1
|
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.
Collapse
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
| |
Collapse
|
2
|
Smiley Evans T, Lowenstine LJ, Ssebide B, Barry PA, Kinani JF, Nizeyimana F, Noheli JB, Okello R, Mudakikwa A, Cranfield MR, Mazet JAK, Johnson CK, Gilardi KV. Simian homologues of human herpesviruses and implications for novel viral introduction to free-living mountain gorillas. Am J Primatol 2023; 85:e23439. [PMID: 36263518 PMCID: PMC11017921 DOI: 10.1002/ajp.23439] [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: 04/22/2022] [Revised: 08/17/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023]
Abstract
The endangered mountain gorilla (Gorilla beringei beringei) in Rwanda, Uganda, and the Democratic Republic of Congo is frequently in contact with humans through tourism, research activities, and illegal entry of people into protected gorilla habitat. Herpesviruses, which are ubiquitous in primates, have the potential to be shared in any setting where humans and gorillas share habitat. Based on serological findings and clinical observations of orofacial ulcerated lesions resembling herpetic lesions, an alpha-herpesvirus resembling human herpes simplex virus type 1 (HSV-1) has long been suspected to be present in human-habituated mountain gorillas in the wild. While the etiology of orofacial lesions in the wild has not been confirmed, HSV-1 has been suspected in captively-housed mountain gorillas and confirmed in a co-housed confiscated Grauer's gorilla (Gorilla beringei graueri). To better characterize herpesviruses infecting mountain gorillas and to determine the presence/absence of HSV-1 in the free-living population, we conducted a population-wide survey to test for the presence of orally shed herpesviruses. DNA was extracted from discarded chewed plants collected from 294 individuals from 26 groups, and samples were screened by polymerase chain reaction using pan-herpesvirus and HSV-1-specific assays. We found no evidence that human herpesviruses had infected free-ranging mountain gorillas. However, we found gorilla-specific homologs to human herpesviruses, including cytomegaloviruses (GbbCMV-1 and 2), a lymphocryptovirus (GbbLCV-1), and a new rhadinovirus (GbbRHV-1) with similar characteristics (i.e., timing of primary infection, shedding in multiple age groups, and potential modes of transmission) to their human counterparts, human cytomegalovirus, Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, respectively.
Collapse
Affiliation(s)
- Tierra Smiley Evans
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Linda J Lowenstine
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Benard Ssebide
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Peter A Barry
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Jean Felix Kinani
- One Health Approach for Conservation (OHAC), Gorilla Health, Kigali, Rwanda
| | - Fred Nizeyimana
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jean Bosco Noheli
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Ricky Okello
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | | | - Michael R Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jonna A K Mazet
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Christine K Johnson
- Epicenter for Disease Dynamics, One Health Institute, University of California Davis, Davis, California, USA
| | - Kirsten V Gilardi
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| |
Collapse
|