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Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
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Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
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2
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Lawrence P, Heung M, Nave J, Henkel C, Escudero-Pérez B. The natural virome and pandemic potential: Disease X. Curr Opin Virol 2023; 63:101377. [PMID: 37995425 DOI: 10.1016/j.coviro.2023.101377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
Over the last decade, the emergence of several zoonotic viruses has demonstrated that previously unknown or neglected pathogens have the potential to cause epidemics and therefore to pose a threat to global public health. Even more concerning are the estimated 1.7 million still-undiscovered viruses present in the natural environment or 'global virome', with many of these as-yet uncharacterized viruses predicted to be pathogenic for humans. Thus, in order to mitigate disease emergence and prevent future pandemics, it is crucial to identify the global extent of viral threats to which humans may become exposed. This requires cataloguing the viruses that exist in the environment within their various and diverse host species, and also understanding the viral, host, and environmental factors that dictate the circumstances that result in viral spillover into humans. We also address here which strategies can be implemented as countermeasure initiatives to reduce the risk of emergence of new diseases.
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Affiliation(s)
- Philip Lawrence
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE: Sciences et Humanités (EA1598), Lyon, France
| | - Michelle Heung
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia Nave
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christoph Henkel
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, Braunschweig, Germany.
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3
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Marchesi E, Gentili V, Bortolotti D, Preti L, Marchetti P, Cristofori V, Fantinati A, Rizzo R, Trapella C, Perrone D, Navacchia ML. Dihydroartemisinin-Ursodeoxycholic Bile Acid Hybrids in the Fight against SARS-CoV-2. ACS OMEGA 2023; 8:45078-45087. [PMID: 38046338 PMCID: PMC10688034 DOI: 10.1021/acsomega.3c07034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/05/2023] [Accepted: 10/13/2023] [Indexed: 12/05/2023]
Abstract
Here, we propose the molecular hybridization of dihydroartemisinin (DHA) and ursodeoxycholic bile acid (UDCA), approved drugs, for the preparation of antiviral agents against SARS-CoV-2. DHA and UDCA were selected on the basis of their recently demonstrated in vitro activity against SARS-CoV-2. A selection of DHA-UDCA-based hybrids obtained by varying the nature of the linkage and the bile acid conjugation point as well as unconjugated DHA and UDCA were tested in vitro for cytotoxicity and anti-SARS-CoV-2 activity on Vero E6 and Calu-3 human lung cells. The hybrid DHA-t-UDCMe, obtained by conjugation via click chemistry on a gram scale, was identified as a potential candidate for SARS-CoV-2 infection treatment due to significant reduction of viral replication, possibly involving ACE2 downregulation, no cytotoxicity, and chemical stability.
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Affiliation(s)
- Elena Marchesi
- Department
of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Valentina Gentili
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Daria Bortolotti
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Lorenzo Preti
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Marchetti
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Virginia Cristofori
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Anna Fantinati
- Department
of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Roberta Rizzo
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Claudio Trapella
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Daniela Perrone
- Department
of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Luisa Navacchia
- Institute
for Organic Synthesis and Photoreactivity (ISOF), National Research
Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
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4
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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5
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Devaux CA, Fantini J. Possible contribution of rare alleles of human ACE2 in the emergence of SARS-CoV-2 variants escaping the immune response. Front Immunol 2023; 14:1252367. [PMID: 37885880 PMCID: PMC10598458 DOI: 10.3389/fimmu.2023.1252367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Since the start of the SARS-CoV-2 pandemic, the rapid replacement of one lineage by another has been observed. Indeed, SARS-CoV-2 is evolving through a quasispecies mechanism leading to post-infection mutation selection under positive evolutionary pressure (host-driven viral evolution). These mutations may reduce the effectiveness of the specific neutralizing immune response against the virus. We provide here evidence that apart from the selection of SARS-CoV-2 variants by the immune system, selection by the cellular receptor can just as well select variants which escape neutralization.
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Affiliation(s)
- Christian A. Devaux
- Institut National des Sciences Biologiques (INSB), Centre National de la Recherche Scientifique (CNRS), Marseille, France
- Microbes, Evolution, Phylogénie et Infections, Faculté de Pharmacie, Aix Marseille Université, Marseille, France
| | - Jacques Fantini
- Institut National de la Santé et de la Recherche Médicale (INSERM) U_1072, Faculté des Sciences, Aix-Marseille Université, Marseille, France
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6
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Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol 2023; 8:1820-1833. [PMID: 37749254 PMCID: PMC10522490 DOI: 10.1038/s41564-023-01476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/14/2023] [Indexed: 09/27/2023]
Abstract
The pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations.
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Affiliation(s)
- Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Moderna Inc., Cambridge, MA, USA
| | - Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vishwaraj Sontake
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Ande West
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Gallant
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Seth J Zost
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lily Adams
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Edgar F Kong
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aleksandra Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Purushothama R Tata
- Department of Cell Biology, Regeneration Next Initiative, Duke University Medical Center, Durham, NC, USA
| | - Peter Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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7
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Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
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Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
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8
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Bernardo L, Lomagno A, Mauri PL, Di Silvestre D. Integration of Omics Data and Network Models to Unveil Negative Aspects of SARS-CoV-2, from Pathogenic Mechanisms to Drug Repurposing. BIOLOGY 2023; 12:1196. [PMID: 37759595 PMCID: PMC10525644 DOI: 10.3390/biology12091196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 health emergency, affecting and killing millions of people worldwide. Following SARS-CoV-2 infection, COVID-19 patients show a spectrum of symptoms ranging from asymptomatic to very severe manifestations. In particular, bronchial and pulmonary cells, involved at the initial stage, trigger a hyper-inflammation phase, damaging a wide range of organs, including the heart, brain, liver, intestine and kidney. Due to the urgent need for solutions to limit the virus' spread, most efforts were initially devoted to mapping outbreak trajectories and variant emergence, as well as to the rapid search for effective therapeutic strategies. Samples collected from hospitalized or dead COVID-19 patients from the early stages of pandemic have been analyzed over time, and to date they still represent an invaluable source of information to shed light on the molecular mechanisms underlying the organ/tissue damage, the knowledge of which could offer new opportunities for diagnostics and therapeutic designs. For these purposes, in combination with clinical data, omics profiles and network models play a key role providing a holistic view of the pathways, processes and functions most affected by viral infection. In fact, in addition to epidemiological purposes, networks are being increasingly adopted for the integration of multiomics data, and recently their use has expanded to the identification of drug targets or the repositioning of existing drugs. These topics will be covered here by exploring the landscape of SARS-CoV-2 survey-based studies using systems biology approaches derived from omics data, paying particular attention to those that have considered samples of human origin.
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Affiliation(s)
| | | | | | - Dario Di Silvestre
- Institute for Biomedical Technologies—National Research Council (ITB-CNR), 20054 Segrate, Italy; (L.B.); (A.L.); (P.L.M.)
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9
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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294416. [PMID: 37662226 PMCID: PMC10473782 DOI: 10.1101/2023.08.22.23294416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. Results We enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive ≥21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR-positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation. Conclusions In this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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10
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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11
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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12
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Messali S, Rondina A, Giovanetti M, Bonfanti C, Ciccozzi M, Caruso A, Caccuri F. Traceability of SARS-CoV-2 transmission through quasispecies analysis. J Med Virol 2023; 95:e28848. [PMID: 37294038 DOI: 10.1002/jmv.28848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023]
Abstract
During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of replicating and closely related viral variants so-called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS-CoV-2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7.
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Affiliation(s)
- Serena Messali
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alessandro Rondina
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy
| | - Carlo Bonfanti
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Massimo Ciccozzi
- Clinical Pathology and Microbiology Laboratory, Unit of Medical Statistics and Molecular Epidemiology, University Hospital Campus Biomedico, Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
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13
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Cheng Y, Ji C, Zhou HY, Zheng H, Wu A. Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking. Viruses 2023; 15:v15051158. [PMID: 37243244 DOI: 10.3390/v15051158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.
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Affiliation(s)
- Yexiao Cheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Chengyang Ji
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
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14
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Riddell AC, Cutino-Moguel T. The origins of new SARS-COV-2 variants in immunocompromised individuals. Curr Opin HIV AIDS 2023; 18:148-156. [PMID: 36977190 DOI: 10.1097/coh.0000000000000794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
PURPOSE OF REVIEW To explore the origins of new severe acute respiratory coronavirus 2 (SARS-CoV-2) variants in immunocompromised individuals and whether the emergence of novel mutations in these individuals is responsible for the development of variants of concern (VOC). RECENT FINDINGS Next generation sequencing of samples from chronically infected immunocompromised patients has enabled identification of VOC- defining mutations in individuals prior to the emergence of these variants worldwide. Whether these individuals are the source of variant generation is uncertain. Vaccine effectiveness in immunocompromised individuals and with respect to VOCs is also discussed. SUMMARY Current evidence on chronic SARS-CoV-2 infection in immunocompromised populations is reviewed including the relevance of this to the generation of novel variants. Continued viral replication in the absence of an effective immune response at an individual level or high levels of viral infection at the population level are likely to have contributed to the appearance of the main VOC.
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Affiliation(s)
- Anna C Riddell
- Department of Virology, Division of Infection, Barts Health NHS Trust, London, UK
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15
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Schiuma G, Beltrami S, Santi E, Scutiero G, Sanz JM, Semprini CM, Rizzo S, Fernandez M, Zidi I, Gafà R, Passaro A, Greco P, Bortolotti D, Rizzo R. Effect of SARS-CoV-2 infection in pregnancy on CD147, ACE2 and HLA-G expression. Placenta 2023; 132:38-43. [PMID: 36628848 PMCID: PMC9814282 DOI: 10.1016/j.placenta.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/20/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Recent studies reported a differential expression of both ACE2 and CD147 in pregnant women associated to SARS-CoV-2 placental infection. The aim of this study is to further investigate the placental SARS-CoV-2 infection and the potential effect on protein expression (ACE2, CD147, HLA-G and CD56). METHODS The study was on three subgroups: i) 18 subjects positive for SARS-CoV-2 swab at delivery; ii) 9 subjects that had a positive SARS-CoV-2 swab during pregnancy but resulted negative at delivery; iii) 11 control subjects with physiological pregnancy and with no previous or concomitant SARS-CoV-2 swab positivity. None of the subjects were vaccinated for SARS-CoV-2 infection. The placenta samples were analyzed for SARS-CoV-2 NP (Nucleocapsid protein) positivity and the expression of ACE2, CD147, HLA-G and CD56. RESULTS We observed a higher percentage of SARS-CoV-2 NP positive placenta samples in the group of SARS-CoV-2 PCR positive at delivery in comparison with SARS-CoV-2 PCR negative at delivery. The localization of SARS-CoV-2 NP positivity in placenta samples was mainly in syncytiotrophoblast (ST) of SARS-CoV-2 PCR positive at delivery group and in extra-villous trophoblast (EVT) of SARS-CoV-2 PCR negative at delivery group. CD147, HLA-G positivity was higher in ST of SARS-CoV-2 PCR positive at delivery group, while CD56-expressing immune cells were decreased in comparison with control subjects. DISCUSSION We confirmed the ability of SARS-CoV-2 to infect placenta tissues. The simultaneous SARS-CoV-2 swab positivity at delivery and the positivity of the placenta tissue for SARS-CoV-2 NP seems to create an environment that modifies the expression of specific molecules, as CD147 and HLA-G. These data suggest a possible impact of SARS-CoV-2 infection during pregnancy, that might be worthy to be monitored also in vaccinated subjects.
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Affiliation(s)
- Giovanna Schiuma
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Silvia Beltrami
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Erica Santi
- Department of Medical Sciences, Obstetric and Gynecological Clinic, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Gennaro Scutiero
- Department of Medical Sciences, Obstetric and Gynecological Clinic, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Juana Maria Sanz
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Chiara Marina Semprini
- Medical Department, University Hospital of Ferrara Arcispedale Sant'Anna, Via Aldo Moro, 8 Cona, 44124, Ferrara, Italy
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Mercedes Fernandez
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Ines Zidi
- Laboratory Microorganismes and Active Biomolecules, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Roberta Gafà
- Department of Translational Medicine, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Angelina Passaro
- Medical Department, University Hospital of Ferrara Arcispedale Sant'Anna, Via Aldo Moro, 8 Cona, 44124, Ferrara, Italy,Department of Translational Medicine, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Pantaleo Greco
- Department of Medical Sciences, Obstetric and Gynecological Clinic, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Daria Bortolotti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy; LTTA-Clinical Research Center, University of Ferrara, Via Luigi Borsari, 46 - 44100, 44121, Ferrara, Italy.
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16
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SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin's Lymphoma. Viruses 2023; 15:v15020377. [PMID: 36851588 PMCID: PMC9962578 DOI: 10.3390/v15020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. CASE PRESENTATION We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin's lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin's lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. CONCLUSIONS This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants.
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17
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Messali S, Bugatti A, Filippini F, Caruso A, Caccuri F. Emergence of S gene-based quasispecies explains an optimal adaptation of Omicron BA.5 subvariant in the immunocompetent vaccinated human host. J Med Virol 2023; 95:e28167. [PMID: 36147029 DOI: 10.1002/jmv.28167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Federica Filippini
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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18
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Lodi G, Gentili V, Casciano F, Romani A, Zauli G, Secchiero P, Zauli E, Simioni C, Beltrami S, Fernandez M, Rizzo R, Voltan R. Cell cycle block by p53 activation reduces SARS-CoV-2 release in infected alveolar basal epithelial A549-hACE2 cells. Front Pharmacol 2022; 13:1018761. [PMID: 36582523 PMCID: PMC9792496 DOI: 10.3389/fphar.2022.1018761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV viruses have been shown to downregulate cellular events that control antiviral defenses. They adopt several strategies to silence p53, key molecule for cell homeostasis and immune control, indicating that p53 has a central role in controlling their proliferation in the host. Specific actions are the stabilization of its inhibitor, MDM2, and the interference with its transcriptional activity. The aim of our work was to evaluate a new approach against SARS-CoV-2 by using MDM2 inhibitors to raise p53 levels and activate p53-dependent pathways, therefore leading to cell cycle inhibition. Experimental setting was performed in the alveolar basal epithelial cell line A549-hACE2, expressing high level of ACE2 receptor, to allow virus entry, as well as p53 wild-type. Cells were treated with several concentrations of Nutlin-3 or RG-7112, two known MDM2 inhibitors, for the instauration of a cell cycle block steady-state condition before and during SARS-CoV-2 infection, and for the evaluation of p53 activation and impact on virus release and related innate immune events. The results indicated an efficient cell cycle block with inhibition of the virion release and a significant inhibition of IL-6, NF-kB and IFN-λ expression. These data suggest that p53 is an efficient target for new therapies against the virus and that MDM2 inhibitors deserve to be further investigated in this field.
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Affiliation(s)
- Giada Lodi
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Fabio Casciano
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy,Interdepartmental Research Center for the Study of Multiple Sclerosis and Inflammatory and Degenerative Diseases of the Nervous System, University of Ferrara, Ferrara, Italy
| | - Arianna Romani
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialistic Hospital, Riyadh, Saudi Arabia
| | - Paola Secchiero
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Enrico Zauli
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Carolina Simioni
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Beltrami
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Mercedes Fernandez
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy,*Correspondence: Roberta Rizzo, ; Rebecca Voltan,
| | - Rebecca Voltan
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy,*Correspondence: Roberta Rizzo, ; Rebecca Voltan,
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19
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Zhou T, Gilliam NJ, Li S, Spaudau S, Osborn RM, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection.. [PMID: 36172120 PMCID: PMC9516852 DOI: 10.1101/2022.09.22.509123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hotspots were identified for DVG recombination and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single cell RNA-seq analysis indicated the IFN stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the NGS dataset from a published cohort study and observed significantly higher DVG amount and frequency in symptomatic patients than that in asymptomatic patients. Finally, we observed unusually high DVG frequency in one immunosuppressive patient up to 140 days after admitted to hospital due to COVID-19, first-time suggesting an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection.
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20
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Martín-Díaz RM, Cabrejas-Ugartondo J, Iglesias-López M, Chulvi-Calvo B, Vélez-Rodriguez D. Persistently positive PCR SARS-CoV-2 at low cycle threshold in an immunosuppressed patient. Braz J Infect Dis 2022; 26:102696. [PMID: 36037848 PMCID: PMC9393159 DOI: 10.1016/j.bjid.2022.102696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 12/27/2022] Open
Abstract
We describe the very prolonged course of the disease in an immunosuppressed patient with persistently positive PCR against SARS-CoV-2 with low cycle threshold for at least 114 days.
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Affiliation(s)
- Rosa-María Martín-Díaz
- Sureste Hospital, Department of Internal Medicine, Arganda del Rey, Madrid, Spain,Corresponding Author.
| | | | - Mar Iglesias-López
- Sureste Hospital, Department of Continuity Care, Arganda del Rey, Madrid, Spain
| | - Beatriz Chulvi-Calvo
- Sureste Hospital, Department of Internal Medicine, Arganda del Rey, Madrid, Spain
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Roggero PF, Calistri A, Palù G. On the intrinsic nature of viral pathogenesis: The assumption of a Darwinian paradigm to describe COVID-19 pandemic. Comput Struct Biotechnol J 2022; 20:5870-5872. [PMID: 36320938 PMCID: PMC9613777 DOI: 10.1016/j.csbj.2022.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Our hypothesis about evolution of the COVID-19 pandemic foresees an inverse relation between infectivity (R0) and lethality (L) of SARS-CoV-2. The above parameters are driven by a continuing mutation process granting the virus a clear survival advantage over virulence. For interpreting this relation we adopted a simple equation, R0 × L ≈ k, by which R0 and L depend upon a constant k, that corresponds to an intrinsic property of the viral species involved. The hypothesis was verified by following changes of the R0 and L terms of the formula in the different variants of SARS-CoV-2 that progressively appeared. A further validation came when the equation was applied to pandemic and epidemic influenza type A viruses, Ebola virus and measles virus. We believe this equation that considers virus biology in Darwinian terms could be extremely useful to better face infectious viral threats and validate virus-host molecular interactions relevant to viral pathogenesis.
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Affiliation(s)
- Pier Francesco Roggero
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy,Italian Medicines Agency, Via del Tritone 181, 00187 Rome, Italy,Corresponding author at: Department of Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy; Italian Medicines Agency, Via del Tritone 181, 00187, Rome, Italy
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