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Terada Y, Amarbayasgalan S, Matsuura Y, Kamitani W. Regulation viral RNA transcription and replication by higher-order RNA structures within the nsp1 coding region of MERS coronavirus. Sci Rep 2024; 14:19594. [PMID: 39179600 PMCID: PMC11343750 DOI: 10.1038/s41598-024-70601-5] [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: 02/08/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024] Open
Abstract
Coronavirus (CoV) possesses numerous functional cis-acting elements in its positive-strand genomic RNA. Although most of these RNA structures participate in viral replication, the functions of RNA structures in the genomic RNA of CoV in viral replication remain unclear. In this study, we investigated the functions of the higher-order RNA stem-loop (SL) structures SL5B, SL5C, and SL5D in the ORF1a coding region of Middle East respiratory syndrome coronavirus (MERS-CoV) in viral replication. Our approach, using reverse genetics of a bacterial artificial chromosome system, revealed that SL5B and SL5C play essential roles in the discontinuous transcription of MERS-CoV. In silico analyses predicted that SL5C interacts with a bulged stem-loop (BSL) in the 3' untranslated region, suggesting that the RNA structure of SL5C is important for viral RNA transcription. Conversely, SL5D did not affect transcription, but mediated the synthesis of positive-strand genomic RNA. Additionally, the RNA secondary structure of SL5 in the revertant virus of the SL5D mutant was similar to that of the wild-type, indicating that the RNA structure of SL5D can finely tune RNA replication in MERS-CoV. Our data indicate novel regulatory mechanisms of viral RNA transcription and replication by higher-order RNA structures in the MERS-CoV genomic RNA.
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Affiliation(s)
- Yutaka Terada
- Laboratory of Clinical Research on Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Vaccine Research and Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sodbayasgalan Amarbayasgalan
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research (CiDER), Suita, Japan
- Research Institute for Microbial Diseases (RIMD), Suita, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Japan
| | - Wataru Kamitani
- Laboratory of Clinical Research on Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Maebashi, Japan.
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Trifonova I, Korsun N, Madzharova I, Velikov P, Alexsiev I, Grigorova L, Voleva S, Yordanova R, Ivanov I, Tcherveniakova T, Christova I. Prevalence and clinical impact of mono- and co-infections with endemic coronaviruses 229E, OC43, NL63, and HKU-1 during the COVID-19 pandemic. Heliyon 2024; 10:e29258. [PMID: 38623185 PMCID: PMC11016702 DOI: 10.1016/j.heliyon.2024.e29258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
Introduction Endemic human coronaviruses (eHCoVs) are found worldwide and usually result in mild to moderate upper respiratory tract infections. They can lead to more severe illnesses such as croup, bronchiolitis, and pneumonia in vulnerable populations. During the coronavirus disease 2019 (COVID-19) pandemic, information on HCoV prevalence and incidence and clinical impact of co-infections of HCoV with SARS-CoV-2 was lacking. Objectives Thus, this study aimed to determine the prevalence and clinical significance of infections caused by eHCoVs during the COVID-19 pandemic in Bulgaria. Methods From January 2021 to December 2022, nasopharyngeal swabs of patients with acute upper or lower respiratory tract infections were tested for 17 respiratory viruses using multiplex real-time polymerase chain reaction assays. The clinical data and laboratory parameters of patients infected with respiratory viruses were analysed. Results Of the 1375 patients screened, 24 (1.7 %) were positive for HCoVs, and 197 (14.3 %) were positive for eight other seasonal respiratory viruses. Five (0.7 %) of 740 patients positive for SARS-CoV-2 were co-infected with eHCoVs. Co-infected patients had a mean C-reactive protein level of 198.5 ± 2.12 mg/mL and a mean oxygen saturation of 82 ± 2.8 mmHg, while those in patients co-infected with SARS-CoV-2 and other respiratory viruses were 61.8 mg/mL and 92.8 ± 4.6 mmHg, respectively (p < 0.05). Pneumonia was diagnosed in 63.3 % of patients with HCoV infection and 6 % of patients positive for other seasonal respiratory viruses (p < 0.05). Patients with SARS-CoV-2 mono-infection stayed in hospital for an average of 5.8 ± 3.7 days, whereas the average hospital stay of patients with eHCoV and SARS-CoV-2 co-infection was 9 ± 1.4 days (p < 0.05). Conclusion These findings indicate the low prevalence of eHCoVs and low co-infection rate between eHCoVs and SARS-CoV-2 during the COVID-19 pandemic in Bulgaria. Despite their low incidence, such mixed infections can cause severe signs that require oxygen therapy and longer hospital stays, underlining the need for targeted testing of severe COVID-19 cases to identify potential co-infections.
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Affiliation(s)
- I. Trifonova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - N. Korsun
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - I. Madzharova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - P. Velikov
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Alexsiev
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - L. Grigorova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - S. Voleva
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - R. Yordanova
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Ivanov
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - T. Tcherveniakova
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Christova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
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Kesika P, Thangaleela S, Sisubalan N, Radha A, Sivamaruthi BS, Chaiyasut C. The Role of the Nuclear Factor-Kappa B (NF-κB) Pathway in SARS-CoV-2 Infection. Pathogens 2024; 13:164. [PMID: 38392902 PMCID: PMC10892479 DOI: 10.3390/pathogens13020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
COVID-19 is a global health threat caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a significant increase in morbidity and mortality. The present review discusses nuclear factor-kappa B (NF-κB) activation and its potential therapeutical role in treating COVID-19. COVID-19 pathogenesis, the major NF-κB pathways, and the involvement of NF-κB in SARS-CoV-2 have been detailed. Specifically, NF-κB activation and its impact on managing COVID-19 has been discussed. As a central player in the immune and inflammatory responses, modulating NF-κB activation could offer a strategic avenue for managing SARS-CoV-2 infection. Understanding the NF-κB pathway's role could aid in developing treatments against SARS-CoV-2. Further investigations into the intricacies of NF-κB activation are required to reveal effective therapeutic strategies for managing and combating the SARS-CoV-2 infection and COVID-19.
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Affiliation(s)
- Periyanaina Kesika
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (N.S.)
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Subramanian Thangaleela
- Institute of Biotechnology, Department of Medical Biotechnology and Integrative Physiology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
| | - Natarajan Sisubalan
- Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (N.S.)
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Arumugam Radha
- Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | | | - Chaiyavat Chaiyasut
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
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Park H, Kim KR, Huh HJ, Yoon Y, Park E, Cho J, Lee J, Lee J, Kim JH, Kim YJ. Complications of the Central Nervous System in Pediatric Patients With Common Cold Coronavirus Infection During 2014-2019. J Korean Med Sci 2023; 38:e358. [PMID: 38013644 PMCID: PMC10681840 DOI: 10.3346/jkms.2023.38.e358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/31/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND In pediatric patients, the common cold coronavirus (ccCoV) usually causes mild respiratory illness. There are reports of coronavirus causing central nervous system (CNS) infection in experimental animal models. Some immunocompromised patients have also been reported to have fatal CNS infections with ccCoV. The aim of this study was to investigate the clinical characteristics of CNS complications related to ccCoV infection. METHODS From January 2014 to December 2019, a retrospective analysis was performed of medical records from hospitalized patients under 19 years of age whose ccCoV was detected through polymerase chain reaction in respiratory specimens. The CNS complications were defined as clinically diagnosed seizure, meningitis, encephalopathy, and encephalitis. RESULTS A total of 436 samples from 420 patients were detected as ccCoV. Among the 420 patients, 269 patients were immunocompetent and 151 patients were immunocompromised. The most common type of ccCoV was OC43 (52% in immunocompetent, 37% in immunocompromised). CNS complications were observed in 9.4% (41/436). The most common type of CNS complication was the fever-provoked seizure under pre-existing neurologic disease (42% in immunocompetent and 60% in immunocompromised patients). Among patients with CNS complications, two immunocompetent patients required intensive care unit admission due to encephalitis. Three patients without underlying neurological disease started anti-seizure medications for the first time at this admission. There was no death related to ccCoV infection. CONCLUSION ccCoV infection may cause severe clinical manifestations such as CNS complications or neurologic sequelae, even in previously healthy children.
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Affiliation(s)
- Hwanhee Park
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung-Ran Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonsun Yoon
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Esther Park
- Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joongbum Cho
- Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Hye Kim
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yae-Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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de Almeida MT, Barbosa AP, Bomfim CG, Visnardi AB, Vinces TC, Ceroni A, Durigon EL, Guzzo CR. Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development. J Immunol Methods 2023; 522:113558. [PMID: 37704125 DOI: 10.1016/j.jim.2023.113558] [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: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped, plus-stranded RNA virus responsible for the Coronavirus Disease 2019 (COVID-19). Patients infected with COVID-19 may be asymptomatic or have symptoms ranging from mild manifestations to severe cases of the disease that could lead to death. The SARS-CoV-2 genome encodes 4 structural proteins, including the Spike protein (S), the Nucleocapsid protein (N), Membrane protein (M) and, the Envelope protein (E). The N protein forms a major component of the ribonucleoprotein complex within the virus particle and play a vital role in its transcription and replication. Nevertheless, the S protein was the most important protein in the development of vaccines against COVID-19. However, the decrease in number of registered immunizations against the disease and the rapid drop in neutralizing antibody titers together with looser preventive measures for virus transmission, favored the rapid appearance of new variants of concerns (VOCs) that primarily show mutations in the S protein. This fact makes the N protein a good candidate for the development of diagnostic tests, due to its stability, amino acid conservation, high immunogenicity, and the smaller likelihood of mutation. With the aim of developing a new diagnostic kit based on the N protein, we evaluated the humoral response in female Wistar rats against this target. Three constructions of the N protein were used to inoculate the animals: the full-length protein (Cfull), the N- (NTD), and the C-terminal (CTD) portion of the protein. The immunizations induced the animal's immune response, with specific polyclonal IgG antibodies against the Cfull protein and its fragments. There were not non-specific bind to the protein used as negative control. Anti-Cfull antibodies demonstrated high efficiency in binding to the NTD protein and the antibodies present in the anti-CTD and anti-NTD sera have recognized the Cfull protein, but they were not able to recognize the NTD and CTD proteins, respectively. Our results indicate an efficient protocol for obtaining high antibody titers against the N recombinant protein of SARS-CoV-2 and its fragments highlighting the Cfull protein, which can be used in the development of new diagnostic kits.
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Affiliation(s)
| | - Ana Paula Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Camila Gasque Bomfim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Aline Biazola Visnardi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tania Churasacari Vinces
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre Ceroni
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Tambe LAM, Mathobo P, Munzhedzi M, Bessong PO, Mavhandu-Ramarumo LG. Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review. Viruses 2023; 15:2146. [PMID: 38005824 PMCID: PMC10675249 DOI: 10.3390/v15112146] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Centre for Global Health Equity, School of Medicine, 1400 University Ave, Charlottesville, VA 22903, USA
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
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George U, George O, Oguzie J, Osasona O, Motayo B, Kamani J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C. Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria. Virus Res 2023; 334:199174. [PMID: 37467933 PMCID: PMC10392604 DOI: 10.1016/j.virusres.2023.199174] [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: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.
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Affiliation(s)
- Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | | | - Judith Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwadamilola Osasona
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde Motayo
- Department of Medical Microbiology, Federal Medical Centre, Abeokuta, Nigeria
| | - Joshua Kamani
- Parasitology Division National Veterinary Research Institute NVRI PMB 01, Vom, Plateau state Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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Rogers JH, Hawes SE, Wolf CR, Hughes JP, Englund JA, Starita LM, Chu HY. Care-seeking correlates of acute respiratory illness among sheltered adults experiencing homelessness in Seattle, WA, 2019: a community-based cross-sectional study. Front Public Health 2023; 11:1090148. [PMID: 37408748 PMCID: PMC10319010 DOI: 10.3389/fpubh.2023.1090148] [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: 11/07/2022] [Accepted: 05/15/2023] [Indexed: 07/07/2023] Open
Abstract
Objective Multifarious barriers to accessing healthcare services among people experiencing homelessness (PEH) lead to delays in seeking care for acute infections, including those caused by respiratory viruses. PEH are at high risk of acute respiratory illness (ARI)-related complications, especially in shelter settings that may facilitate virus spread, yet data characterizing healthcare utilization for ARI episodes among sheltered PEH remained limited. Methods We conducted a cross-sectional study of viral respiratory infection among adult residents at two homeless shelters in Seattle, Washington between January and May 2019. We assessed factors associated with seeking medical care for ARI via self-report. We collected illness questionnaires and nasal swabs were tested for respiratory viruses by reverse transcription quantitative real-time PCR (RT-qPCR). Results We observed 825 encounters from 649 unique participants; 241 (29.2%) encounters reported seeking healthcare for their ARI episode. Seasonal influenza vaccine receipt (adjusted prevalence ratio [aPR] 1.39, 95% CI 1.02-1.88), having health insurance (aPR 2.77, 95% CI 1.27-6.02), chronic lung conditions (aPR 1.55, 95% CI 1.12-2.15), and experiencing influenza-like-illness symptoms (aPR 1.63, 95% CI 1.20 - 2.20) were associated with increased likelihood of seeking care. Smoking (aPR 0.65, 95% CI 0.45-0.92) was associated with decreased likelihood of seeking care. Discussion Findings suggest that care seeking for viral respiratory illness among PEH may be supported by prior engagement with primary healthcare services. Strategies to increase healthcare utilization may lead to earlier detection of respiratory viruses.
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Affiliation(s)
- Julia H. Rogers
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Stephen E. Hawes
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Caitlin R. Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
| | - James P. Hughes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Janet A. Englund
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Seattle Children’s Research Institute, University of Washington, Seattle, WA, United States
| | - Lea M. Starita
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
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Devaux CA, Fantini J. Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies. Pathogens 2023; 12:713. [PMID: 37242383 PMCID: PMC10220573 DOI: 10.3390/pathogens12050713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.
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Affiliation(s)
- Christian A. Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM Institut Hospitalo-Universitaire—Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Jacques Fantini
- Aix-Marseille Université, INSERM UMR_S 1072, 13015 Marseille, France
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10
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Lotti V, Lagni A, Diani E, Sorio C, Gibellini D. Crosslink between SARS-CoV-2 replication and cystic fibrosis hallmarks. Front Microbiol 2023; 14:1162470. [PMID: 37250046 PMCID: PMC10213757 DOI: 10.3389/fmicb.2023.1162470] [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: 02/09/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
SARS-CoV-2, the etiological cause of the COVID-19 pandemic, can cause severe illness in certain at-risk populations, including people with cystic fibrosis (pwCF). Nevertheless, several studies indicated that pwCF do not have higher risks of SARS-CoV-2 infection nor do they demonstrate worse clinical outcomes than those of the general population. Recent in vitro studies indicate cellular and molecular processes to be significant drivers in pwCF lower infection rates and milder symptoms than expected in cases of SARS-CoV-2 infection. These range from cytokine releases to biochemical alterations leading to morphological rearrangements inside the cells associated with CFTR impairment. Based on available data, the reported low incidence of SARS-CoV-2 infection among pwCF is likely a result of several variables linked to CFTR dysfunction, such as thick mucus, IL-6 reduction, altered ACE2 and TMPRSS2 processing and/or functioning, defective anions exchange, and autophagosome formation. An extensive analysis of the relation between SARS-CoV-2 infection and pwCF is essential to elucidate the mechanisms involved in this lower-than-expected infection impact and to possibly suggest potential new antiviral strategies.
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Affiliation(s)
- Virginia Lotti
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Anna Lagni
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Erica Diani
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Claudio Sorio
- General Pathology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Davide Gibellini
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
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11
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Castillo G, Mora-Díaz JC, Breuer M, Singh P, Nelli RK, Giménez-Lirola LG. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023; 327:199078. [PMID: 36813239 PMCID: PMC9944649 DOI: 10.1016/j.virusres.2023.199078] [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: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Mary Breuer
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.
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12
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Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022; 15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.
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Affiliation(s)
| | - Snježana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
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13
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Arsenal of nanobodies shows broad-spectrum neutralization against SARS-CoV-2 variants of concern in vitro and in vivo in hamster models. Commun Biol 2022; 5:933. [PMID: 36085335 PMCID: PMC9461429 DOI: 10.1038/s42003-022-03866-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The nanobodies were collectively shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across existing VoCs; wide-ranging epitopic and mechanistic diversity and high and broad in vitro neutralization potencies. A select set of Fc-fused nanobodies showed high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a potential therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to combat multiple SARS-CoV-2 variants. Isolation and extensive characterization of a collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies show broad neutralization efficacies in vitro and in vivo in a hamster model of SARS-CoV-2 infection.
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14
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Lin Q, Lu C, Hong Y, Li R, Chen J, Chen W, Chen J. Animal models for studying coronavirus infections and developing antiviral agents and vaccines. Antiviral Res 2022; 203:105345. [PMID: 35605699 PMCID: PMC9122840 DOI: 10.1016/j.antiviral.2022.105345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 01/17/2023]
Abstract
In addition to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2 has become the third deadly coronavirus that infects humans and causes the new coronavirus disease (COVID-19). COVID-19 has already caused more than six million deaths worldwide and it is likely the biggest pandemic of this century faced by mankind. Although many studies on SARS-CoV-2 have been conducted, a detailed understanding of SARS-CoV-2 and COVID-19 is still lacking. Animal models are indispensable for studying its pathogenesis and developing vaccines and antivirals. In this review, we analyze animal models of coronavirus infections and explore their applications on antivirals and vaccines.
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Affiliation(s)
- Qisheng Lin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Chunni Lu
- Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Monash University, Clayton, Victoria 3168, Australia
| | - Yuqi Hong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Jinding Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
| | - Jianxin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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15
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Ning T, Liu S, Xu J, Yang Y, Zhang N, Xie S, Min L, Zhang S, Zhu S, Wang Y. Potential intestinal infection and faecal-oral transmission of human coronaviruses. Rev Med Virol 2022; 32:e2363. [PMID: 35584273 PMCID: PMC9348496 DOI: 10.1002/rmv.2363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/25/2022] [Accepted: 05/06/2022] [Indexed: 01/08/2023]
Abstract
Human coronaviruses (HCoVs) were first described in 1960s for patients experiencing common cold. Since then, increasing number of HCoVs have been discovered, including those causing severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the circulating coronavirus disease 2019 (COVID‐19), which can cause fatal respiratory disease in humans on infection. HCoVs are believed to spread mainly through respiratory droplets and close contact. However, studies have shown that a large proportion of patients with HCoV infection develop gastrointestinal (GI) symptoms, and many patients with confirmed HCoV infection have shown detectable viral RNA in their faecal samples. Furthermore, multiple in vitro and in vivo animal studies have provided direct evidence of intestinal HCoV infection. These data highlight the nature of HCoV GI infection and its potential faecal‐oral transmission. Here, we summarise the current findings on GI manifestations of HCoVs. We also discuss how HCoV GI infection might occur and the current evidence to establish the occurrence of faecal‐oral transmission.
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Affiliation(s)
- Tingting Ning
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Si Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Junxuan Xu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Yi Yang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Nan Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Sian Xie
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, China
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16
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Geanes ES, LeMaster C, Fraley ER, Khanal S, McLennan R, Grundberg E, Selvarangan R, Bradley T. Cross-reactive antibodies elicited to conserved epitopes on SARS-CoV-2 spike protein after infection and vaccination. Sci Rep 2022; 12:6496. [PMID: 35444221 PMCID: PMC9019795 DOI: 10.1038/s41598-022-10230-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is a novel betacoronavirus that caused coronavirus disease 2019 and has resulted in millions of deaths worldwide. Novel coronavirus infections in humans have steadily become more common. Understanding antibody responses to SARS-CoV-2, and identifying conserved, cross-reactive epitopes among coronavirus strains could inform the design of vaccines and therapeutics with broad application. Here, we determined that individuals with previous SARS-CoV-2 infection or vaccinated with the Pfizer-BioNTech BNT162b2 vaccine produced antibody responses that cross-reacted with related betacoronaviruses. Moreover, we designed a peptide-conjugate vaccine with a conserved SARS-CoV-2 S2 spike epitope, immunized mice and determined cross-reactive antibody binding to SARS-CoV-2 and other related coronaviruses. This conserved spike epitope also shared sequence homology to proteins in commensal gut microbiota and could prime immune responses in humans. Thus, SARS-CoV-2 conserved epitopes elicit cross-reactive immune responses to both related coronaviruses and host bacteria that could serve as future targets for broad coronavirus therapeutics and vaccines.
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Affiliation(s)
- Eric S Geanes
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Cas LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elizabeth R Fraley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rangaraj Selvarangan
- Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy, Kansas City, MO, USA
| | - Todd Bradley
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO, USA. .,Department of Pediatrics, University of Missouri- Kansas City, Kansas City, MO, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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17
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Designing AbhiSCoVac - A single potential vaccine for all ‘corona culprits’: Immunoinformatics and immune simulation approaches. J Mol Liq 2022; 351:118633. [PMID: 35125571 PMCID: PMC8801591 DOI: 10.1016/j.molliq.2022.118633] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
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18
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He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M, Su S. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell 2022; 185:1117-1129.e8. [PMID: 35298912 PMCID: PMC9942426 DOI: 10.1016/j.cell.2022.02.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Xin Hou
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.,These authors contributed equally
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijian He
- Agricultural College, Jinhua Polytechnic, Jinhua 320017, China
| | - Wei Si
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqing Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Xing
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Meng Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, the United States
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Wenjie Gong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Deyin Guo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Senior authors,Correspondence: Shuo Su (); Mang Shi (); and Edward C. Holmes ()
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
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19
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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20
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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21
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Characterization of SARS-CoV-2-specific humoral immunity and its potential applications and therapeutic prospects. Cell Mol Immunol 2022; 19:150-157. [PMID: 34645940 PMCID: PMC8513558 DOI: 10.1038/s41423-021-00774-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing pandemic that poses a great threat to human health worldwide. As the humoral immune response plays essential roles in disease occurrence and development, understanding the dynamics and characteristics of virus-specific humoral immunity in SARS-CoV-2-infected patients is of great importance for controlling this disease. In this review, we summarize the characteristics of the humoral immune response after SARS-CoV-2 infection and further emphasize the potential applications and therapeutic prospects of SARS-CoV-2-specific humoral immunity and the critical role of this immunity in vaccine development. Notably, serological antibody testing based on the humoral immune response can guide public health measures and control strategies; however, it is not recommended for population surveys in areas with very low prevalence. Existing evidence suggests that asymptomatic individuals have a weaker immune response to SARS-CoV-2 infection, whereas SARS-CoV-2-infected children have a more effective humoral immune response than adults. The correlations between antibody (especially neutralizing antibody) titers and protection against SARS-CoV-2 reinfection should be further examined. In addition, the emergence of cross-reactions among different coronavirus antigens in the development of screening technology and the risk of antibody-dependent enhancement related to SARS-CoV-2 vaccination should be given further attention.
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22
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Li CX, Noreen S, Zhang LX, Saeed M, Wu PF, Ijaz M, Dai DF, Maqbool I, Madni A, Akram F, Naveed M, Li JH. A critical analysis of SARS-CoV-2 (COVID-19) complexities, emerging variants, and therapeutic interventions and vaccination strategies. Biomed Pharmacother 2022; 146:112550. [PMID: 34959116 PMCID: PMC8673752 DOI: 10.1016/j.biopha.2021.112550] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/11/2023] Open
Abstract
Coronavirus is a family of viruses that can cause diseases such as the common cold, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). The universal outbreak of coronavirus disease 2019 (COVID-19) caused by SARS coronaviruses 2 (SARS-CoV-2) has become a global pandemic. The β-Coronaviruses, which caused SARS-CoV-2 (COVID-19), have spread in more than 213 countries, infected over 81 million people, and caused more than 1.79 million deaths. COVID-19 symptoms vary from mild fever, flu to severe pneumonia in severely ill patients. Difficult breathing, acute respiratory distress syndrome (ARDS), acute kidney disease, liver damage, and multi-organ failure ultimately lead to death. Researchers are working on different pre-clinical and clinical trials to prevent this deadly pandemic by developing new vaccines. Along with vaccines, therapeutic intervention is an integral part of healthcare response to address the ongoing threat posed by COVID-19. Despite the global efforts to understand and fight against COVID-19, many challenges need to be addressed. This article summarizes the current pandemic, different strains of SARS-CoV-2, etiology, complexities, surviving medications of COVID-19, and so far, vaccination for the treatment of COVID-19.
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Affiliation(s)
- Chang-Xing Li
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China
| | - Sobia Noreen
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Li-Xue Zhang
- School of Medicine, Northwest Minzu University, Lanzhou 730030, China
| | - Muhammad Saeed
- The Cholistan University of Veterinary and Animal Sciences, Bahawalpur 6300, Pakistan
| | - Pei-Feng Wu
- School of Medicine, Northwest Minzu University, Lanzhou 730030, China
| | - Muhammad Ijaz
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan
| | - Dong-Fang Dai
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China
| | - Irsah Maqbool
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Asadullah Madni
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Faizan Akram
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Muhammad Naveed
- Department of Clinical Pharmacy, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
| | - Jian-Hua Li
- Department of Human Anatomy, Medical College of Qinghai University, 810000 Xining, China.
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23
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Schaeffer R, Temeeyasen G, Hause BM. Alphacoronaviruses Are Common in Bats in the Upper Midwestern United States. Viruses 2022; 14:v14020184. [PMID: 35215778 PMCID: PMC8877427 DOI: 10.3390/v14020184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Bats are a reservoir for coronaviruses (CoVs) that periodically spill over to humans, as evidenced by severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. A collection of 174 bat samples originating from South Dakota, Minnesota, Iowa, and Nebraska submitted for rabies virus testing due to human exposure were analyzed using a pan-coronavirus PCR. A previously partially characterized CoV, Eptesicus bat CoV, was identified in 12 (6.9%) samples by nested RT-PCR. Six near-complete genomes were determined. Genetic analysis found a high similarity between all CoV-positive samples, Rocky Mountain bat CoV 65 and alphacoronavirus HCQD-2020 recently identified in South Korea. Phylogenetic analysis of genome sequences showed EbCoV is closely related to bat CoV HKU2 and swine acute diarrhea syndrome CoV; however, topological incongruences were noted for the spike gene that was more closely related to porcine epidemic diarrhea virus. Similar to some alphaCoVs, a novel gene, ORF7, was discovered downstream of the nucleocapsid, whose protein lacked similarity to known proteins. The widespread circulation of EbCoV with similarities to bat viruses that have spilled over to swine warrants further surveillance.
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24
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Abstract
The coronaviruses belong to the family Coronaviridae in the order Nidovirales. CoVs are found globally and infect a variety of animals, causing illnesses that range from gastrointestinal tract infections, encephalitis and demyelination; and can be fatal. Humans coronaviruses (hCoVs) have traditionally been associated with self-limiting upper respiratory tract infections and gastrointestinal tract infections. In recent years, however, it has become increasingly evident that the hCoVs can cause more severe lower respiratory tract infections such as bronchitis, pneumonia and even acute respiratory distress syndrome (ARDS), and can lead to death. Seven CoVs are known to infect humans, with the four “common cold” CoVs circulating globally on a yearly basis. The remaining three are more pathogenic and have resulted in outbreaks with high mortality rates. This review focussed on the three pathogenic CoVs.
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25
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Bartlow AW, Stromberg ZR, Gleasner CD, Hu B, Davenport KW, Jakhar S, Li PE, Vosburg M, Garimella M, Chain PSG, Erkkila TH, Fair JM, Mukundan H. Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000811. [PMID: 36962439 PMCID: PMC10022352 DOI: 10.1371/journal.pgph.0000811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
Abstract
Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.
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Affiliation(s)
- Andrew W Bartlow
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Zachary R Stromberg
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cheryl D Gleasner
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Karen W Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shailja Jakhar
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Po-E Li
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Molly Vosburg
- Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America
| | - Madhavi Garimella
- Medical Associates of Northern New Mexico, Los Alamos, New Mexico, United States of America
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tracy H Erkkila
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jeanne M Fair
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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26
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Immunological Characterization of HIV and SARS-CoV-2 Coinfected Young Individuals. Cells 2021; 10:cells10113187. [PMID: 34831410 PMCID: PMC8618616 DOI: 10.3390/cells10113187] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/03/2021] [Accepted: 11/13/2021] [Indexed: 01/11/2023] Open
Abstract
While the risk of SARS-CoV-2 infection and/or COVID-19 disease progression in the general population has been largely assessed, its impact on HIV-positive individuals remains unclear. We present clinical and immunological data collected in a cohort of HIV-infected young individuals during the first wave of COVID-19 pandemic. SARS-CoV-2 RNA, virus-specific antibodies, as well as the expression of factors involved in the anti-viral immune response were analyzed. Moreover, we set up an in vitro coinfection assay to study the mechanisms correlated to the coinfection process. Our results did not show any increased risk of severe COVID-19 in HIV-positive young individuals. In those subjects who contracted SARS-CoV-2 infection, an increase in IL-10 expression and production was observed. Furthermore, in the in vitro coinfection assay, we revealed a reduction in SARS-CoV-2 replication associated to an upregulation of IL-10. We speculate that IL-10 could play a crucial role in the course of SARS-CoV-2 infection in HIV-positive individuals. These results might help defining clinical management of HIV/SARS-CoV-2 co-infected young individuals, or putative indications for vaccination schedules in this population.
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27
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Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J. Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol 2021; 12:755599. [PMID: 34691006 PMCID: PMC8529330 DOI: 10.3389/fmicb.2021.755599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Research Institute of Public Heath, Nankai University, Tianjin, China
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28
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Gao H, Zhang Y, Jiang H, Hu X, Zhang Y, Zhou X, Zhong F, Lin C, Li J, Luo J, Zhang J. Crystal structures of human coronavirus NL63 main protease at different pH values. Acta Crystallogr F Struct Biol Commun 2021; 77:348-355. [PMID: 34605439 PMCID: PMC8488857 DOI: 10.1107/s2053230x21009523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022] Open
Abstract
Human coronavirus NL63 (HCoV-NL63), which belongs to the genus Alphacoronavirus, mainly infects children and the immunocompromized and is responsible for a series of clinical manifestations, including cough, fever, rhinorrhoea, bronchiolitis and croup. HCoV-NL63, which was first isolated from a seven-month-old child in 2004, has led to infections worldwide and accounts for 10% of all respiratory illnesses caused by etiological agents. However, effective antivirals against HCoV-NL63 infection are currently unavailable. The HCoV-NL63 main protease (Mpro), also called 3C-like protease (3CLpro), plays a vital role in mediating viral replication and transcription by catalyzing the cleavage of replicase polyproteins (pp1a and pp1ab) into functional subunits. Moreover, Mpro is highly conserved among all coronaviruses, thus making it a prominent drug target for antiviral therapy. Here, four crystal structures of HCoV-NL63 Mpro in the apo form at different pH values are reported at resolutions of up to 1.78 Å. Comparison with Mpro from other human betacoronaviruses such as SARS-CoV-2 and SARS-CoV reveals common and distinct structural features in different genera and extends knowledge of the diversity, function and evolution of coronaviruses.
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Affiliation(s)
- Hongxia Gao
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, People’s Republic of China
| | - Yuting Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
| | - Xiaohui Hu
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
| | - Yuting Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
| | - Xuelan Zhou
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, Jiangxi 341000, People’s Republic of China
| | - Fanglin Zhong
- Shenzhen Crystalo Biopharmaceutical Co. Ltd, Shenzhen, Guangdong 518118, People’s Republic of China
- Jiangxi Jmerry Biopharmaceutical Co. Ltd, Ganzhou, Jiangxi 341000, People’s Republic of China
| | - Cheng Lin
- Shenzhen Crystalo Biopharmaceutical Co. Ltd, Shenzhen, Guangdong 518118, People’s Republic of China
- Jiangxi Jmerry Biopharmaceutical Co. Ltd, Ganzhou, Jiangxi 341000, People’s Republic of China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, Jiangxi 341000, People’s Republic of China
| | - Jun Luo
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, People’s Republic of China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi 330031, People’s Republic of China
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29
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Kong D, Zheng Y, Hu L, Chen J, Wu H, Teng Z, Zhou Y, Qiu Q, Lu Y, Pan H. Epidemiological and co-infection characteristics of common human coronaviruses in Shanghai, 2015-2020: a retrospective observational study. Emerg Microbes Infect 2021; 10:1660-1668. [PMID: 34350810 PMCID: PMC8381891 DOI: 10.1080/22221751.2021.1965498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The coronavirus disease (COVID-19) pandemic is a major challenge worldwide. However, the epidemic potential of common human coronaviruses (HCoVs) remains unclear. This study aimed to determine the epidemiological and co-infection characteristics of common HCoVs in individuals with influenza-like illness (ILI) and severe acute respiratory infection (SARI). This retrospective, observational, multicentre study used data collected from patients admitted to nine sentinel hospitals with ILI and SARI from January 2015 through December 2020 in Shanghai, China. We prospectively tested patients for a total of 22 respiratory pathogens using multi-real-time polymerase chain reaction. Of the 4541 patients tested, 40.37% (1833/4541) tested positive for respiratory pathogens and 3.59% (163/4541) tested positive for common HCoVs. HCoV infection was more common in the non-endemic season for respiratory pathogens (odds ratio: 2.33, 95% confidence interval: 1.64–3.31). HCoV-OC43 (41.72%, 68/163) was the most common type of HCoV detected. The co-infection rate was 31.29% (51/163) among 163 HCoV-positive cases, with HCoV-229E (53.13%, 17/32), the HCoV type that was most frequently associated with co-infection. Respiratory pathogens responsible for co-infections with HCoVs included parainfluenza virus, rhinovirus/enterovirus, influenza A virus, and adenovirus. Furthermore, we identified one patient co-infected with HCoV-OC43 and HCoV-NL63/HKU1. The prevalence of common HCoVs remains low in ILI/SARI cases, in Shanghai. However, the seasonal pattern of HCoVs may be opposite to that of other respiratory pathogens. Moreover, HCoVs are likely to co-exist with specific respiratory pathogens. The potential role of co-infections with HCoVs and other pathogenic microorganisms in infection and pathogenesis of ILI and SARI warrants further study.
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Affiliation(s)
- Dechuan Kong
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yaxu Zheng
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China.,Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Jian Chen
- Department of Logistics Support, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Huanyu Wu
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Zheng Teng
- Institute of Pathogen Examination, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yanqiu Zhou
- Institute of Pathogen Examination, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Qi Qiu
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Hao Pan
- Institute of Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
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30
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Palma M. Perspectives on passive antibody therapy and peptide-based vaccines against emerging pathogens like SARS-CoV-2. Germs 2021; 11:287-305. [PMID: 34422699 DOI: 10.18683/germs.2021.1264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/25/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022]
Abstract
The current epidemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raising awareness of the need to act faster when dealing with new pathogens. Exposure to an emerging pathogen generates an antibody response that can be used for preventing and treating the infection. These antibodies might have a high specificity to a target, few side effects, and are useful in the absence of an effective vaccine for treating immunocompromised individuals. The approved antibodies against the receptor-binding domain (RBD) of the viral spike protein of SARS-CoV-2 (e.g., regdanvimab, bamlanivimab, etesevimab, and casirivimab/imdevimab) have been selected from the antibody repertoire of B cells from convalescent patients using flow cytometry, next-generation sequencing, and phage display. This encourages use of these techniques especially phage display, because it does not require expensive types of equipment and can be performed on the lab bench, thereby making it suitable for labs with limited resources. Also, the antibodies in blood samples from convalescent patients can be used to screen pre-made peptide libraries to identify epitopes for vaccine development. Different types of vaccines against SARS-CoV-2 have been developed, including inactivated virus vaccines, mRNA-based vaccines, non-replicating vector vaccines, and protein subunits. mRNA vaccines have numerous advantages over existing vaccines, such as efficacy, ease of manufacture, safety, and cost-effectiveness. Additionally, epitope vaccination may constitute an attractive strategy to induce high levels of antibodies against a pathogen and phages might be used as immunogenic carriers of such peptides. This is a point worth considering further, as phage-based vaccines have been shown to be safe in clinical trials and phages are easy to produce and tolerate high temperatures. In conclusion, identification of the antibody repertoire of recovering patients, and the epitopes they recognize, should be an attractive alternative option for developing therapeutic and prophylactic antibodies and vaccines against emerging pathogens.
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Affiliation(s)
- Marco Palma
- PhD, Independent researcher, Calle San Jose, Torrevieja, 03181, Spain
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31
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Zhang Z, Zeng E, Zhang L, Wang W, Jin Y, Sun J, Huang S, Yin W, Dai J, Zhuang Z, Chen Z, Sun J, Zhu A, Li F, Cao W, Li X, Shi Y, Gan M, Zhang S, Wei P, Huang J, Zhong N, Zhong G, Zhao J, Wang Y, Shao W, Zhao J. Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. Cell Discov 2021; 7:65. [PMID: 34385423 PMCID: PMC8359631 DOI: 10.1038/s41421-021-00302-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/02/2021] [Indexed: 01/08/2023] Open
Abstract
The current COVID-19 pandemic, caused by SARS-CoV-2, poses a serious public health threat. Effective therapeutic and prophylactic treatments are urgently needed. Angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS-CoV-2, which binds to the receptor binding domain (RBD) of SARS-CoV-2 spike protein. Here, we developed recombinant human ACE2-Fc fusion protein (hACE2-Fc) and a hACE2-Fc mutant with reduced catalytic activity. hACE2-Fc and the hACE2-Fc mutant both efficiently blocked entry of SARS-CoV-2, SARS-CoV, and HCoV-NL63 into hACE2-expressing cells and inhibited SARS-CoV-2 S protein-mediated cell-cell fusion. hACE2-Fc also neutralized various SARS-CoV-2 strains with enhanced infectivity including D614G and V367F mutations, as well as the emerging SARS-CoV-2 variants, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.1 (Kappa), and B.1.617.2 (Delta), demonstrating its potent and broad-spectrum antiviral effects. In addition, hACE2-Fc proteins protected HBE from SARS-CoV-2 infection. Unlike RBD-targeting neutralizing antibodies, hACE2-Fc treatment did not induce the development of escape mutants. Furthermore, both prophylactic and therapeutic hACE2-Fc treatments effectively protected mice from SARS-CoV-2 infection, as determined by reduced viral replication, weight loss, histological changes, and inflammation in the lungs. The protection provided by hACE2 showed obvious dose-dependent efficacy in vivo. Pharmacokinetic data indicated that hACE2-Fc has a relative long half-life in vivo compared to soluble ACE2, which makes it an excellent candidate for prophylaxis and therapy for COVID-19 as well as for SARS-CoV and HCoV-NL63 infections.
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Grants
- This work is supported by the grants from The National Key Research and Development Program of China (2018YFC1200100, 2018ZX10301403, 2020YFC0842400), National Natural Science Foundation of China (82025001), Ministries of Science and Technology, Education of Guangdong province (2020B1111330001, 2020A111128008, 2020B1111320003, 2020A0505100063, 2020KZDZX1158, B195001248, 2020A1515010911, 2019TX05Y120), National Key Technology R&D Program (2018YFC1311900), Guangdong Science and Technology Foundation (2019B030316028), Guangzhou Institute of Respiratory Health Open Project (Funds provided by China Evergrande Group, 2020GIRHHMS07 and 2020GIRHHMS07), State Key Laboratory of Respiratory Disease (SKLRD-QN-201912 and SKLRD-Z-202007), Guangzhou Medical University High-level University Innovation Team Training Program (Guangzhou Medical University released [2017] No.159).
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Affiliation(s)
- Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Eric Zeng
- Nanjing Legend Biotech Co., Ltd, Nanjing, Jiangsu, China
| | - Lu Zhang
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Weiming Wang
- Nanjing GenScript Biotech Co., Ltd, NanJing, Jiangsu, China
| | - Yingkang Jin
- Pediatric Pulmonary Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiye Sun
- Nanjing GenScript Biotech Co., Ltd, NanJing, Jiangsu, China
| | - Shuxiang Huang
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Wenguang Yin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Weitao Cao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaobo Li
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Yongxia Shi
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Peilan Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jicheng Huang
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Guocai Zhong
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China.
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Weihui Shao
- Nanjing GenScript Biotech Co., Ltd, NanJing, Jiangsu, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou laboratory, Bio-island, Guangzhou, Guangdong, China.
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32
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Kalamar Ž, Markota A. Non-SARS-CoV-2 coronavirus severe acute respiratory failure. Minerva Anestesiol 2021; 88:84-85. [PMID: 34337926 DOI: 10.23736/s0375-9393.21.15977-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Žiga Kalamar
- Medical Intensive Care Unit, University Medical Centre Maribor, Maribor, Slovenia -
| | - Andrej Markota
- Medical Intensive Care Unit, University Medical Centre Maribor, Maribor, Slovenia
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33
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Kesheh MM, Hosseini P, Soltani S, Zandi M. An overview on the seven pathogenic human coronaviruses. Rev Med Virol 2021; 32:e2282. [PMID: 34339073 DOI: 10.1002/rmv.2282] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023]
Abstract
To date, seven human coronaviruses (HCoVs) have been detected: HCoV-NL63, HCoV-229E, HCoV-HKU1, HCoV-OC43, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2. Four of these viruses, including HCoV-NL63, -229E, -HKU1 and -OC43, usually cause mild-to-moderate respiratory diseases with a seasonal pattern. Since 2000, three new HCoVs have emerged with a significant mortality rate. Although SARS-CoV and MERS-CoV caused an epidemic in some countries, SARS-CoV-2 escalated into a pandemic. All HCoVs can cause severe complications in the elderly and immunocompromised individuals. The bat origin of HCoVs, the presence of intermediate hosts and the nature of their viral replication suggest that other new coronaviruses may emerge in the future. Despite the fact that all HCoVs share similarities in viral replication, they differ in their accessory proteins, incubation period and pathogenicity. This study aims to review these differences between the seven HCoVs.
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parastoo Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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34
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Sealy RE, Hurwitz JL. Cross-Reactive Immune Responses toward the Common Cold Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Mini-Review and a Murine Study. Microorganisms 2021; 9:1643. [PMID: 34442723 PMCID: PMC8398386 DOI: 10.3390/microorganisms9081643] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022] Open
Abstract
While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious morbidity and mortality in humans (coronavirus disease 2019, COVID-19), there is an enormous range of disease outcomes following virus exposures. Some individuals are asymptomatic while others succumb to virus infection within days. Presently, the factors responsible for disease severity are not fully understood. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to common cold human coronaviruses (HCoVs). Here, we describe previous literature and a new, murine study designed to examine cross-reactive immune responses between SARS-CoV-2 and common cold HCoVs (represented by prototypes OC43, HKU1, 229E, and NL63). Experimental results have been mixed. In SARS-CoV-2-unexposed humans, cross-reactive serum antibodies were identified toward nucleocapsid (N) and the spike subunit S2. S2-specific antibodies were in some cases associated with neutralization. SARS-CoV-2-unexposed humans rarely exhibited antibody responses to the SARS-CoV-2 spike subunit S1, and when naïve mice were immunized with adjuvanted S1 from either SARS-CoV-2 or common cold HCoVs, S1-specific antibodies were poorly cross-reactive. When humans were naturally infected with SARS-CoV-2, cross-reactive antibodies that recognized common cold HCoV antigens increased in magnitude. Cross-reactive T cells, like antibodies, were present in humans prior to SARS-CoV-2 exposures and increased following SARS-CoV-2 infections. Some studies suggested that human infections with common cold HCoVs afforded protection against disease caused by subsequent exposures to SARS-CoV-2. Small animal models are now available for the testing of controlled SARS-CoV-2 infections. Additionally, in the United Kingdom, a program of SARS-CoV-2 human challenge experiments has received regulatory approval. Future, controlled experimental challenge studies may better define how pre-existing, cross-reactive immune responses influence SARS-CoV-2 infection outcomes.
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Affiliation(s)
- Robert E. Sealy
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Julia L. Hurwitz
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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35
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Bhattacharya S, Agarwal S, Shrimali NM, Guchhait P. Interplay between hypoxia and inflammation contributes to the progression and severity of respiratory viral diseases. Mol Aspects Med 2021; 81:101000. [PMID: 34294412 PMCID: PMC8287505 DOI: 10.1016/j.mam.2021.101000] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023]
Abstract
History of pandemics is dominated by viral infections and specifically respiratory viral diseases like influenza and COVID-19. Lower respiratory tract infection is the fourth leading cause of death worldwide. Crosstalk between resultant inflammation and hypoxic microenvironment may impair ventilatory response of lungs. This reduces arterial partial pressure of oxygen, termed as hypoxemia, which is observed in a section of patients with respiratory virus infections including SARS-CoV-2 (COVID-19). In this review, we describe the interplay between inflammation and hypoxic microenvironment in respiratory viral infection and its contribution to disease pathogenesis.
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Affiliation(s)
- Sulagna Bhattacharya
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India; School of Biotechnology, Kalinga Institute of Industrial Technology, Orissa, India
| | - Sakshi Agarwal
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Nishith M Shrimali
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Prasenjit Guchhait
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India.
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36
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Guo W, Lakshminarayanan H, Rodriguez-Palacios A, Salata RA, Xu K, Draz MS. Glycan Nanostructures of Human Coronaviruses. Int J Nanomedicine 2021; 16:4813-4830. [PMID: 34290504 PMCID: PMC8289332 DOI: 10.2147/ijn.s302516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/22/2021] [Indexed: 12/18/2022] Open
Abstract
Human coronaviruses present a substantial global disease burden, causing damage to populations’ health, economy, and social well-being. Glycans are one of the main structural components of all microbes and organismic structures, including viruses—playing multiple essential roles in virus infection and immunity. Studying and understanding virus glycans at the nanoscale provide new insights into the diagnosis and treatment of viruses. Glycan nanostructures are considered potential targets for molecular diagnosis, antiviral therapeutics, and the development of vaccines. This review article describes glycan nanostructures (eg, glycoproteins and glycolipids) that exist in cells, subcellular structures, and microbes. We detail the structure, characterization, synthesis, and functions of virus glycans. Furthermore, we describe the glycan nanostructures of different human coronaviruses, such as human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), severe acute respiratory syndrome-associated coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), human coronavirus HKU1 (HCoV-HKU1), the Middle East respiratory syndrome-associated coronavirus (MERS-CoV), and how glycan nanotechnology can be useful to prevent and combat human coronaviruses infections, along with possibilities that are not yet explored.
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Affiliation(s)
- Wanru Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Harini Lakshminarayanan
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA.,Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Research and Education Institute, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| | - Robert A Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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37
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Barge S, Jade D, Gosavi G, Talukdar NC, Borah J. In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). Eur J Pharm Sci 2021; 162:105820. [PMID: 33775827 PMCID: PMC7997164 DOI: 10.1016/j.ejps.2021.105820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/02/2021] [Accepted: 03/21/2021] [Indexed: 12/24/2022]
Abstract
A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a respiratory infection out broke in December 2019 in Wuhan, Hubei province, China, resulted in pandemic conditions worldwide. COVID-19 spread swiftly around the world over with an alert of an emergency for an adequate drug. Therefore, in this research, we repurposed the FDA-approved medicines to find the prominent drug used to cure the COVID infected patients. We performed homology modeling of the transmembrane serine protease 2 (TMPRSS2), responsible for the viral entry. The prediction of the transmembrane region and the Conserved Domain in TMPRSS2 protein was made for docking. 4182 FDA-approved compounds from the ZINC database were downloaded and used for the calculation of physicochemical properties. Two thousand eight hundred fifteen screened compounds were used for molecular docking against the modelled protein structure. From which top hit compounds based on binding energy were extracted. At 1st site pose, ZINC3830554 showed the highest binding energy -12.91kcal/mol by forming Salt Bridge at LYS143, Hydrogen bond at ALA8, VAL45, HIS47, SER142, ASN277, ASN359, and TRP363. The hydrophobic Interactions at PHE3, LEU4, ALA7, ALA8, ALA139, PRO197, and PHE266. In the 2nd site pose, ZINC203686879 shows the highest binding energy (-12.56 kcal/mol) and forms a hydrophobic interaction with VAL187, VAL189, HIS205, LYS301, GLN347, TRP370 and hydrogen bond was at GLY300, THR302, GLN347, SER350 residues. These hit compounds were subjected to stability checks between the protein-ligand complex through the dynamics simulation (MD), and binding free energy was calculated through the Molecular Mechanics energies combined with Poisson-Boltzmann (MM/PBSA) method. We hope that hit compounds would be an efficient inhibitor that can block the TMPRSS2 activity and resist the entry of the SARS-CoV-2 virus into targeted human cells by reducing the virus's infectivity and transmissibility.
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Affiliation(s)
- Sagar Barge
- Chemical Biology Lab I, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-35, Assam, India
| | - Dhananjay Jade
- JSS College of Pharmacy, Department of Pharmaceutical Chemistry, Ooty, 643001, Tamilnadu, India
| | - Gokul Gosavi
- Institute of Plant Protection Chinese Academy of Agricultural Sciences, Beijing, China
| | - Narayan Chandra Talukdar
- Chemical Biology Lab I, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-35, Assam, India.; Assam Down Town University, Panikhaiti, Guwahati, Assam 781006, India
| | - Jagat Borah
- Chemical Biology Lab I, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati-35, Assam, India..
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38
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Prezioso C, Moens U, Oliveto G, Brazzini G, Piacentini F, Frasca F, Viscido A, Scordio M, Guerrizio G, Rodio DM, Pierangeli A, d’Ettorre G, Turriziani O, Antonelli G, Scagnolari C, Pietropaolo V. KI and WU Polyomavirus in Respiratory Samples of SARS-CoV-2 Infected Patients. Microorganisms 2021; 9:microorganisms9061259. [PMID: 34207902 PMCID: PMC8229673 DOI: 10.3390/microorganisms9061259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been declared a global pandemic. Our goal was to determine whether co-infections with respiratory polyomaviruses, such as Karolinska Institutet polyomavirus (KIPyV) and Washington University polyomavirus (WUPyV) occur in SARS-CoV-2 infected patients. Oropharyngeal swabs from 150 individuals, 112 symptomatic COVID-19 patients and 38 healthcare workers not infected by SARS-CoV-2, were collected from March 2020 through May 2020 and tested for KIPyV and WUPyV DNA presence. Of the 112 SARS-CoV-2 positive patients, 27 (24.1%) were co-infected with KIPyV, 5 (4.5%) were positive for WUPyV, and 3 (2.7%) were infected simultaneously by KIPyV and WUPyV. Neither KIPyV nor WUPyV DNA was detected in samples of healthcare workers. Significant correlations were found in patients co-infected with SARS-CoV-2 and KIPyV (p < 0.05) and between SARS-CoV-2 cycle threshold values and KIPyV, WUPyV and KIPyV and WUPyV concurrently detected (p < 0.05). These results suggest that KIPyV and WUPyV may behave as opportunistic respiratory pathogens. Additional investigations are needed to understand the epidemiology and the prevalence of respiratory polyomavirus in COVID-19 patients and whether KIPyV and WUPyV could potentially drive viral interference or influence disease outcomes by upregulating SARS-CoV-2 replicative potential.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-Degenerative Pathologies, 00163 Rome, Italy
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Giuseppe Oliveto
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Gabriele Brazzini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Francesca Piacentini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Federica Frasca
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Agnese Viscido
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Mirko Scordio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Giuliana Guerrizio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Donatella Maria Rodio
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Alessandra Pierangeli
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
| | - Ombretta Turriziani
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
| | - Guido Antonelli
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Carolina Scagnolari
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, “Sapienza” University of Rome, 00161 Rome, Italy; (G.O.); (F.F.); (A.V.); (M.S.); (G.G.); (D.M.R.); (A.P.); (O.T.); (G.A.); (C.S.)
- Istituto Pasteur Italia, 00161 Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (C.P.); (G.B.); (F.P.); (G.d.)
- Microbiology and Virology Unit, “Sapienza” University Hospital “Policlinico Umberto I”, 00161 Rome, Italy
- Correspondence: ; Tel.: +39-06-49914439
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39
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Variants in ACE2; potential influences on virus infection and COVID-19 severity. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 90:104773. [PMID: 33607284 PMCID: PMC7886638 DOI: 10.1016/j.meegid.2021.104773] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
The third pandemic of coronavirus infection, called COVID-19 disease, was first detected in November 2019th. Various determinants of disease progression such as age, sex, virus mutations, comorbidity, lifestyle, host immune response, and genetic background variation have caused clinical variability of COVID-19. The causative agent of COVID-19 is an enveloped coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that invades host cells using an endocytic pathway. The SARS-CoV-2 spike protein is the main viral protein that contributes to the fusion of the virus particle to the host cell through angiotensin-converting enzyme 2 (ACE2). The highly conserved expression of ACE2 is found in various animals, which indicates its pivotal physiological function. The ACE2 has a crucial role in vascular, renal, and myocardial physiology. Genetic factors contributing to the outcome of SARS-CoV-2 infection are unknown; however, variants in the specific sites of ACE2 gene could be regarded as a main genetic risk factor for COVID-19. Given that ACE2 is the main site for virus landing on host cells, the effect of amino acid sequences of ACE2 on host susceptibility to COVID-19 seems reasonable. It would likely have a substantial role in the occurrence of a wide range of clinical symptoms. Several ACE2 variants can affect the protein stability, influencing the interaction between spike protein and ACE2 through imposing conformational changes while some other variants are known to cause a decrease or an increase in the ligand-receptor affinity. The other variations are located at the proteolytic cleavage site, which can influence virus infection; because soluble ACE2 can act as a decoy receptor for virus and decrease virus intake by cell surface ACE2. Notably, polymorphisms of regulatory and non-coding regions such as promoter in ACE2, can play crucial role in different expression levels of ACE2 among different individuals. Many studies should be performed to investigate the involvement of ACE2 polymorphism with susceptibility to COVID-19. Herein, we discuss some reported associations between variants of ACE2 and COVID-19 in details. In addition, the mode of action of ACE2 and its role in SARS-CoV-2 infection are highlighted which is followed by addressing the effects of several ACE2 variants on its protein stability, viral tropism or ligand-receptor affinity, secondary and tertiary structure or protein conformation, proteolytic cleavage site, and finally inter-individual clinical variability in COVID-19. The polymorphisms of regulatory regions of ACE2 and their effect on expression levels of ACE2 are also provided in this review. Such studies can improve the prediction of the affinity of mutant ACE2 variations with spike protein, and help the biopharmaceutical industry to design effective approaches for recombinant hACE2 therapy and vaccination of COVID-19 disease.
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Zhang Y, Su L, Chen Y, Yu S, Zhang D, Mao H, Fang L. Etiology and clinical characteristics of SARS-CoV-2 and other human coronaviruses among children in Zhejiang Province, China 2017-2019. Virol J 2021; 18:89. [PMID: 33931105 PMCID: PMC8085659 DOI: 10.1186/s12985-021-01562-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND A novel coronavirus (SARS-CoV-2) emerging has put global public health institutes on high alert. Little is known about the epidemiology and clinical characteristics of human coronaviruses infections in relation to infections with other respiratory viruses. METHODS From February 2017 to December 2019, 3660 respiratory samples submitted to Zhejiang Children Hospital with acute respiratory symptoms were tested for four human coronaviruses RNA by a novel two-tube multiplex reverse transcription polymerase chain reaction assays. Samples were also screened for the occurrence of SARS-CoV-2 by reverse transcription-PCR analysis. RESULTS Coronavirus RNAs were detected in 144 (3.93%) specimens: HCoV-HKU1 in 38 specimens, HCoV-NL63 in 62 specimens, HCoV-OC43 in 38 specimens and HCoV-229E in 8 specimens. Genomes for SARS-CoV-2 were absent in all specimens by RT-PCR analysis during the study period. The majority of HCoV infections occurred during fall months. No significant differences in gender, sample type, year were seen across species. 37.5 to 52.6% of coronaviruses detected were in specimens testing positive for other respiratory viruses. Phylogenic analysis identified that Zhejiang coronaviruses belong to multiple lineages of the coronaviruses circulating in other countries and areas. CONCLUSION Common HCoVs may have annual peaks of circulation in fall months in the Zhejiang province, China. Genetic relatedness to the coronaviruses in other regions suggests further surveillance on human coronaviruses in clinical samples are clearly needed to understand their patterns of activity and role in the emergence of novel coronaviruses.
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Affiliation(s)
- Yanjun Zhang
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China.,Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Lingxuan Su
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yin Chen
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Sicong Yu
- Department of Laboratory, School of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Dan Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Haiyan Mao
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China
| | - Lei Fang
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Bincheng Road, Hangzhou, 310051, China.
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Lee J, Bong C, Lim W, Bae PK, Abafogi AT, Baek SH, Shin YB, Bak MS, Park S. Fast and Easy Disinfection of Coronavirus-Contaminated Face Masks Using Ozone Gas Produced by a Dielectric Barrier Discharge Plasma Generator. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:339-344. [PMID: 37566380 PMCID: PMC7931622 DOI: 10.1021/acs.estlett.1c00089] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 05/10/2023]
Abstract
During the COVID-19 pandemic, face masks have become limited in stock. Most of sterilization methods are not applicable for eliminating virus from face masks without compromising the filtration efficiency of the masks. In this study, using a human coronavirus (HCoV-229E) as a surrogate for SARS-CoV-2 contamination on KF94 face masks, we show that the virus loses its infectivity with a 4 log reduction when exposed for 10 s to 120 ppm ozone gas produced by a dielectric barrier discharge plasma generator. Scanning electron microscopy, particulate filtration efficiency (PFE), and inhalation resistance tests revealed that there was no detectable structural or functional deterioration observed in the electrocharged filter layer of Korea Filter (KF) 94 masks even after their excessive exposure to ozone. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) showed decreases in amplification efficiency of HCoV-229E RNA recovered from masks exposed to ozone, indicating the damage to the RNA by the ozone treatment. Our results demonstrate that the plasma generator rapidly disinfects contaminated face masks at least five times without compromising filtration efficiency.
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Affiliation(s)
- Jinyeop Lee
- School of Mechanical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
| | - Cheolwoo Bong
- School of Mechanical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
| | - Wanyoung Lim
- Department of Biomedical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
| | - Pan Kee Bae
- BioNano Health Guard Research Center
(H-GUARD), Daejeon 34141, Korea
| | | | - Seung Ho Baek
- School of Mechanical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
| | - Yong-Beom Shin
- BioNano Health Guard Research Center
(H-GUARD), Daejeon 34141, Korea
- Bionanotechnology Research Center, Korea
Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Bioengineering, KRIBB
School, University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Moon Soo Bak
- School of Mechanical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
- Biomedical Institute for Convergence at SKKU (BICS),
Sungkyunkwan University, Suwon 16419,
Korea
| | - Sungsu Park
- School of Mechanical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
- Department of Biomedical Engineering,
Sungkyunkwan University, Suwon 16419,
Korea
- Biomedical Institute for Convergence at SKKU (BICS),
Sungkyunkwan University, Suwon 16419,
Korea
- Institute of Quantum Biophysics (iQB),
Sungkyunkwan University, Suwon 16419,
Korea
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Chakravarty D, Das Sarma J. Murine-β-coronavirus-induced neuropathogenesis sheds light on CNS pathobiology of SARS-CoV2. J Neurovirol 2021; 27:197-216. [PMID: 33547593 PMCID: PMC7864135 DOI: 10.1007/s13365-021-00945-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/29/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023]
Abstract
The pandemic caused by SARS-CoV-2 has caused widespread infection and significant mortality across the globe. Combined virology perspective of SARS-CoV-2 with a deep-rooted understanding of pathophysiological and immunological processes underlying the clinical manifestations of COVID-19 is of prime importance. The characteristic symptom of COVID-19 is respiratory distress with diffused alveolar damage, but emerging evidence suggests COVID-19 might also have neurologic consequences. Dysregulated homeostasis in the lungs has proven to be fatal, but one cannot ignore that the inability to breathe might be due to defects in the respiratory control center of the brainstem. While the mechanism of pulmonary distress has been documented in the literature, awareness of neurological features and their pathophysiology is still in the nascent state. This review makes references to the neuro-immune axis and neuro-invasive potential of SARS-CoV and SARS-CoV2, as well as the prototypic H-CoV strains in human brains. Simultaneously, considerable discussion on relevant experimental evidence of mild to severe neurological manifestations of fellow neurotropic murine-β-CoVs (m-CoVs) in the mouse model will help understand the underpinning mechanisms of Neuro-COVID. In this review, we have highlighted the neuroimmunopathological processes in murine CoVs. While MHV infection in mice and SARS-CoV-2 infection in humans share numerous parallels, there are critical differences in viral recognition and viral entry. These similarities are highlighted in this review, while differences have also been emphasized. Though CoV-2 Spike does not favorably interact with murine ACE2 receptor, modification of murine SARS-CoV2 binding domain or development of transgenic ACE-2 knock-in mice might help in mediating consequential infection and understanding human CoV2 pathogenesis in murine models. While a global animal model that can replicate all aspects of the human disease remains elusive, prior insights and further experiments with fellow m-β-CoV-induced cause-effect experimental models and current human COVID-19 patients data may help to mitigate the SARS-CoV-2-induced multifactorial multi-organ failure.
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Affiliation(s)
- Debanjana Chakravarty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Haringhata, 741246, Mohanpur, India
| | - Jayasri Das Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Haringhata, 741246, Mohanpur, India.
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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González N, Marquès M, Domingo JL. Respiratory viruses in foods and their potential transmission through the diet: A review of the literature. ENVIRONMENTAL RESEARCH 2021; 195:110826. [PMID: 33529649 PMCID: PMC7963685 DOI: 10.1016/j.envres.2021.110826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 05/04/2023]
Abstract
Respiratory viruses are the main agents causing respiratory tract diseases. Nowadays, coronaviruses - and specifically, SARS-CoV-1, MERS-CoV and SARS-CoV-2 - are the principal responsible for the major epidemic outbreaks of the 21st century. The major routes of transmission for respiratory viruses - including coronaviruses - are via direct and indirect contacts. However, transmission through contaminated foods has not been extensively assessed. The present paper was aimed at reviewing scientific data on the transmission of respiratory viruses through potentially contaminated foods. While the current data seem to suggest that this route of transmission is not likely to occur, in order to increase the knowledge on this issue further investigations are still clearly necessary for a more complete prevention of the risks. Studies should include fresh produce and cooked foods. Anyway, prevention measures and good hygienic practices for both consumers and workers are mandatory when handling and cooking foods.
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Affiliation(s)
- Neus González
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain.
| | - Montse Marquès
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
| | - José L Domingo
- Laboratory of Toxicology and Environmental Health, School of Medicine, Universitat Rovira I Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
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Sermet-Gaudelus I, Temmam S, Huon C, Behillil S, Gajdos V, Bigot T, Lurier T, Chrétien D, Backovic M, Delaunay-Moisan A, Donati F, Albert M, Foucaud E, Mesplées B, Benoist G, Faye A, Duval-Arnould M, Cretolle C, Charbit M, Aubart M, Auriau J, Lorrot M, Kariyawasam D, Fertitta L, Orliaguet G, Pigneur B, Bader-Meunier B, Briand C, Enouf V, Toubiana J, Guilleminot T, van der Werf S, Leruez-Ville M, Eloit M. Prior infection by seasonal coronaviruses, as assessed by serology, does not prevent SARS-CoV-2 infection and disease in children, France, April to June 2020. Euro Surveill 2021; 26:2001782. [PMID: 33797390 PMCID: PMC8017906 DOI: 10.2807/1560-7917.es.2021.26.13.2001782] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/07/2021] [Indexed: 01/10/2023] Open
Abstract
BackgroundChildren have a low rate of COVID-19 and secondary severe multisystem inflammatory syndrome (MIS) but present a high prevalence of symptomatic seasonal coronavirus infections.AimWe tested if prior infections by seasonal coronaviruses (HCoV) NL63, HKU1, 229E or OC43 as assessed by serology, provide cross-protective immunity against SARS-CoV-2 infection.MethodsWe set a cross-sectional observational multicentric study in pauci- or asymptomatic children hospitalised in Paris during the first wave for reasons other than COVID (hospitalised children (HOS), n = 739) plus children presenting with MIS (n = 36). SARS-CoV-2 antibodies directed against the nucleoprotein (N) and S1 and S2 domains of the spike (S) proteins were monitored by an in-house luciferase immunoprecipitation system assay. We randomly selected 69 SARS-CoV-2-seropositive patients (including 15 with MIS) and 115 matched SARS-CoV-2-seronegative patients (controls (CTL)). We measured antibodies against SARS-CoV-2 and HCoV as evidence for prior corresponding infections and assessed if SARS-CoV-2 prevalence of infection and levels of antibody responses were shaped by prior seasonal coronavirus infections.ResultsPrevalence of HCoV infections were similar in HOS, MIS and CTL groups. Antibody levels against HCoV were not significantly different in the three groups and were not related to the level of SARS-CoV-2 antibodies in the HOS and MIS groups. SARS-CoV-2 antibody profiles were different between HOS and MIS children.ConclusionPrior infection by seasonal coronaviruses, as assessed by serology, does not interfere with SARS-CoV-2 infection and related MIS in children.
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Affiliation(s)
- Isabelle Sermet-Gaudelus
- Institut Necker Enfants Malades, INSERM U 1171, Paris, France
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Paris, France
- These authors contributed equally to the work
| | - Sarah Temmam
- These authors contributed equally to the work
- Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France
| | - Christèle Huon
- Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France
| | - Sylvie Behillil
- Molecular Genetics of RNA Viruses, Department of Virology, CNRS UMR3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Vincent Gajdos
- Hôpital Antoine Beclere, Clamart, France
- Centre for Research in Epidemiology and Population Health, INSERM UMR1018, Villejuif, France
| | - Thomas Bigot
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
- Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France
| | - Thibaut Lurier
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université de Lyon, INRAE, VetAgro Sup, Usc 1233 UR RS2GP, Marcy l'Etoile, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France
| | - Marija Backovic
- Unité de Virologie Structurale, Institut Pasteur, Département de Virologie, CNRS, UMR3569, Paris, France
| | - Agnès Delaunay-Moisan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Flora Donati
- Molecular Genetics of RNA Viruses, Department of Virology, CNRS UMR3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Mélanie Albert
- Molecular Genetics of RNA Viruses, Department of Virology, CNRS UMR3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Célia Cretolle
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Marina Charbit
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Mélodie Aubart
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Johanne Auriau
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | | | | | - Laura Fertitta
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Gilles Orliaguet
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Bénédicte Pigneur
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | | | | | - Vincent Enouf
- Plateforme de microbiologie mutualisée (P2M), Pasteur International Bioresources Network (PIBnet), Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, CNRS UMR3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Julie Toubiana
- Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Unité Biodiversité et Epidemiologie des Bacteries Pathogènes, Institut Pasteur, Paris, France
- Université de Paris, Paris, France
| | | | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, CNRS UMR3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | | | - Marc Eloit
- Ecole Nationale Vétérinaire d'Alfort, Maisons Alfort, France
- Pathogen Discovery Laboratory, Department of Virology, Institut Pasteur, Paris, France
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Stone NE, Jaramillo SA, Jones AN, Vazquez AJ, Martz M, Versluis LM, Raniere MO, Nunnally HE, Zarn KE, Nottingham R, Ng KR, Sahl JW, Wagner DM, Knudsen S, Settles EW, Keim P, French CT. Stenoparib, an Inhibitor of Cellular Poly(ADP-Ribose) Polymerase, Blocks Replication of the SARS-CoV-2 and HCoV-NL63 Human Coronaviruses In Vitro. mBio 2021; 12:e03495-20. [PMID: 33468703 PMCID: PMC7845641 DOI: 10.1128/mbio.03495-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/22/2020] [Indexed: 02/08/2023] Open
Abstract
By late 2020, the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had caused tens of millions of infections and over 1 million deaths worldwide. A protective vaccine and more effective therapeutics are urgently needed. We evaluated a new poly(ADP-ribose) polymerase (PARP) inhibitor, stenoparib, that recently advanced to phase II clinical trials for treatment of ovarian cancer, for activity against human respiratory coronaviruses, including SARS-CoV-2, in vitro Stenoparib exhibits dose-dependent suppression of SARS-CoV-2 multiplication and spread in Vero E6 monkey kidney and Calu-3 human lung adenocarcinoma cells. Stenoparib was also strongly inhibitory to the human seasonal respiratory coronavirus HCoV-NL63. Compared to remdesivir, which inhibits viral replication downstream of cell entry, stenoparib impedes entry and postentry processes, as determined by time-of-addition (TOA) experiments. Moreover, a 10 μM dosage of stenoparib-below the approximated 25.5 μM half-maximally effective concentration (EC50)-combined with 0.5 μM remdesivir suppressed coronavirus growth by more than 90%, indicating a potentially synergistic effect for this drug combination. Stenoparib as a stand-alone or as part of combinatorial therapy with remdesivir should be a valuable addition to the arsenal against COVID-19.IMPORTANCE New therapeutics are urgently needed in the fight against COVID-19. Repurposing drugs that are either already approved for human use or are in advanced stages of the approval process can facilitate more rapid advances toward this goal. The PARP inhibitor stenoparib may be such a drug, as it is currently in phase II clinical trials for the treatment of ovarian cancer and its safety and dosage in humans have already been established. Our results indicate that stenoparib possesses strong antiviral activity against SARS-CoV-2 and other coronaviruses in vitro. This activity appears to be based on multiple modes of action, where both pre-entry and postentry viral replication processes are impeded. This may provide a therapeutic advantage over many current options that have a narrower target range. Moreover, our results suggest that stenoparib and remdesivir in combination may be especially potent against coronavirus infection.
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Affiliation(s)
- Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Sierra A Jaramillo
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ashley N Jones
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Adam J Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Madison Martz
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Lora M Versluis
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Marlee O Raniere
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Haley E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Katherine E Zarn
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Roxanne Nottingham
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ken R Ng
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | | | - Erik W Settles
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Christopher T French
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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Vougogiannopoulou K, Corona A, Tramontano E, Alexis MN, Skaltsounis AL. Natural and Nature-Derived Products Targeting Human Coronaviruses. Molecules 2021; 26:448. [PMID: 33467029 PMCID: PMC7831024 DOI: 10.3390/molecules26020448] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.
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Affiliation(s)
- Konstantina Vougogiannopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Michael N. Alexis
- Molecular Endocrinology Team, Inst of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Ave., 11635 Athens, Greece;
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
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Hu Y, Buehler MJ. Comparative Analysis of Nanomechanical Features of Coronavirus Spike Proteins and Correlation with Lethality and Infection Rate. MATTER 2021; 4:265-275. [PMID: 33163958 PMCID: PMC7605853 DOI: 10.1016/j.matt.2020.10.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/19/2020] [Accepted: 10/28/2020] [Indexed: 05/08/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) has spread rapidly around the world. Its causative virus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), enters human cells through the physical interaction between the receptor-binding domain (RBD) of its spike protein and the human cell receptor ACE2. Here, we provide a novel way of understanding coronavirus spike proteins, connecting their nanomechanical features, specifically their vibrational spectrum and quantitative measures of mobility, with virus lethality and infection rate. The key result of our work is that both the overall flexibility of upward RBD and the mobility ratio of RBDs in different conformations represent two significant factors that show a positive scaling with virus lethality and an inverse correlation with the infection rate. Our analysis shows that epidemiological virus properties can be linked directly to pure nanomechanical, vibrational aspects, offering an alternative way of screening new viruses and mutations, and potentially exploring novel ways to prevent infections from occurring.
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Affiliation(s)
- Yiwen Hu
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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The zoonotic potential of bat-borne coronaviruses. Emerg Top Life Sci 2020; 4:353-369. [PMID: 33258903 DOI: 10.1042/etls20200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Seven zoonoses - human infections of animal origin - have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.
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Abstract
Animal and human endemic coronaviruses have been known for decades, as has their capacity to re-infect. In the COVID-19 pandemic, it is key to reveal the factors that influence reinfection susceptibility. In this commentary, I provide a view on endemic animal and human coronaviruses and the correlates of protection to reinfection.
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Zhao X, Ding Y, Du J, Fan Y. 2020 update on human coronaviruses: One health, one world. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2020; 8:100043. [PMID: 33521622 PMCID: PMC7836940 DOI: 10.1016/j.medntd.2020.100043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/04/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023] Open
Abstract
Since human coronavirus (HCoVs) was first described in the 1960s, seven strains of respiratory human coronaviruses have emerged and caused human infections. After the emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), a pneumonia outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has represented a pandemic threat to global public health in the 21st century. Without effectively prophylactic and therapeutic strategies including vaccines and antiviral drugs, these three coronaviruses have caused severe respiratory syndrome and high case-fatality rates around the world. In this review, we detail the emergence event, origin and reservoirs of all HCoVs, compare the differences with regard to structure and receptor usage, and summarize therapeutic strategies for COVID-19 that cause severe pneumonia and global pandemic.
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Affiliation(s)
- Xinbin Zhao
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yuecheng Ding
- School of Public Health, Peking University, Beijing, 100871, China
| | - Jing Du
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
- Key Laboratory of Human Motion Analysis and Rehabilitation Technology of the Ministry of Civil Affairs, National Research Center for Rehabilitation Technical Aids, Beijing, 100176, China
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