1
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Mo Y, Lim LS, Ng SK. A systematic review on current approaches in bat virus discovered between 2018 and 2022. J Virol Methods 2024; 329:115005. [PMID: 39128772 DOI: 10.1016/j.jviromet.2024.115005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.
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Affiliation(s)
- Yaxin Mo
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Lee-Sim Lim
- School of Distance Education, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Siew Kit Ng
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia.
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2
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Patarca R, Haseltine WA. Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2. Int J Mol Sci 2024; 25:8012. [PMID: 39125583 PMCID: PMC11311688 DOI: 10.3390/ijms25158012] [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: 06/26/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions.
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Affiliation(s)
- Roberto Patarca
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
| | - William A. Haseltine
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
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3
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Martínez-Puchol S, Tarradas-Alemany M, Mejías-Molina C, Itarte M, Rusiñol M, Baliellas J, Abasolo N, Canela N, Monastiri A, López-Roig M, Serra-Cobo J, Abril JF, Bofill-Mas S. Target enrichment metaviromics enables comprehensive surveillance of coronaviruses in environmental and animal samples. Heliyon 2024; 10:e31556. [PMID: 38845944 PMCID: PMC11153099 DOI: 10.1016/j.heliyon.2024.e31556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
The COVID-19 pandemic has underscored the importance of understanding the role of animals in the transmission of coronaviruses (CoVs) and their impact on human health. A One Health approach, integrating human, animal, and environmental health, is essential for effective CoVs control. Next-generation sequencing has played a pivotal role in identifying and monitoring the evolution of novel CoVs strains, like SARS-CoV-2. However, viral occurrence and diversity studies in environmental and animal samples are challenging because of the complexity of viral communities and low abundance of viruses in these samples. Target enrichment sequencing (TES) has emerged as a valuable tool for investigating viral families in challenging samples. This approach involves the specific capture and enrichment of viral genomes using sequence-specific probes, thereby enhancing the efficiency of detection and characterization. In this study, we aimed to develop and validate a TES panel to study CoVs in various complex environmental and animal derived samples. The results demonstrated the panel's effectiveness in capturing and sequencing a wide diversity of CoVs providing valuable insights into their abundance and host diversity in urban wastewater, farm animal corpses lixiviates and bat guano samples. In sewage samples, CoVs were detected solely when TES was employed while in guano samples, sequencing of CoVs species was achieved in 2 out of 4 samples showing an almost three-logarithmic increase in the number of reads obtained in comparison with the untargeted approach. For animal lixiviates, only the TES application enabled the acquisition of CoVs reads. The information obtained can significantly contribute to early detection, surveillance, and control measures for CoVs, including viral discovery and potential spillover events. Additionally, this sequencing panel shows potential for studying other significant viral families and monitoring viral diversity in different animal populations.
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Vicerectorat de Recerca. Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Maria Tarradas-Alemany
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Computational Genomics Lab, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de l’Aigua (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de l’Aigua (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de l’Aigua (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | - Nerea Abasolo
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Catalonia, Spain
| | - Abir Monastiri
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBiO), Universitat de Barcelona, Catalonia, Spain
| | - Marc López-Roig
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBiO), Universitat de Barcelona, Catalonia, Spain
| | - Jordi Serra-Cobo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBiO), Universitat de Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Computational Genomics Lab, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de l’Aigua (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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4
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Paskey AC, Schully KL, Voegtly LJ, Arnold CE, Cer RZ, Frey KG, Blair PW, Clark DV, Ge H, Richards AL, Farris CM, Bishop-Lilly KA. A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens. Front Microbiol 2024; 15:1387208. [PMID: 38659991 PMCID: PMC11039911 DOI: 10.3389/fmicb.2024.1387208] [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: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Paul W. Blair
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Danielle V. Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Allen L. Richards
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Christina M. Farris
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
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5
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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6
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Habeebur‐Rahman SP, Noni V, Khan FAA, Tan C. Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo. Vet Med Sci 2023; 9:2634-2641. [PMID: 37658663 PMCID: PMC10650259 DOI: 10.1002/vms3.1251] [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: 02/07/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia. OBJECTIVES Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi). METHODS Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi-nested consensus RNA-dependent RNA polymerase consensus primers. RESULTS The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and Betacoronavirus (β-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats. CONCLUSIONS This study provides the first available data on CoVs circulating in P. lucasi.
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Affiliation(s)
- Sultana Parvin Habeebur‐Rahman
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Vaenessa Noni
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Faisal Ali Anwarali Khan
- Faculty of Resource Science and TechnologyUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
| | - Cheng‐Siang Tan
- Center for Tropical and Emerging DiseasesFaculty of Medicine and Health SciencesUniversiti Malaysia SarawakKota SamarahanSarawakMalaysia
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7
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Jones BD, Kaufman EJ, Peel AJ. Viral Co-Infection in Bats: A Systematic Review. Viruses 2023; 15:1860. [PMID: 37766267 PMCID: PMC10535902 DOI: 10.3390/v15091860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Co-infection is an underappreciated phenomenon in contemporary disease ecology despite its ubiquity and importance in nature. Viruses, and other co-infecting agents, can interact in ways that shape host and agent communities, influence infection dynamics, and drive evolutionary selective pressures. Bats are host to many viruses of zoonotic potential and have drawn increasing attention in their role as wildlife reservoirs for human spillover. However, the role of co-infection in driving viral transmission dynamics within bats is unknown. Here, we systematically review peer-reviewed literature reporting viral co-infections in bats. We show that viral co-infection is common in bats but is often only reported as an incidental finding. Biases identified in our study database related to virus and host species were pre-existing in virus studies of bats generally. Studies largely speculated on the role co-infection plays in viral recombination and few investigated potential drivers or impacts of co-infection. Our results demonstrate that current knowledge of co-infection in bats is an ad hoc by-product of viral discovery efforts, and that future targeted co-infection studies will improve our understanding of the role it plays. Adding to the broader context of co-infection studies in other wildlife species, we anticipate our review will inform future co-infection study design and reporting in bats. Consideration of detection strategy, including potential viral targets, and appropriate analysis methodology will provide more robust results and facilitate further investigation of the role of viral co-infection in bat reservoirs.
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Affiliation(s)
- Brent D. Jones
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | | | - Alison J. Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD 4111, Australia
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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8
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Huang X, Fu R, Qiao S, Zhang J, Xianyu Y. Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification. BIOSENSORS & BIOELECTRONICS: X 2023; 13:100289. [PMID: 36530849 PMCID: PMC9733970 DOI: 10.1016/j.biosx.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.
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Affiliation(s)
- Xucheng Huang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Ruijie Fu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Sai Qiao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jun Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yunlei Xianyu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
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9
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Kuchinski KS, Loos KD, Suchan DM, Russell JN, Sies AN, Kumakamba C, Muyembe F, Mbala Kingebeni P, Ngay Lukusa I, N’Kawa F, Atibu Losoma J, Makuwa M, Gillis A, LeBreton M, Ayukekbong JA, Lerminiaux NA, Monagin C, Joly DO, Saylors K, Wolfe ND, Rubin EM, Muyembe Tamfum JJ, Prystajecky NA, McIver DJ, Lange CE, Cameron ADS. Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats. eLife 2022; 11:e79777. [PMID: 36346652 PMCID: PMC9643004 DOI: 10.7554/elife.79777] [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: 04/26/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.
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Affiliation(s)
- Kevin S Kuchinski
- Department of Pathology and Laboratory Medicine, University of British ColumbiaVancouverCanada
- Public Health Laboratory, British Columbia Centre for Disease ControlVancouverCanada
| | - Kara D Loos
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
| | - Danae M Suchan
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
| | - Jennifer N Russell
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
| | - Ashton N Sies
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
| | | | | | - Placide Mbala Kingebeni
- Metabiota IncKinshasaDemocratic Republic of the Congo
- Institut National de Recherche BiomédicaleKinshasaDemocratic Republic of the Congo
| | | | - Frida N’Kawa
- Metabiota IncKinshasaDemocratic Republic of the Congo
| | | | - Maria Makuwa
- Metabiota IncKinshasaDemocratic Republic of the Congo
- Labyrinth Global Health IncSt. PetersburgUnited States
| | - Amethyst Gillis
- Metabiota IncSan FranciscoUnited States
- Development AlternativesWashingtonUnited States
| | | | | | - Nicole A Lerminiaux
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
| | - Corina Monagin
- Metabiota IncSan FranciscoUnited States
- One Health Institute, School of Veterinary Medicine, University of California, DavisDavisUnited States
| | - Damien O Joly
- MetabiotaNanaimoCanada
- Nyati Health ConsultingNanaimoCanada
| | - Karen Saylors
- Labyrinth Global Health IncSt. PetersburgUnited States
- Metabiota IncSan FranciscoUnited States
| | | | | | | | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British ColumbiaVancouverCanada
- Public Health Laboratory, British Columbia Centre for Disease ControlVancouverCanada
| | - David J McIver
- MetabiotaNanaimoCanada
- Institute for Global Health Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Christian E Lange
- Labyrinth Global Health IncSt. PetersburgUnited States
- MetabiotaNanaimoCanada
| | - Andrew DS Cameron
- Department of Biology, Faculty of Science, University of ReginaReginaCanada
- Institute for Microbial Systems and Society, Faculty of Science, University of ReginaReginaCanada
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10
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Kouhpayeh H. Evaluation of the diagnosis and treatment options for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Family Med Prim Care 2022; 11:4219-4227. [PMID: 36352961 PMCID: PMC9638654 DOI: 10.4103/jfmpc.jfmpc_1735_21] [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: 08/30/2021] [Revised: 02/07/2022] [Accepted: 03/16/2022] [Indexed: 11/04/2022] Open
Abstract
Viruses are non-living organisms that cause many problems for human societies annually. The outbreak of some dangerous viruses causing acute pneumonia has been the leading cause of death in the world. The epidemiological findings showed that the virus is developing different and dangerous species by creating new mutations, which makes it difficult to treat. The diagnosis and treatment of corona virus disease (COVID-19) has been one of the most important topics in the scientific community for the past 2 years. There are several diagnostic methods available for the detection of COVID-19 that are highly accurate and require less time. The use of some therapies such as remdesivir with basic therapy has shown high therapeutic effectiveness, but the therapeutic side effects such as decreased glomerular filtration rate, decreased lymphocyte count, respiratory failure, and increased blood creatinine levels in most treatments have been observed. The COVID-19 infection and the associated deaths are still very worrying, therefore, rapid diagnosis and timely management of this deadly infection and the necessary measures for eradicating COVID-19 are important.
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Affiliation(s)
- Hamidreza Kouhpayeh
- Tropical and Infectious Diseases Department, Zahedan University of Medical Sciences, Zahedan, Iran
- Zahedan University of Medical Sciences Research Center Department, Emam Ali Hospital, Zahedan, Iran
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11
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
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12
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Zhu F, Duong V, Lim XF, Hul V, Chawla T, Keatts L, Goldstein T, Hassanin A, Tu VT, Buchy P, Sessions OM, Wang LF, Dussart P, Anderson DE. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats. Viruses 2022; 14:v14020176. [PMID: 35215769 PMCID: PMC8877364 DOI: 10.3390/v14020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/04/2022] Open
Abstract
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
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Affiliation(s)
- Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Unité des Virus Émergents, (UVÉ: Aix-Marseille Univ-IRD 190-INSERM 1207), 13005 Marseille, France
| | - Tanu Chawla
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lucy Keatts
- Wildlife Conservation Society, Health Program, Bronx, NY 10460, USA;
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité, Sorbonne Université, MNHN, CNRS, EPHE, UA, 75005 Paris, France;
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam;
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - October M. Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne 3000, Australia
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
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13
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Martínez-Puchol S, Itarte M, Rusiñol M, Forés E, Mejías-Molina C, Andrés C, Antón A, Quer J, Abril JF, Girones R, Bofill-Mas S. Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don't miss the forest for the trees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149562. [PMID: 34391155 PMCID: PMC8349739 DOI: 10.1016/j.scitotenv.2021.149562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 05/07/2023]
Abstract
In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Josep F Abril
- Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona; Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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14
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Giles JR, Peel AJ, Wells K, Plowright RK, McCallum H, Restif O. Optimizing noninvasive sampling of a zoonotic bat virus. Ecol Evol 2021; 11:12307-12321. [PMID: 34594501 PMCID: PMC8462156 DOI: 10.1002/ece3.7830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Outbreaks of infectious viruses resulting from spillover events from bats have brought much attention to bat-borne zoonoses, which has motivated increased ecological and epidemiological studies on bat populations. Field sampling methods often collect pooled samples of bat excreta from plastic sheets placed under-roosts. However, positive bias is introduced because multiple individuals may contribute to pooled samples, making studies of viral dynamics difficult. Here, we explore the general issue of bias in spatial sample pooling using Hendra virus in Australian bats as a case study. We assessed the accuracy of different under-roost sampling designs using generalized additive models and field data from individually captured bats and pooled urine samples. We then used theoretical simulation models of bat density and under-roost sampling to understand the mechanistic drivers of bias. The most commonly used sampling design estimated viral prevalence 3.2 times higher than individual-level data, with positive bias 5-7 times higher than other designs due to spatial autocorrelation among sampling sheets and clustering of bats in roosts. Simulation results indicate using a stratified random design to collect 30-40 pooled urine samples from 80 to 100 sheets, each with an area of 0.75-1 m2, and would allow estimation of true prevalence with minimum sampling bias and false negatives. These results show that widely used under-roost sampling techniques are highly sensitive to viral presence, but lack specificity, providing limited information regarding viral dynamics. Improved estimation of true prevalence can be attained with minor changes to existing designs such as reducing sheet size, increasing sheet number, and spreading sheets out within the roost area. Our findings provide insight into how spatial sample pooling is vulnerable to bias for a wide range of systems in disease ecology, where optimal sampling design is influenced by pathogen prevalence, host population density, and patterns of aggregation.
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Affiliation(s)
- John R. Giles
- Department of EpidemiologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreMDUSA
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Alison J. Peel
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Hamish McCallum
- Environmental Futures Research InstituteGriffith UniversityBrisbaneQldAustralia
| | - Olivier Restif
- Disease Dynamics UnitDepartment of Veterinary MedicineUniversity of CambridgeCambridgeUK
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15
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Muzeniek T, Perera T, Siriwardana S, Bas D, Kaplan F, Öruc M, Becker-Ziaja B, Schwarz F, Premawansa G, Premawansa S, Perera I, Yapa W, Nitsche A, Kohl C. Detection of Alpha- and Betacoronaviruses in Miniopterus fuliginosus and Rousettus leschenaultii, two species of Sri Lankan Bats. Vaccines (Basel) 2021; 9:vaccines9060650. [PMID: 34203592 PMCID: PMC8232336 DOI: 10.3390/vaccines9060650] [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: 05/12/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 12/21/2022] Open
Abstract
Bats are known to be potential reservoirs of numerous human-pathogenic viruses. They have been identified as natural hosts for coronaviruses, causing Severe Acute Respiratory Syndrome (SARS) in humans. Since the emergence of SARS-CoV-2 in 2019 interest in the prevalence of coronaviruses in bats was newly raised. In this study we investigated different bat species living in a sympatric colony in the Wavul Galge cave (Koslanda, Sri Lanka). In three field sessions (in 2018 and 2019), 395 bats were captured (Miniopterus, Rousettus, Hipposideros and Rhinolophus spp.) and either rectal swabs or fecal samples were collected. From these overall 396 rectal swab and fecal samples, the screening for coronaviruses with nested PCR resulted in 33 positive samples, 31 of which originated from Miniopterus fuliginosus and two from Rousettus leschenaultii. Sanger sequencing and phylogenetic analysis of the obtained 384-nt fragment of the RNA-dependent RNA polymerase revealed that the examined M. fuliginosus bats excrete alphacoronaviruses and the examined R. leschenaultii bats excrete betacoronaviruses. Despite the sympatric roosting habitat, the coronaviruses showed host specificity and seemed to be limited to one species. Our results represent an important basis to better understand the prevalence of coronaviruses in Sri Lankan bats and may provide a basis for pursuing studies on particular bat species of interest.
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Affiliation(s)
- Therese Muzeniek
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Thejanee Perera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka;
| | - Sahan Siriwardana
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (S.P.); (I.P.); (W.Y.)
| | - Dilara Bas
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Fatimanur Kaplan
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Mizgin Öruc
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Beate Becker-Ziaja
- Robert Koch Institute, Centre for International Health Protection, Public Health Laboratory Support (ZIG 4), 13353 Berlin, Germany;
| | - Franziska Schwarz
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | | | - Sunil Premawansa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (S.P.); (I.P.); (W.Y.)
| | - Inoka Perera
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (S.P.); (I.P.); (W.Y.)
| | - Wipula Yapa
- IDEA (Identification of Emerging Agents) Laboratory, Department of Zoology and Environment Sciences, University of Colombo, Colombo 00300, Sri Lanka; (S.S.); (S.P.); (I.P.); (W.Y.)
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
| | - Claudia Kohl
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), 13353 Berlin, Germany; (T.M.); (D.B.); (F.K.); (M.Ö.); (F.S.); (A.N.)
- Correspondence: ; Tel.: +49-30-187-542-144
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16
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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17
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Tabibzadeh A, Esghaei M, Soltani S, Yousefi P, Taherizadeh M, Safarnezhad Tameshkel F, Golahdooz M, Panahi M, Ajdarkosh H, Zamani F, Karbalaie Niya MH. Evolutionary study of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an emerging coronavirus: Phylogenetic analysis and literature review. Vet Med Sci 2021; 7:559-571. [PMID: 33210477 PMCID: PMC7753621 DOI: 10.1002/vms3.394] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/12/2020] [Accepted: 10/25/2020] [Indexed: 12/22/2022] Open
Abstract
Since emerging coronaviruses have always become a human health concern globally especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV) and Middle East respiratory syndrome coronavirus and a novel coronavirus was introduced in Wuhan, China, in December 2019 (called SARS-CoV-2), many researchers focused on its epidemics, virological and clinical features. SARS-CoV-2 is classified as Betacoronaviruses genus and Sarbecovirus subgenus (lineage B). The virus shows a great similarity with SARS-CoV and bat SARS-like coronaviruses. In this study, we evaluate SARS-CoV-2 virus phylogeny and evolution by using current virus and related sequences.
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Affiliation(s)
- Alireza Tabibzadeh
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Maryam Esghaei
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Saber Soltani
- Department of VirologyFaculty of Public HealthTehran University of Medical SciencesTehranIran
| | - Parastoo Yousefi
- Department of VirologyFaculty of MedicineIran University of Medical SciencesTehranIran
| | - Mahsa Taherizadeh
- Department of VirologyRabies Research CenterPasteur Institute of IranTehranIran
| | | | - Mahsa Golahdooz
- Department of VirologyRabies Research CenterPasteur Institute of IranTehranIran
| | - Mahshid Panahi
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
| | - Farhad Zamani
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
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18
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Khade SM, Yabaji SM, Srivastava J. An update on COVID-19: SARS-CoV-2 life cycle, immunopathology, and BCG vaccination. Prep Biochem Biotechnol 2020; 51:650-658. [PMID: 33226885 DOI: 10.1080/10826068.2020.1848869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The causative agent of novel coronavirus disease (COVID-19) is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 possesses RNA as a genetic material with 79% of the match with the bat SARS-CoV genome, which became epidemic in 2002. The SARS-CoV-2 peripheral Spike-Fc protein binds specifically to the ACE2 receptors present on bronchial epithelial cells and alveolar pneumocytes to downmodulates its expression which leads to severe acute respiratory failure. The disease is super infectious from human to human and the symptoms are similar to flu. The old aged and immunocompromised population are severely affected, and healthcare providers globally applied various strategies for treatment including the repurposing of drugs including antimalarial drug, hydroxychloroquine and anti-viral drugs.Herein, we described the SARS-CoV-2 pandemic, immune responses, possible drug targets, vaccines under the trials and correlated the possibility of trained immunity induced by BCG vaccination over control of SARS-CoV-2 infection. The countries with constraint BCG vaccination policy are struggling badly compared to countries with BCG vaccination policy. The BCG vaccination policy supports either lowering the total number of COVID-19 cases or the increasing recovery rate.
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Affiliation(s)
- Shankar M Khade
- Department of Biosciences, Sri Sathya Sai University for Human Excellence, Kalaburgi, India
| | - Shivraj M Yabaji
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Jyoti Srivastava
- Department of Biosciences, Sri Sathya Sai University for Human Excellence, Kalaburgi, India
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19
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Jamshaid H, Zahid F, Din IU, Zeb A, Choi HG, Khan GM, Din FU. Diagnostic and Treatment Strategies for COVID-19. AAPS PharmSciTech 2020; 21:222. [PMID: 32748244 PMCID: PMC7398284 DOI: 10.1208/s12249-020-01756-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
The world is facing lockdown for the first time in decades due to the novel coronavirus COVID-19 (SARS-CoV-2) pandemic. This has led to massive global economic disruption, placed additional strain on local and global public health resources and, above all, threatened human health. We conducted a review of peer-reviewed and unpublished data, written in English, reporting on the current COVID-19 pandemic. This data includes previously used strategies against infectious disease, recent clinical trials and FDA-approved diagnostic and treatment strategies. The literature was obtained through a systematic search using PubMed, Web of Sciences, and FDA, NIH and WHO websites. Of the 98 references included in the review, the majority focused on pathogen and host targeting, symptomatic treatment and convalescent plasma utilization. Other sources investigated vaccinations in the pipeline for the possible prevention of COVID-19 infection. The results demonstrate various conventional as well as potentially advanced in vitro diagnostic approaches (IVD) for the diagnosis of COVID-19. Mixed results have been observed so far when utilising these approaches for the treatment of COVID-19 infection. Some treatments have been found highly effective in specific regions of the world while others have not altered the disease process. The responsiveness of currently available options is not conclusive. The novelty of this disease, the rapidity of its global outbreak and the unavailability of vaccines have contributed to the global public's fear. It is concluded that the exploration of a range of diagnostic and treatment strategies for the management of COVID-19 is the need of the hour.
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Affiliation(s)
- Humzah Jamshaid
- Department of Pharmacy, Nanomedicine Research Group, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fatima Zahid
- Department of Pharmacy, Nanomedicine Research Group, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Intisar Ud Din
- College of Resources and Environment, Huanzhong Agricultural University (Hazu), Wuhan, Hubei, China
| | - Alam Zeb
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Sector G-7/4, Islamabad, 44000, Pakistan
| | - Han Gon Choi
- College of Pharmacy & Institute of Pharmaceutical Science and Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
| | - Gul Majid Khan
- Department of Pharmacy, Nanomedicine Research Group, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Fakhar Ud Din
- Department of Pharmacy, Nanomedicine Research Group, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Evaluations of the serological test in the diagnosis of 2019 novel coronavirus (SARS-CoV-2) infections during the COVID-19 outbreak. Eur J Clin Microbiol Infect Dis 2020; 39:2271-2277. [PMID: 32681308 PMCID: PMC7367508 DOI: 10.1007/s10096-020-03978-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
We developed a chemiluminescence immunoassay method based on the recombinant nucleocapsid antigen and assessed its performance for the clinical diagnosis of severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infections by detecting SARS-CoV-2–specific IgM and IgG antibodies in patients. Full-length recombinant nucleocapsid antigen and tosyl magnetic beads were used to develop the chemiluminescence immunoassay approach. Plasmas from 29 healthy cohorts, 51 tuberculosis patients, and 79 confirmed SARS-CoV-2 patients were employed to evaluate the chemiluminescence immunoassay method performance for the clinical diagnosis of SARS-CoV-2 infections. A commercial ELISA kit (Darui Biotech, China) using the same nucleocapsid antigen was used for the in-parallel comparison with our chemiluminescence immunoassay method. The IgM and IgG manner of testing in the chemiluminescence immunoassay method showed a sensitivity and specificity of 60.76% (95% CI 49.1 to 71.6) and 92.25% (95% CI 83.4 to 97.2) and 82.28% (95% CI 72.1 to 90.0) and 97.5% (95% CI 91.3 to 99.7), respectively. Higher sensitivity and specificity were observed in the chemiluminescence immunoassay method compared with the Darui Biotech ELISA kit. The developed high sensitivity and specificity chemiluminescence immunoassay IgG testing method combined with the RT-PCR approach can improve the clinical diagnosis for SARS-CoV-2 infections and thus contribute to the control of COVID-19 expansion.
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Yadav PD, Shete-Aich A, Nyayanit DA, Pardeshi P, Majumdar T, Balasubramanian R, Ullas PT, Mohandas S, Dighe H, Sawant P, Patil S, Patil D, Gokhale MD, Mathapati B, Sudeep AB, Baradkar S, Kumar A, Kharde R, Salve M, Joshi Y, Gupta N, Mourya DT. Detection of coronaviruses in Pteropus & Rousettus species of bats from different States of India. Indian J Med Res 2020; 151:226-235. [PMID: 32317409 PMCID: PMC7366549 DOI: 10.4103/ijmr.ijmr_795_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background & objectives: Bats are considered to be the natural reservoir for many viruses, of which some are potential human pathogens. In India, an association of Pteropus medius bats with the Nipah virus was reported in the past. It is suspected that the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also has its association with bats. To assess the presence of CoVs in bats, we performed identification and characterization of bat CoV (BtCoV) in P. medius and Rousettus species from representative States in India, collected during 2018 and 2019. Methods: Representative rectal swab (RS) and throat swab specimens of Pteropus and Rousettus spp. bats were screened for CoVs using a pan-CoV reverse transcription-polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase (RdRp) gene. A single-step RT-PCR was performed on the RNA extracted from the bat specimens. Next-generation sequencing (NGS) was performed on a few representative bat specimens that were tested positive. Phylogenetic analysis was carried out on the partial sequences of RdRp gene sequences retrieved from both the bat species and complete viral genomes recovered from Rousettus spp. Results: Bat samples from the seven States were screened, and the RS specimens of eight Rousettus spp. and 21 Pteropus spp. were found positive for CoV RdRp gene. Among these, by Sanger sequencing, partial RdRp sequences could be retrieved from three Rousettus and eight Pteropus bat specimens. Phylogenetic analysis of the partial RdRp region demonstrated distinct subclustering of the BtCoV sequences retrieved from these Rousettus and Pteropus spp. bats. NGS led to the recovery of four sequences covering approximately 94.3 per cent of the whole genome of the BtCoVs from Rousettus bats. Three BtCoV sequences had 93.69 per cent identity to CoV BtRt-BetaCoV/GX2018. The fourth BtCoV sequence was 96.8 per cent identical to BtCoV HKU9-1. Interpretation & conclusions: This study was a step towards understanding the CoV circulation in Indian bats. Detection of potentially pathogenic CoVs in Indian bats stresses the need for enhanced screening for novel viruses in them. One Health approach with collaborative activities by the animal health and human health sectors in these surveillance activities shall be of use to public health. This would help in the development of diagnostic assays for novel viruses with outbreak potential and be useful in disease interventions. Proactive surveillance remains crucial for identifying the emerging novel viruses with epidemic potential and measures for risk mitigation.
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Affiliation(s)
- Pragya D Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Anita Shete-Aich
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Dimpal A Nyayanit
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Prachi Pardeshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Triparna Majumdar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - R Balasubramanian
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra; ICMR-National Institute of Virology Kerala Unit, Alappuzha, Kerala, India
| | | | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Hitesh Dighe
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Pradeep Sawant
- Enteric Virus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Savita Patil
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Dilip Patil
- Animal House, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - M D Gokhale
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Basavaraj Mathapati
- Poliovirus Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A B Sudeep
- Entomology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sreekant Baradkar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Abhimanyu Kumar
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Rutuja Kharde
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Malvika Salve
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Yash Joshi
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 DOI: 10.1002/jmv.v92.410.1002/jmv.25674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 05/24/2023]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 PMCID: PMC7166954 DOI: 10.1002/jmv.25674] [Citation(s) in RCA: 284] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 12/20/2022]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019‐nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray‐based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections. Respiratory tract viral infection including 2019‐nCoV poses great threats worldwide. Currently available and novel emerging diagnostic methods are summarized for several common respiratory viruses, including influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. This review is aimed to assist researchers and clinicians to develop timely and effective diagnostic strategies to detect respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing. mSphere 2020; 5:5/1/e00807-19. [PMID: 31996413 PMCID: PMC6992374 DOI: 10.1128/msphere.00807-19] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coronaviruses (CoVs) of bat origin have caused two pandemics in this century. Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV both originated from bats, and it is highly likely that bat coronaviruses will cause future outbreaks. Active surveillance is both urgent and essential to predict and mitigate the emergence of these viruses in humans. Next-generation sequencing (NGS) is currently the preferred methodology for virus discovery to ensure unbiased sequencing of bat CoVs, considering their high genetic diversity. However, unbiased NGS is an expensive methodology and is prone to missing low-abundance CoV sequences due to the high background level of nonviral sequences present in surveillance field samples. Here, we employ a capture-based NGS approach using baits targeting most of the CoV species. Using this technology, we effectively reduced sequencing costs by increasing the sensitivity of detection. We discovered nine full genomes of bat CoVs in this study and revealed great genetic diversity for eight of them.IMPORTANCE Active surveillance is both urgent and essential to predict and mitigate the emergence of bat-origin CoV in humans and livestock. However, great genetic diversity increases the chance of homologous recombination among CoVs. Performing targeted PCR, a common practice for many surveillance studies, would not reflect this diversity. NGS, on the other hand, is an expensive methodology and is prone to missing low-abundance CoV sequences. Here, we employ a capture-based NGS approach using baits targeting all CoVs. Our work demonstrates that targeted, cost-effective, large-scale, genome-level surveillance of bat CoVs is now highly feasible.
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