014, respectively) or subgenomic E RNA (14.3- and 6.9-fold increase; P < 0.0001, P = 0.004, respectively). In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity for Delta may further explain increased spread, suggesting a need for increased measures to prevent viral transmission.
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Affiliation(s)
- Hannah W Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405
| | - Margaret G Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105
| | - David J Shirley
- Data Science Department, Faraday, Inc., Burlington, VT 05405
| | - Madaline M Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Keith R Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Alexander L Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Emily A Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405;
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15
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Mao T, Israelow B, Lucas C, Vogels CB, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice. J Exp Med 2022; 219:e20211818. [PMID: 34757384 PMCID: PMC8590200 DOI: 10.1084/jem.20211818] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
As SARS-CoV-2 continues to cause morbidity and mortality around the world, there is an urgent need for the development of effective medical countermeasures. Here, we assessed the antiviral capacity of a minimal RIG-I agonist, stem-loop RNA 14 (SLR14), in viral control, disease prevention, post-infection therapy, and cross-variant protection in mouse models of SARS-CoV-2 infection. A single dose of SLR14 prevented viral infection in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I)-dependent manner. SLR14 demonstrated remarkable prophylactic protective capacity against lethal SARS-CoV-2 infection and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity in the absence of the adaptive immune system. In the context of infection with variants of concern (VOCs), SLR14 conferred broad protection against emerging VOCs. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and treatment of chronically infected immunosuppressed patients.
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Affiliation(s)
- Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Benjamin Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | | | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
| | | | - Huiping Dong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Melissa Linehan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | | | - Craig B. Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Marie L. Landry
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Anna M. Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Department of Chemistry, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
- Howard Hughes Medical Institute, Chevy Chase, MD
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16
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Lee JY, Wing PAC, Gala DS, Noerenberg M, Järvelin AI, Titlow J, Zhuang X, Palmalux N, Iselin L, Thompson MK, Parton RM, Prange-Barczynska M, Wainman A, Salguero FJ, Bishop T, Agranoff D, James W, Castello A, McKeating JA, Davis I. Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences. eLife 2022; 11:74153. [PMID: 35049501 PMCID: PMC8776252 DOI: 10.7554/elife.74153] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022] Open
Abstract
Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, subgenomic RNAs, and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.
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Affiliation(s)
- Jeffrey Y Lee
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Peter AC Wing
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Dalia S Gala
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Marko Noerenberg
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Aino I Järvelin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Joshua Titlow
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Louisa Iselin
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Mary Kay Thompson
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Richard M Parton
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
| | - Maria Prange-Barczynska
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Alan Wainman
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | | | - Tammie Bishop
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Ludwig Institute for Cancer Research, The University of OxfordOxfordUnited Kingdom
| | - Daniel Agranoff
- Department of Infectious Diseases, University Hospitals Sussex NHS Foundation TrustBrightonUnited Kingdom
| | - William James
- Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom,James & Lillian Martin Centre, Sir William Dunn School of Pathology, The University of OxfordOxfordUnited Kingdom
| | - Alfredo Castello
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom,MRC-University of Glasgow Centre for Virus Research, The University of GlasgowGlasgowUnited Kingdom
| | - Jane A McKeating
- Nuffield Department of Medicine, The University of OxfordOxfordUnited Kingdom,Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), The University of OxfordOxfordUnited Kingdom
| | - Ilan Davis
- Department of Biochemistry, The University of OxfordOxfordUnited Kingdom
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17
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Montenegro YHA, Zanatta G, Quincozes-Santos A, Leipnitz G. TOM70 in Glial Cells as a Potential Target for Treatment of COVID-19. Front Cell Neurosci 2021; 15:811376. [PMID: 35002631 PMCID: PMC8740195 DOI: 10.3389/fncel.2021.811376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Geancarlo Zanatta
- Programa de Pós-Graduação em Bioquímica, Universidade Federal do Ceará, Fortaleza, Brazil
- Departamento de Física, Universidade Federal do Ceará, Fortaleza, Brazil
| | - André Quincozes-Santos
- Programa de Pós-Graduação em Neurociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilhian Leipnitz
- Programa de Pós-Graduação em Neurociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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18
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Mathema B, Chen L, Chow KF, Zhao Y, Zody MC, Mediavilla JR, Cunningham MH, Composto K, Lee A, Oschwald DM, Germer S, Fennessey S, Patel K, Wilson D, Cassell A, Pascual L, Ip A, Corvelo A, Dar S, Kramer Y, Maniatis T, Perlin DS, Kreiswirth BN. Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Microbiol Spectr 2021; 9:e0188221. [PMID: 34787439 PMCID: PMC8597639 DOI: 10.1128/spectrum.01882-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called variants of concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated health care professionals (HCP). Our postvaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network identified all vaccinated HCPs who tested positive for COVID-19 after routine screening or after self-reporting. From 1 January 2021 to 30 April 2021, 23,687 HCPs received either mRNA-1273 or BNT162b2 mRNA vaccine. All available postvaccination SARS-CoV-2 samples and a random collection from nonvaccinated patients during the similar time frame were subjected to VOC screening and whole-genome sequencing (WGS). Sixty-two percent (23,697/37,500) of HCPs received at least one vaccine dose, with 60% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; percentage of concurrent nonvaccinated samples was 37% (523/1,404) and 20% (284/1,394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and nonvaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any receptor-binding domain (RBD)/N-terminal domain (NTD) polymorphism between groups (P > 0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent VOCs among nonvaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants with high transmission potential and immune evasion properties, the so-called variants of concern (VOC), continue to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from partial/fully vaccinated health care professionals and probe specifically for VOC enrichment. Our findings support the high level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the nonvaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered postvaccination appears to proportionally represent the observed viral diversity within the community.
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Affiliation(s)
- Barun Mathema
- Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Kar Fai Chow
- Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA
| | - Yanan Zhao
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | | | - Jose R. Mediavilla
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Marcus H. Cunningham
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Kaelea Composto
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Annie Lee
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | | | | | | | - Kishan Patel
- Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA
| | - David Wilson
- Hackensack Meridian Health BI Analytics, Edison, New Jersey, USA
| | - Ann Cassell
- Hackensack Meridian Health BI Analytics, Edison, New Jersey, USA
| | - Lauren Pascual
- John Theurer Cancer Center, Outcomes Division, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Andrew Ip
- John Theurer Cancer Center, Outcomes Division, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | | | - Sophia Dar
- Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA
| | - Yael Kramer
- Hackensack Meridian Health Biorepository, Hackensack, New Jersey, USA
| | | | - David S. Perlin
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
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19
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Guo K, Barrett BS, Mickens KL, Vladar EK, Morrison JH, Hasenkrug KJ, Poeschla EM, Santiago ML. Interferon Resistance of Emerging SARS-CoV-2 Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.20.436257. [PMID: 33758840 PMCID: PMC7986999 DOI: 10.1101/2021.03.20.436257] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The emergence of SARS-CoV-2 variants with enhanced transmissibility, pathogenesis and resistance to vaccines presents urgent challenges for curbing the COVID-19 pandemic. While Spike mutations that enhance virus infectivity or neutralizing antibody evasion may drive the emergence of these novel variants, studies documenting a critical role for interferon responses in the early control of SARS-CoV-2 infection, combined with the presence of viral genes that limit these responses, suggest that interferons may also influence SARS-CoV-2 evolution. Here, we compared the potency of 17 different human interferons against multiple viral lineages sampled during the course of the global outbreak, including ancestral and four major variants of concern. Our data reveal increased interferon resistance in emerging SARS-CoV-2 variants, suggesting that evasion of innate immunity may be a significant, ongoing driving force for SARS-CoV-2 evolution. These findings have implications for the increased lethality of emerging variants and highlight the interferon subtypes that may be most successful in the treatment of early infections.
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Affiliation(s)
- Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Bradley S. Barrett
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kaylee L. Mickens
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Ezster K. Vladar
- Division of Pulmonary Sciences and Critical Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - James H. Morrison
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Kim J. Hasenkrug
- Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Eric M. Poeschla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA 80045
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20
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 599] [Impact Index Per Article: 199.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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21
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The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature 2021; 602:294-299. [PMID: 34818667 DOI: 10.1038/s41586-021-04245-0] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom. This B.1.1.7 variant, also known as Alpha, increased rapidly in prevalence, attributed to an increase in infection and/or transmission efficiency1. The Alpha variant has 19 nonsynonymous mutations across its viral genome, including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 Alpha spike mutations, suggesting it is a major determinant of increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil, South Africa, and elsewhere2,3, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.
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22
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Fleites YA, Aguiar J, Cinza Z, Bequet M, Marrero E, Vizcaíno M, Esquivel I, Diaz M, Sin-Mayor A, Garcia M, Martinez SM, Beato A, Galarraga AG, Mendoza-Mari Y, Valdés I, García G, Lemos G, González I, Canaán-Haden C, Figueroa N, Oquendo R, Akbar SM, Mahtab MA, Uddin MH, Guillén GE, Muzio VL, Pentón E, Aguilar JC. HeberNasvac, a Therapeutic Vaccine for Chronic Hepatitis B, Stimulates Local and Systemic Markers of Innate Immunity: Potential Use in SARS-CoV-2 Postexposure Prophylaxis. Euroasian J Hepatogastroenterol 2021; 11:59-70. [PMID: 34786358 PMCID: PMC8566153 DOI: 10.5005/jp-journals-10018-1344] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction More than 180 million people have been infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and more than 4 million coronavirus disease-2019 (COVID-19) patients have died in 1.5 years of the pandemic. A novel therapeutic vaccine (NASVAC) has shown to be safe and to have immunomodulating and antiviral properties against chronic hepatitis B (CHB). Materials and methods A phase I/II, open-label controlled and randomized clinical trial of NASVAC as a postexposure prophylaxis treatment was designed with the primary aim of assessing the local and systemic immunomodulatory effect of NASVAC in a cohort of suspected and SARS-CoV-2 risk-contact patients. A total of 46 patients, of both sexes, 60 years or older, presenting with symptoms of COVID-19 were enrolled in the study. Patients received NASVAC (100 μg per Ag per dose) via intranasal at days 1, 7, and 14 and sublingual, daily for 14 days. Results and discussion The present study detected an increased expression of toll-like receptors (TLR)-related genes in nasopharyngeal tonsils, a relevant property considering these are surrogate markers of SARS protection in the mice model of lethal infection. The HLA-class II increased their expression in peripheral blood mononuclear cell's (PBMC's) monocytes and lymphocytes, which is an attractive property taking into account the functional impairment of innate immune cells from the periphery of COVID-19-infected subjects. NASVAC was safe and well tolerated by the patients with acute respiratory infections and evidenced a preliminary reduction in the number of days with symptoms that needs to be confirmed in larger studies. Conclusions Our data justify the use of NASVAC as preemptive therapy or pre-/postexposure prophylaxis of SARS-CoV-2 and acute respiratory infections in general. The use of NASVAC or their active principles has potential as immunomodulatory prophylactic therapies in other antiviral settings like dengue as well as in malignancies like hepatocellular carcinoma where these markers have shown relation to disease progression. How to cite this article Fleites YA, Aguiar J, Cinza Z, et al. HeberNasvac, a Therapeutic Vaccine for Chronic Hepatitis B, Stimulates Local and Systemic Markers of Innate Immunity: Potential Use in SARS-CoV-2 Postexposure Prophylaxis. Euroasian J Hepato-Gastroenterol 2021;11(2):59–70.
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Affiliation(s)
- Yoel A Fleites
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Jorge Aguiar
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Zurina Cinza
- Department of Vaccines, Clinical Trials Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Monica Bequet
- Department of Pharmaceuticals, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Elieser Marrero
- Department of Quality Control Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | | | - Idelsis Esquivel
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Marisol Diaz
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Adriana Sin-Mayor
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Maura Garcia
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Sara M Martinez
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Abrahan Beato
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Ana G Galarraga
- Department of Clinical Trials, Luis Diaz Soto Hospital, Havana, Cuba
| | - Yssel Mendoza-Mari
- Department of Pharmaceuticals, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Iris Valdés
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Gerardo García
- Department of Quality Control Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Gilda Lemos
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Isabel González
- Department of Pharmaceuticals, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Camila Canaán-Haden
- Department of Pharmaceuticals, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Nelvis Figueroa
- Department of Vaccines, Clinical Trials Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Rachel Oquendo
- Department of Vaccines, Clinical Trials Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Sheikh Mf Akbar
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Mamun A Mahtab
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Mohammad H Uddin
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Gerardo E Guillén
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Verena L Muzio
- Department of Vaccines, Clinical Trials Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Eduardo Pentón
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Julio C Aguilar
- Department of Vaccines, Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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23
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McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen LE, Dang HV, De Marco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. SCIENCE (NEW YORK, N.Y.) 2021; 374:1621-1626. [PMID: 34751595 DOI: 10.1126/science.abl8506] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jennifer Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Margaret Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | | | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Li JY, Zhou ZJ, Wang Q, He QN, Zhao MY, Qiu Y, Ge XY. Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2. Front Microbiol 2021; 12:770656. [PMID: 34777324 PMCID: PMC8586461 DOI: 10.3389/fmicb.2021.770656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
In the past two decades, coronavirus (CoV) has emerged frequently in the population. Three CoVs (SARS-CoV, MERS-CoV, SARS-CoV-2) have been identified as highly pathogenic human coronaviruses (HP-hCoVs). Particularly, the ongoing COVID-19 pandemic caused by SARS-CoV-2 warns that HP-hCoVs present a high risk to human health. Like other viruses, HP-hCoVs interact with their host cells in sophisticated manners for infection and pathogenesis. Here, we reviewed the current knowledge about the interference of HP-hCoVs in multiple cellular processes and their impacts on viral infection. HP-hCoVs employed various strategies to suppress and evade from immune response, including shielding viral RNA from recognition by pattern recognition receptors (PRRs), impairing IFN-I production, blocking the downstream pathways of IFN-I, and other evasion strategies. This summary provides a comprehensive view of the interplay between HP-hCoVs and the host cells, which is helpful to understand the mechanism of viral pathogenesis and develop antiviral therapies.
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Affiliation(s)
- Jin-Yan Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Qing-Nan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ming-Yi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
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25
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Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Khan K, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Muema D, Ramjit D, Ndung'u T, Hanekom W, Gosnell B, Lessells RJ, Wong EB, de Oliveira T, Moosa MYS, Lustig G, Leslie A, Kløverpris H, Sigal A. HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV-2 infection wave. eLife 2021; 10:e67397. [PMID: 34608862 PMCID: PMC8676326 DOI: 10.7554/elife.67397] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/07/2021] [Indexed: 01/08/2023] Open
Abstract
There are conflicting reports on the effects of HIV on COVID-19. Here, we analyzed disease severity and immune cell changes during and after SARS-CoV-2 infection in 236 participants from South Africa, of which 39% were people living with HIV (PLWH), during the first and second (Beta dominated) infection waves. The second wave had more PLWH requiring supplemental oxygen relative to HIV-negative participants. Higher disease severity was associated with low CD4 T cell counts and higher neutrophil to lymphocyte ratios (NLR). Yet, CD4 counts recovered and NLR stabilized after SARS-CoV-2 clearance in wave 2 infected PLWH, arguing for an interaction between SARS-CoV-2 and HIV infection leading to low CD4 and high NLR. The first infection wave, where severity in HIV negative and PLWH was similar, still showed some HIV modulation of SARS-CoV-2 immune responses. Therefore, HIV infection can synergize with the SARS-CoV-2 variant to change COVID-19 outcomes.
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Affiliation(s)
- Farina Karim
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | - Inbal Gazy
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
| | - Sandile Cele
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Robert Krause
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Khadija Khan
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Hylton Rodel
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | | | - Daniel Muema
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Thumbi Ndung'u
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-NatalDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
| | - Willem Hanekom
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bernadett Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalDurbanSouth Africa
| | - Richard J Lessells
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
| | - Emily B Wong
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infectious Diseases, Department of Medicine, University of Alabama at BirminghamBirminghamUnited States
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch UniversityStellenboschSouth Africa
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalDurbanSouth Africa
| | - Gil Lustig
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
| | - Alasdair Leslie
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Henrik Kløverpris
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
| | - Alex Sigal
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
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26
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Longo SK, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat Rev Genet 2021; 22:627-644. [PMID: 34145435 PMCID: PMC9888017 DOI: 10.1038/s41576-021-00370-8] [Citation(s) in RCA: 343] [Impact Index Per Article: 114.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
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Affiliation(s)
- Sophia K. Longo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Margaret G. Guo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA,Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Andrew L. Ji
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA,Stanford Cancer Institute, Stanford University, Stanford, CA, USA,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
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Abstract
Mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can enhance the spread and the infectiousness and decrease the protective effect of antibodies present after infection, vaccination or antibody treatment. The alpha variant (B.1.1.7), first seen in Kent/United Kingdom, has increased the R‑value and therefore the infectiousness by 75%; however, the effectiveness of the vaccines against SARS-CoV‑2 available in Germany seems to be only slightly impaired by these mutations. In the case of the beta variant (B.1.351), first described in South Africa, the neutralization ability of antibodies towards SARS-CoV‑2 is decreased. The monoclonal antibodies bamlanivimab and etesivimab, which are used therapeutically, are ineffective. The AstraZeneca vaccine offers almost no protection against mild or moderate disease caused by the beta variant. The gamma variant (P.1 or B.1.1.28.1), which was first found in Brazil, is probably 1.7-2.6 times more transmissible than previous virus strains circulating in Brazil. In addition to the infectiousness, the mortality risk of the gamma variant also seems to be increased between 1.2 and 1.9-fold in adults and between 5 and 8-fold in young persons. The delta variant (B.1.617), first described in India, is now dominant in most countries. It is 50% more infectious than the alpha variant, and the protective effect of vaccinations against symptomatic disease can be decreased (Biontech: delta variant 88%, alpha variant 93.7%; AstraZeneca: delta variant 67%, alpha variant 74.5%). Furthermore, the course of the disease with the delta variant is often more severe than with the wild type. Disease courses with the delta variant are less severe in vaccinated than in nonvaccinated persons, and fatal outcomes are substantially rarer. A high vaccination rate is essential in order to approach herd immunity and to bring the pandemic under control. Even where the protective effect towards mild or moderate disease is decreased, as a rule, vaccination still offers excellent protection against life-threatening and fatal disease courses.
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Affiliation(s)
- Christoph J Hemmer
- Abteilung für Tropenmedizin und Infektionskrankheiten, Universitätsmedizin Rostock, Ernst-Heydemann-Straße 5, 18057, Rostock, Deutschland.
| | - M Löbermann
- Abteilung für Tropenmedizin und Infektionskrankheiten, Universitätsmedizin Rostock, Ernst-Heydemann-Straße 5, 18057, Rostock, Deutschland
| | - E C Reisinger
- Abteilung für Tropenmedizin und Infektionskrankheiten, Universitätsmedizin Rostock, Ernst-Heydemann-Straße 5, 18057, Rostock, Deutschland
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28
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Begemann M, Gross O, Wincewicz D, Hardeland R, Daguano Gastaldi V, Vieta E, Weissenborn K, Miskowiak KW, Moerer O, Ehrenreich H. Addressing the 'hypoxia paradox' in severe COVID-19: literature review and report of four cases treated with erythropoietin analogues. Mol Med 2021; 27:120. [PMID: 34565332 PMCID: PMC8474703 DOI: 10.1186/s10020-021-00381-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Since fall 2019, SARS-CoV-2 spread world-wide, causing a major pandemic with estimated ~ 220 million subjects affected as of September 2021. Severe COVID-19 is associated with multiple organ failure, particularly of lung and kidney, but also grave neuropsychiatric manifestations. Overall mortality reaches > 2%. Vaccine development has thrived in thus far unreached dimensions and will be one prerequisite to terminate the pandemic. Despite intensive research, however, few treatment options for modifying COVID-19 course/outcome have emerged since the pandemic outbreak. Additionally, the substantial threat of serious downstream sequelae, called 'long COVID' and 'neuroCOVID', becomes increasingly evident. Among candidates that were suggested but did not yet receive appropriate funding for clinical trials is recombinant human erythropoietin. Based on accumulating experimental and clinical evidence, erythropoietin is expected to (1) improve respiration/organ function, (2) counteract overshooting inflammation, (3) act sustainably neuroprotective/neuroregenerative. Recent counterintuitive findings of decreased serum erythropoietin levels in severe COVID-19 not only support a relative deficiency of erythropoietin in this condition, which can be therapeutically addressed, but also made us coin the term 'hypoxia paradox'. As we review here, this paradox is likely due to uncoupling of physiological hypoxia signaling circuits, mediated by detrimental gene products of SARS-CoV-2 or unfavorable host responses, including microRNAs or dysfunctional mitochondria. Substitution of erythropoietin might overcome this 'hypoxia paradox' caused by deranged signaling and improve survival/functional status of COVID-19 patients and their long-term outcome. As supporting hints, embedded in this review, we present 4 male patients with severe COVID-19 and unfavorable prognosis, including predicted high lethality, who all profoundly improved upon treatment which included erythropoietin analogues. SHORT CONCLUSION Substitution of EPO may-among other beneficial EPO effects in severe COVID-19-circumvent downstream consequences of the 'hypoxia paradox'. A double-blind, placebo-controlled, randomized clinical trial for proof-of-concept is warranted.
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Affiliation(s)
- Martin Begemann
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Hermann-Rein-Str.3, 37075, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany
| | - Oliver Gross
- Department of Nephrology and Rheumatology, University Medical Center, Göttingen, Germany
| | - Dominik Wincewicz
- Hospital Clinic, Institute of Neuroscience, IDIBAPS, CIBERSAM, Barcelona, Spain
| | - Rüdiger Hardeland
- Johann Friedrich Blumenbach Institute of Zoology & Anthropology, University of Göttingen, Göttingen, Germany
| | - Vinicius Daguano Gastaldi
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Hermann-Rein-Str.3, 37075, Göttingen, Germany
| | - Eduard Vieta
- Hospital Clinic, Institute of Neuroscience, IDIBAPS, CIBERSAM, Barcelona, Spain
| | | | - Kamilla W Miskowiak
- Psychiatric Centre Copenhagen, University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Onnen Moerer
- Department of Anaesthesiology, University Medical Center Göttingen, Göttingen, Germany
| | - Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Hermann-Rein-Str.3, 37075, Göttingen, Germany.
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Torbati E, Krause KL, Ussher JE. The Immune Response to SARS-CoV-2 and Variants of Concern. Viruses 2021; 13:1911. [PMID: 34696342 PMCID: PMC8537260 DOI: 10.3390/v13101911] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/07/2023] Open
Abstract
At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. Subsequently, SARS-CoV-2 rapidly spread globally, resulting in a pandemic that has to date infected over 200 million individuals and resulted in more than 4.3 million deaths. While SARS-CoV-2 results in severe disease in 13.8%, with increasing frequency of severe disease with age, over 80% of infections are asymptomatic or mild. The immune response is an important determinant of outcome following SARS-CoV-2 infection. While B cell and T cell responses are associated with control of infection and protection against subsequent challenge with SARS-CoV-2, failure to control viral replication and the resulting hyperinflammation are associated with severe COVID-19. Towards the end of 2020, several variants of concern emerged that demonstrate increased transmissibility and/or evasion of immune responses from prior SARS-CoV-2 infection. This article reviews what is known about the humoral and cellular immune responses to SARS-CoV-2 and how mutation and structural/functional changes in the emerging variants of concern impact upon the immune protection from prior infection or vaccination.
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Affiliation(s)
- Elham Torbati
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
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30
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Mok BWY, Liu H, Deng S, Liu J, Zhang AJ, Lau SY, Liu S, Tam RCY, Cremin CJ, Ng TTL, Leung JSL, Lee LK, Wang P, To KKW, Chan JFW, Chan KH, Yuen KY, Siu GKH, Chen H. Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Commun Biol 2021; 4:1102. [PMID: 34545191 PMCID: PMC8452646 DOI: 10.1038/s42003-021-02640-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/01/2021] [Indexed: 11/09/2022] Open
Abstract
Emerging variants of SARS-CoV-2 have been shown to rapidly replace original circulating strains in humans soon after they emerged. There is a lack of experimental evidence to explain how these natural occurring variants spread more efficiently than existing strains of SARS-CoV-2 in transmission. We found that the Alpha variant (B.1.1.7) increased competitive fitness over earlier parental D614G lineages in in-vitro and in-vivo systems. Using hamster transmission model, we further demonstrated that the Alpha variant is able to replicate and shed more efficiently in the nasal cavity of hamsters than other variants with low dose and short duration of exposure. The capability to initiate effective infection with low inocula may be one of the key factors leading to the rapid transmission of emerging variants of SARS-CoV-2.
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Affiliation(s)
- Bobo Wing-Yee Mok
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Honglian Liu
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shaofeng Deng
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jiayan Liu
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Anna Jinxia Zhang
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Siu-Ying Lau
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Siwen Liu
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rachel Chun-Yee Tam
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Conor J Cremin
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Pui Wang
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kelvin Kai-Wang To
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Hung Chan
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Honglin Chen
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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31
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Despres HW, Mills MG, Shirley DJ, Schmidt MM, Huang ML, Jerome KR, Greninger AL, Bruce EA. Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.09.07.21263229. [PMID: 34580674 PMCID: PMC8475961 DOI: 10.1101/2021.09.07.21263229] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Novel SARS-CoV-2 Variants of Concern (VoC) pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between viral RNA and infectious virus for individual variants is unknown. METHODS We measured infectious viral titer (using a micro-focus forming assay) as well as total and subgenomic viral RNA levels (using RT-PCR) in a set of 165 clinical samples containing SARS-CoV-2 Alpha, Delta and Epsilon variants that were processed within two days of collection from the patient. RESULTS We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite the variability we observed for individual samples the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (6 and 4 times as much, p=0.0002 and 0.009 respectively) or subgenomic E RNA (11 and 7 times as much, p<0.0001 and 0.006 respectively). CONCLUSION In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may also be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity of the Delta variant may further explain increased spread and suggests a need for increased measures to prevent viral transmission. SIGNIFICANCE STATEMENT Current and future SARS-CoV-2 variants threaten our ability to control the COVID-19 pandemic. Variants with increased transmission, higher viral loads, or greater immune evasion are of particular concern. Viral loads are currently measured by the amount of viral RNA in a clinical sample rather than the amount of infectious virus. We measured both RNA and infectious virus levels directly in a set of 165 clinical specimens from Alpha, Epsilon or Delta variants. Our data shows that Delta is more infectious compared to Alpha, with ∼ six times as much infectious virus for the same amount of RNA. This increase in infectivity suggests increased measures (vaccination, masking, distancing, ventilation) are needed to control Delta compared to Alpha.
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Affiliation(s)
- Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
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Christie MJ, Irving AT, Forster SC, Marsland BJ, Hansbro PM, Hertzog PJ, Nold-Petry CA, Nold MF. Of bats and men: Immunomodulatory treatment options for COVID-19 guided by the immunopathology of SARS-CoV-2 infection. Sci Immunol 2021; 6:eabd0205. [PMID: 34533977 DOI: 10.1126/sciimmunol.abd0205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Michael J Christie
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Aaron T Irving
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW 2050, Australia.,Centre for Inflammation, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Melbourne, Victoria, Australia
| | - Claudia A Nold-Petry
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Marcel F Nold
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria, Australia
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections trigger viral RNA sensors such as TLR7 and RIG-I, thereby leading to production of type I interferon (IFN) and other inflammatory mediators. Expression of viral proteins in the context of this inflammation leads to stereotypical antigen-specific antibody and T cell responses that clear the virus. Immunity is then maintained through long-lived antibody-secreting plasma cells and by memory B and T cells that can initiate anamnestic responses. Each of these steps is consistent with prior knowledge of acute RNA virus infections. Yet there are certain concepts, while not entirely new, that have been resurrected by the biology of severe SARS-CoV-2 infections and deserve further attention. These include production of anti-IFN autoantibodies, early inflammatory processes that slow adaptive humoral immunity, immunodominance of antibody responses, and original antigenic sin. Moreover, multiple different vaccine platforms allow for comparisons of pathways that promote robust and durable adaptive immunity.
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Affiliation(s)
- Dominik Schenten
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, United States.
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, United States.
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34
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Annavajhala MK, Mohri H, Wang P, Nair M, Zucker JE, Sheng Z, Gomez-Simmonds A, Kelley AL, Tagliavia M, Huang Y, Bedford T, Ho DD, Uhlemann AC. Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Nature 2021; 597:703-708. [PMID: 34428777 PMCID: PMC8481122 DOI: 10.1038/s41586-021-03908-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/13/2021] [Indexed: 12/21/2022]
Abstract
SARS-CoV-2 infections have surged across the globe in recent months, concomitant with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten the efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies that are in clinical use and is less susceptible to neutralization by plasma from individuals who had recovered from SARS-CoV-2 infection or serum from vaccinated individuals, posing a modest antigenic challenge. The presence of the B.1.526 lineage has now been reported in all 50 states in the United States and in many other countries. B.1.526 rapidly replaced earlier lineages in New York, with an estimated transmission advantage of 35%. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrently with the rise of B.1.1.7 and ensuing variants.
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Affiliation(s)
- Medini K Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jason E Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anne L Kelley
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maya Tagliavia
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David D Ho
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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35
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Phosphorylation of SARS-CoV-2 Orf9b Regulates Its Targeting to Two Binding Sites in TOM70 and Recruitment of Hsp90. Int J Mol Sci 2021; 22:ijms22179233. [PMID: 34502139 PMCID: PMC8430508 DOI: 10.3390/ijms22179233] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the causative agent of the COVID19 pandemic. The SARS-CoV-2 genome encodes for a small accessory protein termed Orf9b, which targets the mitochondrial outer membrane protein TOM70 in infected cells. TOM70 is involved in a signaling cascade that ultimately leads to the induction of type I interferons (IFN-I). This cascade depends on the recruitment of Hsp90-bound proteins to the N-terminal domain of TOM70. Binding of Orf9b to TOM70 decreases the expression of IFN-I; however, the underlying mechanism remains elusive. We show that the binding of Orf9b to TOM70 inhibits the recruitment of Hsp90 and chaperone-associated proteins. We characterized the binding site of Orf9b within the C-terminal domain of TOM70 and found that a serine in position 53 of Orf9b and a glutamate in position 477 of TOM70 are crucial for the association of both proteins. A phosphomimetic variant Orf9bS53E showed drastically reduced binding to TOM70 and did not inhibit Hsp90 recruitment, suggesting that Orf9b–TOM70 complex formation is regulated by phosphorylation. Eventually, we identified the N-terminal TPR domain of TOM70 as a second binding site for Orf9b, which indicates a so far unobserved contribution of chaperones in the mitochondrial targeting of the viral protein.
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36
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Leary S, Gaudieri S, Parker MD, Chopra A, James I, Pakala S, Alves E, John M, Lindsey BB, Keeley AJ, Rowland-Jones SL, Swanson MS, Ostrov DA, Bubenik JL, Das SR, Sidney J, Sette A, de Silva TI, Phillips E, Mallal S. Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Pathog Immun 2021; 6:27-49. [PMID: 34541432 PMCID: PMC8439434 DOI: 10.20411/pai.v6i2.460] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 07/31/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host's anti-viral immune response, in turn affecting the frequency of variants over time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. METHODS Deep-sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. Results: Sequence analysis suggests that the 3 adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep-sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames. CONCLUSIONS The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans, resulting in both coding changes and novel sub-genomic RNA transcripts, suggests this as a mechanism for diversification and adaptation within its new host.
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Affiliation(s)
- Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Matthew D. Parker
- Sheffield Biomedical Research Centre, Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Suman Pakala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Benjamin B. Lindsey
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease and The Florey Institute for Host-Pathogen Interactions, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Alexander J. Keeley
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease and The Florey Institute for Host-Pathogen Interactions, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Sarah L. Rowland-Jones
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease and The Florey Institute for Host-Pathogen Interactions, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Maurice S. Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, Gainesville, Florida, United States
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States
| | - Jodi L. Bubenik
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, Gainesville, Florida, United States
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, United States
| | - COVID-19 Genomics UK (COG-UK) consortium
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Sheffield Biomedical Research Centre, Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease and The Florey Institute for Host-Pathogen Interactions, Medical School, University of Sheffield, Sheffield, United Kingdom
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, Gainesville, Florida, United States
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, California, United States
| | - Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease and The Florey Institute for Host-Pathogen Interactions, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
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37
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McCallum M, Walls AC, Sprouse KR, Bowen JE, Rosen L, Dang HV, deMarco A, Franko N, Tilles SW, Logue J, Miranda MC, Ahlrichs M, Carter L, Snell G, Pizzuto MS, Chu HY, Van Voorhis WC, Corti D, Veesler D. Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34401880 DOI: 10.1101/2021.08.11.455956] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Worldwide SARS-CoV-2 transmission leads to the recurrent emergence of variants, such as the recently described B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.617.2+ (delta+). The B.1.617.2 (delta) variant of concern is causing a new wave of infections in many countries, mostly affecting unvaccinated individuals, and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing the impact of individual mutations on immune evasion. Mutations in the B.1.617.1 (kappa) and B.1.617.2 (delta) spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including an unexpected remodeling of the B.1.617.2 (delta) N-terminal domain. The binding affinity of the B.1.617.1 (kappa) and B.1.617.2 (delta) receptor-binding domain for ACE2 is comparable to the ancestral virus whereas B.1.617.2+ (delta+) exhibits markedly reduced affinity. We describe a previously uncharacterized class of N-terminal domain-directed human neutralizing monoclonal antibodies cross-reacting with several variants of concern, revealing a possible target for vaccine development.
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38
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Patients Admitted for Variant Alpha COVID-19 Have Poorer Outcomes than Those Infected with the Old Strain. J Clin Med 2021; 10:jcm10163550. [PMID: 34441844 PMCID: PMC8396910 DOI: 10.3390/jcm10163550] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES The variant alpha COVID-19 rapidly spread across Europe in early 2021. While this variant's increased infectivity has been proven, little is known of its clinical presentation and outcomes compared to the old strain. METHODS We identified patients admitted to the Cannes General Hospital for variant alpha-related COVID-19 infection from January to April 2021. Their main demographic parameters, inflammatory markers and clinical characteristics were recorded. Patients admitted from October to December 2020 for 20E (EU1) COVID-19 were selected as controls. Differences between groups were analyzed. RESULTS We included 157 patients (mean age 73 years; 58% men; mean delay of symptoms 6.9 days). Comorbidities were present in 92% (mainly hypertension, diabetes and obesity or overweight). The prevalence of comorbidities did not differ between groups. In 28% of cases, patients either died or required transfer to the Intensive Care Unit (ICU). The cause of death or of transfer to the ICU was presumably associated with severe pneumonia. Variant alpha COVID-19 had 3.8-fold higher risk of death or transfer to the ICU compared to the old strain. DISCUSSION Patients infected with variant alpha COVID-19, despite similar background characteristics, had a higher risk of unfavorable outcomes than those infected with the old strain, suggesting increased virulence related to this variant.
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39
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Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33880475 DOI: 10.1101/2020.04.10.029454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host’s anti-viral immune response, in turn affecting the frequency of variants over-time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. Methods Deep sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. Results Sequence analysis suggests that the three adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence (CS) of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames. Conclusions The finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans resulting in both coding changes and novel sub-genomic RNA transcripts suggests this as a mechanism for diversification and adaptation within its new host.
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40
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Annavajhala MK, Mohri H, Wang P, Nair M, Zucker JE, Sheng Z, Gomez-Simmonds A, Kelley AL, Tagliavia M, Huang Y, Bedford T, Ho DD, Uhlemann AC. Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.23.21252259. [PMID: 33655278 PMCID: PMC7924303 DOI: 10.1101/2021.02.23.21252259] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent months have seen surges of SARS-CoV-2 infection across the globe with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature mutations of concern are E484K, which plays a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here, we report the emergence of variant lineage B.1.526 that contains E484K and its alarming rise to dominance in New York City in early 2021. This variant is partially or completely resistant to two therapeutic monoclonal antibodies in clinical use and less susceptible to neutralization by convalescent plasma or vaccinee sera, posing a modest antigenic challenge. The B.1.526 lineage has now been reported from all 50 states in the US and numerous other countries. B.1.526 rapidly replaced earlier lineages in New York upon its emergence, with an estimated transmission advantage of 35%. Such transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, likely contributed to the sharp rise and rapid spread of B.1.526. Although SARS-CoV-2 B.1.526 initially outpaced B.1.1.7 in the region, its growth subsequently slowed concurrent with the rise of B.1.1.7 and ensuing variants.
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Affiliation(s)
- Medini K. Annavajhala
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jason E. Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Anne L. Kelley
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maya Tagliavia
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David D. Ho
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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41
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Goldhill DH, Barclay WS. 2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic? Evolution 2021; 75:2311-2316. [PMID: 34342897 PMCID: PMC8444725 DOI: 10.1111/evo.14317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022]
Affiliation(s)
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London, UK
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42
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Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.23.21252268. [PMID: 33688681 PMCID: PMC7941658 DOI: 10.1101/2021.02.23.21252268] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARSCoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.
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Affiliation(s)
- Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Houryiah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sureshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Yeshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Ravindra K Gupta
- Clinical Microbiology, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anton Nekturenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western cape, Bellville, South Africa
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, Scotland, UK
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, US
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
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Gori Savellini G, Anichini G, Gandolfo C, Cusi MG. SARS-CoV-2 N Protein Targets TRIM25-Mediated RIG-I Activation to Suppress Innate Immunity. Viruses 2021; 13:1439. [PMID: 34452305 PMCID: PMC8402637 DOI: 10.3390/v13081439] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
A weak production of INF-β along with an exacerbated release of pro-inflammatory cytokines have been reported during infection by the novel SARS-CoV-2 virus. SARS-CoV-2 encodes several proteins able to counteract the host immune system, which is believed to be one of the most important features contributing to the viral pathogenesis and development of a severe clinical picture. Previous reports have demonstrated that SARS-CoV-2 N protein, along with some non-structural and accessory proteins, efficiently suppresses INF-β production by interacting with RIG-I, an important pattern recognition receptor (PRR) involved in the recognition of pathogen-derived molecules. In the present study, we better characterized the mechanism by which the SARS-CoV-2 N counteracts INF-β secretion and affects RIG-I signaling pathways. In detail, when the N protein was ectopically expressed, we noted a marked decrease in TRIM25-mediated RIG-I activation. The capability of the N protein to bind to, and probably mask, TRIM25 could be the consequence of its antagonistic activity. Furthermore, this interaction occurred at the SPRY domain of TRIM25, harboring the RNA-binding activity necessary for TRIM25 self-activation. Here, we describe new findings regarding the interplay between SARS-CoV-2 and the IFN system, filling some gaps for a better understanding of the molecular mechanisms affecting the innate immune response in COVID-19.
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Affiliation(s)
- Gianni Gori Savellini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (M.G.C.)
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (M.G.C.)
| | - Claudia Gandolfo
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (M.G.C.)
| | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (M.G.C.)
- “S. Maria delle Scotte” Hospital, Viale Bracci, 1, 53100 Siena, Italy
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34282424 DOI: 10.1101/2021.07.12.21260208] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimate viral reproduction and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome load often peaked days earlier in saliva than in nasal swabs, indicating strong compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of B.1.1.7 and non-B.1.1.7 viruses in nasal swabs were indistinguishable, however B.1.1.7 exhibited a significantly slower pre-peak growth rate in saliva. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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Mallapaty S. How a rampant coronavirus variant blunts our immune defences. Nature 2021:10.1038/d41586-021-01540-8. [PMID: 34108727 DOI: 10.1038/d41586-021-01540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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