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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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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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3
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Köndgen S, Oh DY, Thürmer A, Sedaghatjoo S, Patrono LV, Calvignac-Spencer S, Biere B, Wolff T, Dürrwald R, Fuchs S, Reiche J. A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples. J Clin Microbiol 2024; 62:e0111123. [PMID: 38407068 PMCID: PMC10935636 DOI: 10.1128/jcm.01111-23] [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: 08/31/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses. IMPORTANCE Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.
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Affiliation(s)
- Sophie Köndgen
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Djin-Ye Oh
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Andrea Thürmer
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | | | - Livia V. Patrono
- Epidemiology of highly pathogenic microorganisms, Robert Koch-Institute, Berlin, Germany
| | | | - Barbara Biere
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Thorsten Wolff
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Ralf Dürrwald
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center, Robert Koch-Institute, Berlin, Germany
| | - Janine Reiche
- Influenza and Other Respiratory Viruses, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch-Institute, Berlin, Germany
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4
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Shi C, Wang Q, Liu Y, Wang S, Zhang Y, Liu C, Hu Y, Zheng D, Sun C, Song F, Yu X, Zhao Y, Bao J, Wang Z. Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing. Viruses 2024; 16:312. [PMID: 38400087 PMCID: PMC10891787 DOI: 10.3390/v16020312] [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: 12/25/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has caused severe effects on the global pig industry. Whole-genome sequencing provides crucial information for virus strain characterization, epidemiology analysis and vaccine development. Here, we evaluated the performance of next-generation sequencing (NGS) in generating ASFV genome sequences from clinical samples. Thirty-four ASFV-positive field samples including spleen, lymph node, lung, liver and blood with a range of Ct values from 14.73 to 25.95 were sequenced. For different tissue samples collected from the same sick pigs, the proportion of ASFV reads obtained from the spleen samples was 3.69-9.86 times higher than other tissues. For the high-viral-load spleen samples (Ct < 20), a minimum of a 99.8% breadth of ≥10× coverage was revealed for all the samples. For the spleen samples with Ct ≥ 20, 6/12 samples had a minimum of a 99.8% breadth of ≥10× coverage. A high average depth of sequencing coverage was also achieved from the blood samples. According to our results, high-quality ASFV whole-genome sequences could be obtained from the spleen or blood samples with Ct < 20. The high-quality ASFV genome sequence generated in this study was further used for the high-resolution phylogenetic analysis of the ASFV genomes in the early stage of the ASF epidemic in China. Our study demonstrates that NGS may act as a useful tool for efficient ASFV genome characterization, providing valuable information for disease control.
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Affiliation(s)
- Chuan Shi
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
| | - Qinghua Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yutian Liu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Shujuan Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yongqiang Zhang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Chunju Liu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yongxin Hu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Dongxia Zheng
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Chengyou Sun
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Fangfang Song
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Xiaojing Yu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yunling Zhao
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Jingyue Bao
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
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5
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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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6
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Garbuglia AR, Lapa D, Pauciullo S, Raoul H, Pannetier D. Nipah Virus: An Overview of the Current Status of Diagnostics and Their Role in Preparedness in Endemic Countries. Viruses 2023; 15:2062. [PMID: 37896839 PMCID: PMC10612039 DOI: 10.3390/v15102062] [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: 09/20/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Nipah virus (NiV) is a paramyxovirus responsible for a high mortality rate zoonosis. As a result, it has been included in the list of Blueprint priority pathogens. Bats are the main reservoirs of the virus, and different clinical courses have been described in humans. The Bangladesh strain (NiV-B) is often associated with severe respiratory disease, whereas the Malaysian strain (NiV-M) is often associated with severe encephalitis. An early diagnosis of NiV infection is crucial to limit the outbreak and to provide appropriate care to the patient. Due to high specificity and sensitivity, qRT-PCR is currently considered to be the optimum method in acute NiV infection assessment. Nasal swabs, cerebrospinal fluid, urine, and blood are used for RT-PCR testing. N gene represents the main target used in molecular assays. Different sensitivities have been observed depending on the platform used: real-time PCR showed a sensitivity of about 103 equivalent copies/reaction, SYBRGREEN technology's sensitivity was about 20 equivalent copies/reaction, and in multiple pathogen card arrays, the lowest limit of detection (LOD) was estimated to be 54 equivalent copies/reaction. An international standard for NiV is yet to be established, making it difficult to compare the sensitivity of the different methods. Serological assays are for the most part used in seroprevalence studies owing to their lower sensitivity in acute infection. Due to the high epidemic and pandemic potential of this virus, the diagnosis of NiV should be included in a more global One Health approach to improve surveillance and preparedness for the benefit of public health. Some steps need to be conducted in the diagnostic field in order to become more efficient in epidemic management, such as development of point-of-care (PoC) assays for the rapid diagnosis of NiV.
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Affiliation(s)
- Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Silvia Pauciullo
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Hervé Raoul
- French National Agency for Research on AIDS—Emerging Infectious Diseases (ANRS MIE), Maladies Infectieuses Émergentes, 75015 Paris, France;
| | - Delphine Pannetier
- Institut National de la Santé et de la Recherche Médicale, Jean Mérieux BSL4 Laboratory, 69002 Lyon, France;
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Chang Y, Wang Y, Li W, Wei Z, Tang S, Chen R. Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085471. [PMID: 37107752 PMCID: PMC10138381 DOI: 10.3390/ijerph20085471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.
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Affiliation(s)
- Yuqing Chang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Yuqian Wang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Wen Li
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Shichuan Tang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Rui Chen
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
- Correspondence:
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8
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Ahrens AK, Selinka HC, Wylezich C, Wonnemann H, Sindt O, Hellmer HH, Pfaff F, Höper D, Mettenleiter TC, Beer M, Harder TC. Investigating Environmental Matrices for Use in Avian Influenza Virus Surveillance-Surface Water, Sediments, and Avian Fecal Samples. Microbiol Spectr 2023; 11:e0266422. [PMID: 36700688 PMCID: PMC10100768 DOI: 10.1128/spectrum.02664-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Surveillance of avian influenza viruses (AIV) in wild water bird populations is important for early warning to protect poultry from incursions of high-pathogenicity (HP) AIV. Access to individual water birds is difficult and restricted and limits sampling depth. Here, we focused on environmental samples such as surface water, sediments, and environmentally deposited fresh avian feces as matrices for AIV detection. Enrichment of viral particles by ultrafiltration of 10-L surface water samples using Rexeed-25-A devices was validated using a bacteriophage ϕ6 internal control system, and AIV detection was attempted using real-time RT-PCR and virus isolation. While validation runs suggested an average enrichment of about 60-fold, lower values of 10 to 15 were observed for field water samples. In total 25/36 (60%) of water samples and 18/36 (50%) of corresponding sediment samples tested AIV positive. Samples were obtained from shallow water bodies in habitats with large numbers of waterfowl during an HPAIV epizootic. Although AIV RNA was detected in a substantial percentage of samples virus isolation failed. Virus loads in samples often were too low to allow further sub- and pathotyping. Similar results were obtained with environmentally deposited avian feces. Moreover, the spectrum of viruses detected by these active surveillance methods did not fully mirror an ongoing HPAIV epizootic among waterfowl as detected by passive surveillance, which, in terms of sensitivity, remains unsurpassed. IMPORTANCE Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds. Environmental matrices comprising surface water, sediments, and avian fecal matter deposited in the environment were examined for their usefulness in AIV surveillance. Despite virus enrichment efforts, environmental samples regularly revealed very low virus loads, which hampered further sub- and pathotyping. Passive surveillance based on oral and cloacal swabs of diseased and dead wild birds remained unsurpassed with respect to sensitivity.
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Affiliation(s)
- Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Ole Sindt
- State Laboratory of Schleswig-Holstein, Neumuenster, Germany
| | - Hartmut H. Hellmer
- Climate Sciences, Physical Oceanography of the Polar Seas, Alfred Wegener Institute, Bremerhaven, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Timm C. Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
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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; 11:79777. [DOI: 10.7554/elife.79777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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 Columbia
- Public Health Laboratory, British Columbia Centre for Disease Control
| | - Kara D Loos
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Danae M Suchan
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Jennifer N Russell
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Ashton N Sies
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | | | | | | | | | | | | | | | | | | | | | - Nicole A Lerminiaux
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
| | - Corina Monagin
- Metabiota Inc
- One Health Institute, School of Veterinary Medicine, University of California, Davis
| | | | | | | | | | | | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia
- Public Health Laboratory, British Columbia Centre for Disease Control
| | - David J McIver
- Metabiota
- Institute for Global Health Sciences, University of California, San Francisco
| | | | - Andrew DS Cameron
- Department of Biology, Faculty of Science, University of Regina
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina
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10
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Kuchinski KS, Duan J, Himsworth C, Hsiao W, Prystajecky NA. ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa. BMC Genomics 2022; 23:579. [PMID: 35953803 PMCID: PMC9371634 DOI: 10.1186/s12864-022-08790-4] [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: 02/25/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Background Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico. In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools’ suitability for challenging viral probe design applications. Results Based on ProbeTool’s in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools’ in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results. Conclusions ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools’ design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08790-4.
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Affiliation(s)
- Kevin S Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. .,, Vancouver, Canada.
| | - Jun Duan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, Food, and Fisheries, Abbotsford, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - William Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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11
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High viral loads: what drives fatal cases of COVID-19 in vaccinees? - an autopsy study. Mod Pathol 2022; 35:1013-1021. [PMID: 35365771 PMCID: PMC8974809 DOI: 10.1038/s41379-022-01069-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 01/07/2023]
Abstract
The rate of SARS-CoV-2 infections in vaccinees has become a relevant serious issue. This study aimed to determine the causes of death, histological organ alteration, and viral spread in relation to demographic, clinical-pathological, viral variants, and vaccine types for deceased individuals with proven SARS-CoV-2 infection after vaccination who died between January and November 2021. Twenty-nine consecutively collected cases were analyzed and compared to 141 nonvaccinated control cases. Autopsies were performed on 16 partially and 13 fully vaccinated individuals. Most patients were elderly and suffered from several relevant comorbidities. Real-time RT-PCR (RT-qPCR) identified a significantly increased rate of generalized viral dissemination within organ systems in vaccinated cases versus nonvaccinated cases (45% vs. 16%, respectively; P = 0.008) mainly with Ct-values of higher than 25 in non-respiratory samples. However, vaccinated cases also showed high viral loads, reaching Ct-values below 10, especially in the upper airways and lungs. This was accompanied by high rates of pulmonal bacterial or mycotic superinfections and the occurrence of immunocompromising factors, such as malignancies, immunosuppressive drug intake, or decreased immunoglobulin levels. All these findings were particularly accentuated in partially vaccinated patients compared to fully vaccinated individuals. The virus dissemination observed in our case study may indicate that patients with an impaired immune system have a decreased ability to eliminate the virus. However, the potential role of antibody-dependent enhancement must also be ruled out in future studies. Fatal cases of COVID-19 in vaccinees were rare and often associated with severe comorbidities or other immunosuppressive conditions.
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12
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Schlottau K, Feldmann F, Hanley PW, Lovaglio J, Tang-Huau TL, Meade-White K, Callison J, Williamson BN, Rosenke R, Long D, Wylezich C, Höper D, Herden C, Scott D, Hoffmann D, Saturday G, Beer M, Feldmann H. Development of a nonhuman primate model for mammalian bornavirus infection. PNAS NEXUS 2022; 1:pgac073. [PMID: 35860599 PMCID: PMC9291224 DOI: 10.1093/pnasnexus/pgac073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023]
Abstract
Until recently, it was assumed that members of the family Bornaviridae could not induce severe disease in humans. Today, however, Borna disease virus 1 (BoDV-1), as well as the more recently emerged variegated squirrel bornavirus 1 (VSBV-1), are known as causative agents of lethal encephalitis in humans. In order to establish animal models reflecting the pathogenesis in humans and for countermeasure efficacy testing, we infected twelve rhesus macaques (Macaca mulatta) either with VSBV-1 or with BoDV-1. For each virus, three monkeys each were inoculated with 2 × 104 focus forming units by the intracerebral route or by multiple peripheral routes (intranasal, conjunctival, intramuscular, and subcutaneous; same dose in total). All BoDV-1 and VSBV-1 intracerebrally infected monkeys developed severe neurological signs around 5 to 6 or 8 to 12 weeks postinfection, respectively. Focal myoclonus and tremors were the most prominent observations in BoDV-1 and VSBV-1-infected animals. VSBV-1-infected animals also showed behavioral changes. Only one BoDV-1 peripherally infected animal developed similar disease manifestations. All animals with severe clinical disease showed high viral loads in brain tissues and displayed perivascular mononuclear cuffs with a predominance of lymphocytes and similar meningeal inflammatory infiltrates. In summary, rhesus macaques intracerebrally infected with mammalian bornaviruses develop a human-like disease and may serve as surrogate models for human bornavirus infection.
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Affiliation(s)
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Tsing-Lee Tang-Huau
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Julie Callison
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Brandi N Williamson
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Dan Long
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Christiane Herden
- Justus-Liebig-Universität, Institute of Veterinary Pathology, 35390 Gießen, Germany
| | - Dana Scott
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
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13
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Mohapatra S, Menon NG. Factors responsible for the emergence of novel viruses: An emphasis on SARS-CoV-2. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 27:100358. [PMID: 35369608 PMCID: PMC8958772 DOI: 10.1016/j.coesh.2022.100358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Structural and genetic differences among various viruses play a significant factor in host infectivity and vulnerability to environmental stressors. Zoonoses of viruses require several recombinations and mutations in their genetic material and among several viruses allowing them to switch hosts and infect new species. Additionally, the host genetics play a significant role in successful viral transmission among various hosts. For example, human immunodeficiency virus (HIV), Ebola virus and influenza viruses. In efficient zoonotic events, selective stresses in the host milieu-interieur are critical during viral infection of the first human host. The genetic rearrangement of the virus and the selective environmental pressure of the host immune system dominate the emergence of new viral disease outbreaks.
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Affiliation(s)
- Sanjeeb Mohapatra
- NUS Environmental Research Institute, National University of Singapore, 1 Create Way, Create Tower, #15-02, 138602, Singapore
| | - N Gayathri Menon
- Centre for Research in Nanotechnology and Science (CRNTS), Indian Institute of Technology Bombay, India
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Abstract
Rustrela virus (RusV; species Rubivirus strelense) is a recently discovered relative of rubella virus (RuV) that has been detected in cases of encephalitis in diverse mammals. Here, we diagnosed two additional cases of fatal RusV-associated meningoencephalitis in a South American coati (Nasua nasua) and a Eurasian or European otter (Lutra lutra) that were detected in a zoological garden with history of prior RusV infections. Both animals showed abnormal movement or unusual behavior and their brains tested positive for RusV using specific reverse transcription quantitative PCR (RT-qPCR) and RNA in situ hybridization. As previous sequencing of the RusV genome proved to be very challenging, we employed a sophisticated target-specific capture enrichment with specifically designed RNA baits to generate complete RusV genome sequences from both detected encephalitic animals and apparently healthy wild yellow-necked field mice (Apodemus flavicollis). Furthermore, the technique was used to revise three previously published RusV genomes from two encephalitic animals and a wild yellow-necked field mouse. When comparing the newly generated RusV sequences to the previously published RusV genomes, we identified a previously undetected stretch of 309 nucleotides predicted to represent the intergenic region and the sequence encoding the N terminus of the capsid protein. This indicated that the original RusV sequence was likely incomplete due to misassembly of the genome at a region with an exceptionally high G+C content of >80 mol%. The new sequence data indicate that RusV has an overall genome length of 9,631 nucleotides with the longest intergenic region (290 nucleotides) and capsid protein-encoding sequence (331 codons) within the genus Rubivirus. IMPORTANCE The detection of rustrela virus (RusV)-associated encephalitis in two carnivoran mammal species further extends the knowledge on susceptible species. Furthermore, we provide clinical and pathological data for the two new RusV cases, which were until now limited to the initial description of this fatal encephalitis. Using a sophisticated enrichment method prior to sequencing of the viral genome, we markedly improved the virus-to-background sequence ratio compared to that of standard procedures. Consequently, we were able to resolve and update the intergenic region and the coding region for the N terminus of the capsid protein of the initial RusV genome sequence. The updated putative capsid protein now resembles those of rubella and ruhugu virus in size and harbors a predicted RNA-binding domain that had not been identified in the initial RusV genome version. The newly determined complete RusV genomes strongly improve our knowledge of the genome structure of this novel rubivirus.
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15
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Stoek F, Barry Y, Ba A, Schulz A, Rissmann M, Wylezich C, Sadeghi B, Beyit AD, Eisenbarth A, N’diaye FB, Haki ML, Doumbia BA, Gueya MB, Bah MY, Eiden M, Groschup MH. Mosquito survey in Mauritania: Detection of Rift Valley fever virus and dengue virus and the determination of feeding patterns. PLoS Negl Trop Dis 2022; 16:e0010203. [PMID: 35427361 PMCID: PMC9113561 DOI: 10.1371/journal.pntd.0010203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/17/2022] [Accepted: 01/26/2022] [Indexed: 11/28/2022] Open
Abstract
In Mauritania, several mosquito-borne viruses have been reported that can cause devastating diseases in animals and humans. However, monitoring data on their occurrence and local distribution are limited. Rift Valley fever virus (RVFV) is an arthropod-borne virus that causes major outbreaks throughout the African continent and the Arabian Peninsula. The first Rift Valley fever (RVF) epidemic in Mauritania occurred in 1987 and since then the country has been affected by recurrent outbreaks of the disease. To gain information on the occurrence of RVFV as well as other mosquito-borne viruses and their vectors in Mauritania, we collected and examined 4,950 mosquitoes, belonging to four genera and 14 species. The mosquitoes were captured during 2018 in the capital Nouakchott and in southern parts of Mauritania. Evidence of RVFV was found in a mosquito pool of female Anopheles pharoensis mosquitoes collected in December on a farm near the Senegal River. At that time, 37.5% of 16 tested Montbéliarde cattle on the farm showed RVFV-specific IgM antibodies. Additionally, we detected IgM antibodies in 10.7% of 28 indigenous cattle that had been sampled on the same farm one month earlier. To obtain information on potential RVFV reservoir hosts, blood meals of captured engorged mosquitoes were analyzed. The mosquitoes mainly fed on humans (urban areas) and cattle (rural areas), but also on small ruminants, donkeys, cats, dogs and straw-colored fruit bats. Results of this study demonstrate the circulation of RVFV in Mauritania and thus the need for further research to investigate the distribution of the virus and its vectors. Furthermore, factors that may contribute to its maintenance should be analyzed more closely. In addition, two mosquito pools containing Aedes aegypti and Culex quinquefasciatus mosquitoes showed evidence of dengue virus (DENV) 2 circulation in the city of Rosso. Further studies are therefore needed to also examine DENV circulation in Mauritania. In Mauritania, various mosquito-borne viruses responsible for devastating diseases in livestock and/or humans occur, threatening both human and animal health. One of these viruses is the Rift Valley fever phlebovirus (RVFV), which is widespread throughout the African continent and the Arabian Peninsula. The first outbreak in Mauritania occurred in 1987, and epidemics have recurred since then. However, little is known about the maintenance of RVFV during inter-epidemic periods, in the absence of reported outbreaks, and although there is evidence of an active circulation of the virus during these times, only limited data are available on the abundance of RVFV and its vectors in Mauritania. Therefore, this study aimed to collect and examine mosquitoes in different areas where outbreaks have already occurred. Additionally, blood of collected blood-fed mosquitoes was analyzed to identify feeding patterns and thus wildlife potentially acting as RVFV reservoir hosts. Furthermore, the collected mosquitoes were analyzed for the presence of other neglected viruses in order to participate in an elucidation of the circulation of different viruses within the mosquito population in Mauritania and to be able to better prevent disease outbreaks.
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Affiliation(s)
- Franziska Stoek
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Yahya Barry
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | - Aliou Ba
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | - Ansgar Schulz
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Melanie Rissmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Abdellahi Diambar Beyit
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | - Albert Eisenbarth
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Mohamed Lemine Haki
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | | | | | | | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- * E-mail:
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16
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Müller T, Hassel R, Jago M, Khaiseb S, van der Westhuizen J, Vos A, Calvelage S, Fischer S, Marston DA, Fooks AR, Höper D, Freuling CM. Rabies in kudu: Revisited. Adv Virus Res 2022; 112:115-173. [DOI: 10.1016/bs.aivir.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Nature 2021; 602:307-313. [PMID: 34937050 PMCID: PMC8828469 DOI: 10.1038/s41586-021-04342-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/13/2021] [Indexed: 11/27/2022]
Abstract
Emerging variants of concern (VOCs) are driving the COVID-19 pandemic1,2. Experimental assessments of replication and transmission of major VOCs and progenitors are needed to understand the mechanisms of replication and transmission of VOCs3. Here we show that the spike protein (S) from Alpha (also known as B.1.1.7) and Beta (B.1.351) VOCs had a greater affinity towards the human angiotensin-converting enzyme 2 (ACE2) receptor than that of the progenitor variant S(D614G) in vitro. Progenitor variant virus expressing S(D614G) (wt-S614G) and the Alpha variant showed similar replication kinetics in human nasal airway epithelial cultures, whereas the Beta variant was outcompeted by both. In vivo, competition experiments showed a clear fitness advantage of Alpha over wt-S614G in ferrets and two mouse models—the substitutions in S were major drivers of the fitness advantage. In hamsters, which support high viral replication levels, Alpha and wt-S614G showed similar fitness. By contrast, Beta was outcompeted by Alpha and wt-S614G in hamsters and in mice expressing human ACE2. Our study highlights the importance of using multiple models to characterize fitness of VOCs and demonstrates that Alpha is adapted for replication in the upper respiratory tract and shows enhanced transmission in vivo in restrictive models, whereas Beta does not overcome Alpha or wt-S614G in naive animals. The Alpha variant of SARS-CoV-2 outcompetes progenitor SARS-CoV-2 in upper respiratory tract replication competition in vivo.
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18
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Santos PD, Ziegler U, Szillat KP, Szentiks CA, Strobel B, Skuballa J, Merbach S, Grothmann P, Tews BA, Beer M, Höper D. In action-an early warning system for the detection of unexpected or novel pathogens. Virus Evol 2021; 7:veab085. [PMID: 34703624 PMCID: PMC8542707 DOI: 10.1093/ve/veab085] [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: 05/29/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Proactive approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or invitro and invivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize the whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018–9 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus (UMAV), whereas a new peribunyavirid, tentatively named ‘Hedwig virus’ (HEDV), belonged to a putative novel genus of the family Peribunyaviridae. In follow-up studies, newly developed molecular diagnostic assays detected fourteen UMAV-positive wild birds from different German cities and eight HEDV-positive captive birds from two zoological gardens. UMAV was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.
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Affiliation(s)
- Pauline Dianne Santos
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Ute Ziegler
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Kevin P Szillat
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Claudia A Szentiks
- 4Department of Wildlife Diseases, Leibniz-Institute for Zoo- and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin 10315, Germany
| | - Birte Strobel
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Jasmin Skuballa
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Sabine Merbach
- State Institute for Chemical and Veterinary Analysis (CVUA) Westfalen, Zur Taubeneiche 10-12, Arnsberg 59821, Germany
| | - Pierre Grothmann
- Practice for Zoo, Game and Wild Animals, Lintiger Str. 74, Geestland 27624, Germany
| | - Birke Andrea Tews
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Infectology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
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19
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Santos PD, Michel F, Wylezich C, Höper D, Keller M, Holicki CM, Szentiks CA, Eiden M, Muluneh A, Neubauer-Juric A, Thalheim S, Globig A, Beer M, Groschup MH, Ziegler U. Co-infections: Simultaneous detections of West Nile virus and Usutu virus in birds from Germany. Transbound Emerg Dis 2021; 69:776-792. [PMID: 33655706 DOI: 10.1111/tbed.14050] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022]
Abstract
The emergence of West Nile virus (WNV) and Usutu virus (USUV) in Europe resulted in significant outbreaks leading to avifauna mortality and human infections. Both viruses have overlapping geographical, host and vector ranges, and are often co-circulating in Europe. In Germany, a nationwide bird surveillance network was established to monitor these zoonotic arthropod-borne viruses in migratory and resident birds. In this framework, co-infections with WNV and USUV were detected in six dead birds collected in 2018 and 2019. Genomic sequencing and phylogenetic analyses classified the detected WNV strains as lineage 2 and the USUV strains as lineages Africa 2 (n = 2), Africa 3 (n = 3) and Europe 2 (n = 1). Preliminary attempts to co-propagate both viruses in vitro failed. However, we successfully cultivated WNV from two animals. Further evidence for WNV-USUV co-infection was obtained by sampling live birds in four zoological gardens with confirmed WNV cases. Three snowy owls had high neutralizing antibody titres against both WNV and USUV, of which two were also positive for USUV-RNA. In conclusion, further reports of co-infections in animals as well as in humans are expected in the future, particularly in areas where both viruses are present in the vector population.
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Affiliation(s)
- Pauline Dianne Santos
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Friederike Michel
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Cora M Holicki
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | | | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Aemero Muluneh
- Saxon State Laboratory of Health and Veterinary Affairs, Dresden, Germany
| | | | - Sabine Thalheim
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.,German Centre for Infection Research, partner site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.,German Centre for Infection Research, partner site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
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