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Kadokura K, Kato H, Yoshizumi K, Kamikuri M, Kamenosono A, Shinkawa N, Hamada Y, Kawamura H, Shimada T, Kuroda M, Sunagawa T. Rapid response to a COVID-19 outbreak at a nightclub in Kagoshima prefecture, Japan, in the early phase of the COVID-19 pandemic, June and July 2020: A descriptive epidemiological study. J Infect Chemother 2024; 30:1001-1007. [PMID: 38521457 DOI: 10.1016/j.jiac.2024.03.014] [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: 10/11/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
INTRODUCTION During COVID-19 pandemic in Japan, nightclubs were identified as high-risk locations for COVID-19 outbreaks, but an outbreak investigation in this setting is challenging because of the anonymous and opportunistic nature of interactions. METHODS The joint rapid response team collected epidemiological data, conducted descriptive epidemiology to determine the characteristics of cases associated with the nightclub, and implemented countermeasures. Polymerase chain reaction (PCR) tests were performed by the Local Institute of Public Health, Kagoshima University, and several commercial laboratories. RESULTS Between June 15 and July 20, 2020, 121 individuals tested positive for SARS-CoV-2 (59 confirmed and 62 asymptomatic) of whom 8 were nightclub staff who had no travel history of outside Kagoshima, 66 were guests, and 47 were subsequent contacts. The median age was 32 years (interquartile range: 24-43 years). One individual showed severe symptoms but there were no fatal. The epidemic curve showed one peak on June 30 and July 1 with a limited number of cases subsequently. Of the 121 cases, 116 and 5 were in individuals living in and outside Kagoshima Prefecture, respectively. Haplotype network analysis showed 5 genome-wide single-nucleotide variants between the isolates before and during this outbreak. CONCLUSIONS There is a possibility that unidentified guests from outside Kagoshima Prefecture could infect staff who could subsequently spread the virus to guests and other staff, who were mainly a younger population. The rapid outbreak response enabled onward transmission in the community to be minimized. This outbreak investigation could provide insights for effective responses to challenging situations in future pandemic.
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Affiliation(s)
- Keisuke Kadokura
- Field Epidemiology Training Program, National Institute of Infectious Diseases, Tokyo, Japan; Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Hirofumi Kato
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Kayoko Yoshizumi
- Kagoshima City Public Health and Welfare Bureau, Kagoshima, Japan
| | - Miyuki Kamikuri
- Kagoshima City Public Health and Welfare Bureau, Kagoshima, Japan
| | - Akira Kamenosono
- Kagoshima Prefectural Health Promotion Division, Life, Health and Social Welfare Department, Kagoshima, Japan
| | - Naomi Shinkawa
- Department of Microbiology, Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Yuka Hamada
- Department of Microbiology, Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Hideki Kawamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan
| | - Tomoe Shimada
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan.
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2
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Sivertsen A, Mortensen N, Solem U, Valen E, Bullita MF, Wensaas KA, Litleskare S, Rørtveit G, Grewal HMS, Ulvestad E. Comprehensive contact tracing during an outbreak of alpha-variant SARS-CoV-2 in a rural community reveals less viral genomic diversity and higher household secondary attack rates than expected. mSphere 2024; 9:e0011424. [PMID: 39109863 DOI: 10.1128/msphere.00114-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/03/2024] [Indexed: 08/29/2024] Open
Abstract
Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes throughout the COVID-19 pandemic has generated a wealth of data on viral evolution across populations, but only a few studies have so far explored SARS-CoV-2 evolution across large connected transmission networks. Here, we couple data from SARS-CoV-2 sequencing with contact tracing data from an outbreak with a single origin in a rural Norwegian community where samples from all exposed persons were collected prospectively. A total of 134 nasopharyngeal samples were positive by PCR. Among the 121 retrievable genomes, 81 were identical to the genome of the introductor, thus demonstrating that genomics beyond clustering genotypically similar viral genomes to confirm relatedness offers limited additional value to manual contact tracing. In the cases where mutations were discovered, five small genetic clusters were identified. We observed a household secondary attack rate of 77%, with 92% of household members infected among households with secondary transmission, suggesting that SARS-CoV-2 introduction into large families is likely to affect all household members. IMPORTANCE In outbreak investigations, obtaining a full overview of infected individuals within a population is seldom achieved. We here present an example where a single introduction of B1.1.7 SARS-CoV-2 within a rural community allowed for tracing of the virus from an introductor via dissemination through larger gatherings into households. The outbreak occurred before widespread vaccination, allowing for a "natural" outbreak development with community lockdown. We show through sequencing that the virus can infect up to five consecutive persons without gaining mutations, thereby showing that contact tracing seems more important than sequencing for local outbreak investigations in settings with few alternative introductory transmission pathways. We also show how larger households where a child introduced transmission appeared more likely to promote further spread of the virus compared to households with an adult as the primary introductor.
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Affiliation(s)
- Audun Sivertsen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Nicolay Mortensen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Knut-Arne Wensaas
- NORCE Norwegian Research Centre, Research Unit for General Practice, Bergen, Norway
| | - Sverre Litleskare
- NORCE Norwegian Research Centre, Research Unit for General Practice, Bergen, Norway
| | - Guri Rørtveit
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Harleen M S Grewal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Elling Ulvestad
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
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3
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Kar M, Johnson KEE, Vanderheiden A, Elrod EJ, Floyd K, Geerling E, Stone ET, Salinas E, Banakis S, Wang W, Sathish S, Shrihari S, Davis-Gardner ME, Kohlmeier J, Pinto A, Klein R, Grakoui A, Ghedin E, Suthar MS. CD4 + and CD8 + T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment. SCIENCE ADVANCES 2024; 10:eadp2636. [PMID: 39178263 PMCID: PMC11343035 DOI: 10.1126/sciadv.adp2636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/19/2024] [Indexed: 08/25/2024]
Abstract
SARS-CoV-2 infection induces the generation of virus-specific CD4+ and CD8+ effector and memory T cells. However, the contribution of T cells in controlling SARS-CoV-2 during infection is not well understood. Following infection of C57BL/6 mice, SARS-CoV-2-specific CD4+ and CD8+ T cells are recruited to the respiratory tract, and a vast proportion secrete the cytotoxic molecule granzyme B. Using depleting antibodies, we found that T cells within the lungs play a minimal role in viral control, and viral clearance occurs in the absence of both CD4+ and CD8+ T cells through 28 days postinfection. In the nasal compartment, depletion of both CD4+ and CD8+ T cells, but not individually, results in persistent, culturable virus replicating in the nasal epithelial layer through 28 days postinfection. Viral sequencing analysis revealed adapted mutations across the SARS-CoV-2 genome, including a large deletion in ORF6. Overall, our findings highlight the importance of T cells in controlling virus replication within the respiratory tract during SARS-CoV-2 infection.
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Affiliation(s)
- Meenakshi Kar
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Katherine E. E. Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Abigail Vanderheiden
- Center for Neuroimmunology and Neuroinfectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth J. Elrod
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Katharine Floyd
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Eduardo Salinas
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Stephanie Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Wei Wang
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Shruti Sathish
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Swathi Shrihari
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Meredith E. Davis-Gardner
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
| | - Jacob Kohlmeier
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Amelia Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Robyn Klein
- Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, Western Institute of Neuroscience, Western University, London, Ontario, Canada
| | - Arash Grakoui
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Medicine, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Mehul S. Suthar
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Emory National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
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Jauhiainen MK, Pyöriä L, Viitasalo S, Aaltonen LM, Söderlund-Venermo M, Hagström J, Mäkitie AA, Perdomo MF, Sinkkonen ST. Multiple DNA Viruses and HPV Integration in Inverted Papilloma and Associated Sinonasal Carcinoma. Laryngoscope 2024. [PMID: 39171991 DOI: 10.1002/lary.31714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVES Sinonasal inverted papilloma (IP) has a locally destructive growth pattern, can relapse, and can undergo malignant transformation (IP-associated sinonasal squamous cell carcinoma (IP-SNSCC)). Human papillomaviruses (HPV)-6 and -16 are frequently detected in IPs. To clarify the possible roles of other DNA viruses in IPs, we explored viruses not studied in this context before. With the setting of pre- and post-malignant transformation samples, we investigated HPV genomes in depth to assess the integration of HPV into the human genome and the presence of minor intratypic variants. MATERIALS AND METHODS We analyzed 35 IP samples representing 28 individuals, of which six had IP-SNSCC. For virus screening, we applied qPCR to detect 16 different DNA viruses in three virus families, comprising herpesviruses, parvoviruses, and polyomaviruses. In addition, targeted next generation sequencing (NGS) was used for detailed HPV analysis. RESULTS We detected herpes-, parvo-, and polyomaviruses in 13/28 (46%) patients, with codetections of multiple viruses in six (21%) patients. NGS revealed HPV16 DNA in 2/6 IP-SNSCC and in their respective earlier benign IP samples, as well as in a plasma sample from one of these patients. HPV6 was detected in two IP samples without subsequent malignant transformation. We identified sequence reads containing junctions of HPV6 and HPV16 and host genome suggestive of viral integration. HPV6 and HPV16 minor intratypic variants were present across pre- and post-malignant transformation, with mostly nonsynonymous mutations. CONCLUSIONS Multiple DNA viruses were present in IPs. HPV16 was detected only in IP-SNSCCs or in tumors that later underwent malignant transformation. LEVEL OF EVIDENCE 3 Laryngoscope, 2024.
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Affiliation(s)
- Maria K Jauhiainen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- The Doctoral Programme in Clinical Research, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lari Pyöriä
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sanna Viitasalo
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Leena-Maija Aaltonen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology, University Hospital of Helsinki, Helsinki, Finland
- Department of Oral Pathology and Radiology, University of Turku, Turku, Finland
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, HusLab, Helsinki University Hospital, Helsinki, Finland
| | - Antti A Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Maria F Perdomo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saku T Sinkkonen
- Department of Otorhinolaryngology - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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5
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Khurana MP, Curran-Sebastian J, Scheidwasser N, Morgenstern C, Rasmussen M, Fonager J, Stegger M, Tang MHE, Juul JL, Escobar-Herrera LA, Møller FT, Albertsen M, Kraemer MUG, du Plessis L, Jokelainen P, Lehmann S, Krause TG, Ullum H, Duchêne DA, Mortensen LH, Bhatt S. High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark. Nat Commun 2024; 15:7123. [PMID: 39164246 PMCID: PMC11335946 DOI: 10.1038/s41467-024-51371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.
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Affiliation(s)
- Mark P Khurana
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Curran-Sebastian
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Neil Scheidwasser
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas L Juul
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Sune Lehmann
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tyra G Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut Copenhagen, Copenhagen, Denmark
| | | | - David A Duchêne
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Laust H Mortensen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Statistics Denmark, Copenhagen, Denmark
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
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6
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Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
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Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
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7
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Jung A, Droit L, Febles B, Fronick C, Cook L, Handley SA, Parikh BA, Wang D. Tracking the prevalence and emergence of SARS-CoV-2 variants of concern using a regional genomic surveillance program. Microbiol Spectr 2024; 12:e0422523. [PMID: 38912809 PMCID: PMC11302336 DOI: 10.1128/spectrum.04225-23] [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: 12/19/2023] [Accepted: 05/14/2024] [Indexed: 06/25/2024] Open
Abstract
SARS-CoV-2 molecular testing coupled with whole-genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOCs) as well as discovery of novel variants. Since the beginning of the pandemic, millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. In this study, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOCs and recapitulate national trends. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories. IMPORTANCE In our manuscript, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of variants of concern (VOCs). Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories. While the SARS-CoV-2 pandemic has evolved into a more endemic form, we still believe that additional real-world information about sampling, procedures, and data interpretation is valuable for ongoing as well as future genomic surveillance efforts. Our study should be of substantial interest to clinical virologists.
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Affiliation(s)
- Ana Jung
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Binita Febles
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Catarina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lisa Cook
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bijal A. Parikh
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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8
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Bundschuh C, Weidner N, Klein J, Rausch T, Azevedo N, Telzerow A, Jost KL, Schnitzler P, Kräusslich HG, Benes V. Optimization data for an ARTIC-/Illumina-based whole-genome sequencing protocol and pipeline for SARS-CoV-2 analysis. Data Brief 2024; 55:110607. [PMID: 39006345 PMCID: PMC11239479 DOI: 10.1016/j.dib.2024.110607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
In January 2021, Germany commenced surveillance of SARS-CoV-2 variants under the Corona Surveillance Act, which ceased in July 2023. The objective was to bolster pandemic control, as specific alterations in amino acids, particularly within the spike protein, were linked to heightened transmission and decreased vaccine effectiveness. Consequently, our team conducted whole genome sequencing using the commercially accessible ARTIC protocol on Illumina's NextSeq500 platform and MiSeq for SARS-CoV-2 positive samples obtained from patients at Heidelberg University Hospital, affiliated hospitals, and the public health office in the Rhine-Neckar/Heidelberg region. Throughout the pandemic, we refined the existing ARTIC V4 protocol as well as our bioinformatics pipeline, the details of which are outlined in this report. This report reflects the protocol for the MiSeq analysis, the protocol for the NextSeq500 can be found in our previous publication.
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Affiliation(s)
- Christian Bundschuh
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
| | - Niklas Weidner
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
- Medical Faculty Heidelberg, Department of Infectious Diseases, Microbiology and Hygiene, Heidelberg University, Heidelberg, Germany
| | - Julian Klein
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nayara Azevedo
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anja Telzerow
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Katharina Laurence Jost
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
| | - Paul Schnitzler
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Medical Faculty Heidelberg, Department of Infectious Diseases Virology, Heidelberg University, Heidelberg, Germany
- Deutsches Zentrum für Infektionsforschung, partner site Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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9
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Zambre S, Katarmal P, Pawar S, Dawkhar S, Iyer P, Rajput V, Kadam P, Bhalerao U, Tupekar M, Shah P, Karmodiya K, Dharne M, Roy B, Koraktar S. Wastewater surveillance of severe acute respiratory syndrome coronavirus-2 in open drains of two Indian megacities captures evolutionary lineage transitions: a zonation approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:49670-49681. [PMID: 39078552 DOI: 10.1007/s11356-024-34448-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
Wastewater-based environmental surveillance (WBES) has been proven as proxy tool for monitoring nucleic acids of pathogens shed by infected population before clinical outcomes. The poor sewershed network of low to middle-income countries (LMICs) leads to most of the wastewater flow through open drains. We studied the effectiveness of WBES using open drain samples to monitor the emergence of the SARS-CoV-2 variants in 2 megacities of India having dense population through zonation approach. Samples from 28 locations spanned into 5 zones of Pune region, Maharashtra, India, were collected on a weekly basis during October 2021 to July 2022. Out of 1115 total processed samples, 303 (~ 27%) tested positive for SARS-CoV-2. The periodical rise and fall in the percentage positivity of the samples was found to be in sync with the abundance of SARS-CoV-2 RNA and the reported COVID-19 active cases for Pune city. Sequencing of the RNA obtained from wastewater samples confirmed the presence of SARS-CoV-2. Of 337 sequences, lineage identification for 242 samples revealed 265 distinct SARS-CoV-2 variants including 10 highly transmissible ones. Importantly, transition from Delta to Omicron variant could be detected in wastewater samples 2 weeks prior to any clinically reported Omicron cases in India. Thus, this study demonstrates the usefulness of open drain samples for real-time monitoring of a viral pathogen's evolutionary dynamics and could be implemented in LMICs.
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Affiliation(s)
- Saee Zambre
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Poonam Katarmal
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Shubhankar Pawar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Snehal Dawkhar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Parvati Iyer
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Priyanki Shah
- Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Bishnudeo Roy
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Santosh Koraktar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India.
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10
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Peña-Hernández MA, Alfajaro MM, Filler RB, Moriyama M, Keeler EL, Ranglin ZE, Kong Y, Mao T, Menasche BL, Mankowski MC, Zhao Z, Vogels CBF, Hahn AM, Kalinich CC, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach BD, Homer R, Pyle AM, Martinez DR, Grubaugh ND, Israelow B, Iwasaki A, Wilen CB. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nat Microbiol 2024; 9:2038-2050. [PMID: 39075235 DOI: 10.1038/s41564-024-01765-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/19/2024] [Indexed: 07/31/2024]
Abstract
Circulating bat coronaviruses represent a pandemic threat. However, our understanding of bat coronavirus pathogenesis and transmission potential is limited by the lack of phenotypically characterized strains. We created molecular clones for the two closest known relatives of SARS-CoV-2, BANAL-52 and BANAL-236. We demonstrated that BANAL-CoVs and SARS-CoV-2 have similar replication kinetics in human bronchial epithelial cells. However, BANAL-CoVs have impaired replication in human nasal epithelial cells and in the upper airway of mice. We also observed reduced pathogenesis in mice and diminished transmission in hamsters. Further, we observed that diverse bat coronaviruses evade interferon and downregulate major histocompatibility complex class I. Collectively, our study demonstrates that despite high genetic similarity across bat coronaviruses, prediction of pandemic potential of a virus necessitates functional characterization. Finally, the restriction of bat coronavirus replication in the upper airway highlights that transmission potential and innate immune restriction can be uncoupled in this high-risk family of emerging viruses.
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Affiliation(s)
- Mario A Peña-Hernández
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Emma L Keeler
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zara E Ranglin
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yong Kong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Madeleine C Mankowski
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zhe Zhao
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Shuo Zhang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Nicholas Huston
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rafael Araujo-Tavares
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David R Martinez
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
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11
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Ndione MHD, Diagne MM, Mencattelli G, Diallo A, Ndiaye EH, Di Domenico M, Diallo D, Kane M, Curini V, Top NM, Marcacci M, Sankhe S, Ancora M, Secondini B, Di Lollo V, Teodori L, Leone A, Puglia I, Gaye A, Sall AA, Loucoubar C, Rosà R, Diallo M, Monaco F, Faye O, Cammà C, Rizzoli A, Savini G, Faye O. An amplicon-based sequencing approach for Usutu virus characterization. Virol J 2024; 21:163. [PMID: 39044231 PMCID: PMC11267690 DOI: 10.1186/s12985-024-02426-7] [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: 02/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024] Open
Abstract
Usutu virus (USUV), an arbovirus from the Flaviviridae family, genus Flavivirus, has recently gained increasing attention because of its potential for emergence. After his discovery in South Africa, USUV spread to other African countries, then emerged in Europe where it was responsible for epizootics. The virus has recently been found in Asia. USUV infection in humans is considered to be most often asymptomatic or to cause mild clinical signs. However, a few cases of neurological complications such as encephalitis or meningo-encephalitis have been reported in both immunocompromised and immunocompetent patients. USUV natural life cycle involves Culex mosquitoes as its main vector, and multiple bird species as natural viral reservoirs or amplifying hosts, humans and horses can be incidental hosts. Phylogenetic studies carried out showed eight lineages, showing an increasing genetic diversity for USUV. This work describes the development and validation of a novel whole-genome amplicon-based sequencing approach to Usutu virus. This study was carried out on different strains from Senegal and Italy. The new approach showed good coverage using samples derived from several vertebrate hosts and may be valuable for Usutu virus genomic surveillance to better understand the dynamics of evolution and transmission of the virus.
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Affiliation(s)
| | | | - Giulia Mencattelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, 38010, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38010, Italy
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - El Hadji Ndiaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Diawo Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Ndeye Marieme Top
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Safiétou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Alessandra Leone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Alioune Gaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Roberto Rosà
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, 38010, Italy
| | - Mawlouth Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Federica Monaco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38010, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, 64100, Italy
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, BP220, Senegal
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12
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Nsengimana I, Juma J, Roesel K, Gasana MN, Ndayisenga F, Muvunyi CM, Hakizimana E, Hakizimana JN, Eastwood G, Chengula AA, Bett B, Kasanga CJ, Oyola SO. Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda. Viruses 2024; 16:1148. [PMID: 39066310 PMCID: PMC11281637 DOI: 10.3390/v16071148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Rift Valley fever (RVF), a mosquito-borne transboundary zoonosis, was first confirmed in Rwanda's livestock in 2012 and since then sporadic cases have been reported almost every year. In 2018, the country experienced its first large outbreak, which was followed by a second one in 2022. To determine the circulating virus lineages and their ancestral origin, two genome sequences from the 2018 outbreak, and thirty-six, forty-one, and thirty-eight sequences of small (S), medium (M), and large (L) genome segments, respectively, from the 2022 outbreak were generated. All of the samples from the 2022 outbreak were collected from slaughterhouses. Both maximum likelihood and Bayesian-based phylogenetic analyses were performed. The findings showed that RVF viruses belonging to a single lineage, C, were circulating during the two outbreaks, and shared a recent common ancestor with RVF viruses isolated in Uganda between 2016 and 2019, and were also linked to the 2006/2007 largest East Africa RVF outbreak reported in Kenya, Tanzania, and Somalia. Alongside the wild-type viruses, genetic evidence of the RVFV Clone 13 vaccine strain was found in slaughterhouse animals, demonstrating a possible occupational risk of exposure with unknown outcome for people working in meat-related industry. These results provide additional evidence of the ongoing wide spread of RVFV lineage C in Africa and emphasize the need for an effective national and international One Health-based collaborative approach in responding to RVF emergencies.
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Affiliation(s)
- Isidore Nsengimana
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania
- Rwanda Inspectorate, Competition and Consumer Protection Authority, Kigali P.O. Box 375, Rwanda
- Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
| | - Kristina Roesel
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
| | - Methode N. Gasana
- Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda
| | - Fabrice Ndayisenga
- Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda
| | | | | | - Jean N. Hakizimana
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania
| | - Gillian Eastwood
- Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Augustino A. Chengula
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
| | - Bernard Bett
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
| | - Christopher J. Kasanga
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
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13
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Zhang Z, He F, Yi L, Deng Z, Wang R, Shen L, Fu S. Wastewater surveillance together with metaviromic data revealed the unusual resurgence of infectious diseases after the first wave of the COVID-19 outbreak. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134635. [PMID: 38772110 DOI: 10.1016/j.jhazmat.2024.134635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/01/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
How to address public health priorities after COVID-19 is becoming a critical task. To this end, we conducted wastewater surveillance for six leading pathogens, namely, SARS-CoV-2, norovirus, rotavirus, influenza A virus (IAV), enteroviruses and respiratory syncytial virus (RSV), in Nanchang city from January to April 2023. Metaviromic sequencing was conducted at the 1st, 4th, 7th, 9th, 12th and 14th weeks to reveal the dynamics of viral pathogens that were not covered by qPCR. Amplicon sequencing of the conserved region of norovirus GI and GII and the rotavirus and region encoding nonstructural protein of RSV was also conducted weekly. The results showed that after a rapid decrease in SARS-CoV-2 sewage concentrations occurred in January 2023, surges of norovirus, rotavirus, IAV and RSV started at the 6th, 7th, 8th and 11th weeks, respectively. The dynamics of the sewage concentrations of norovirus, rotavirus, IAV and RSV were consistent with the off-season resurgence of the above infectious diseases. Notably, peak sewage concentrations of norovirus GI, GII, rotavirus, IAV and RSV were found at the 6th, 3rd, 7th, 7th and 8th weeks, respectively. Astroviruses also resurge after the 7th week, as revealed by metaviromic data, suggesting that wastewater surveillance together with metaviromic data provides an essential early warning tool for revealing patterns of infectious disease resurgence.
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Affiliation(s)
- Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Liu Yi
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Zhiqiang Deng
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang 330038, Jiangxi, China
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, Dalian Ocean University, Dalian 116023, China
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, China.
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14
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Butel-Simoes G, Steinig E, Savic I, Zhanduisenov M, Papadakis G, Tran T, Moselen J, Caly L, Williamson DA, Lim CK. Optimising nucleic acid recovery from rapid antigen tests for whole genome sequencing of respiratory viruses. J Clin Virol 2024; 174:105714. [PMID: 39038394 DOI: 10.1016/j.jcv.2024.105714] [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: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Whole genome sequencing (WGS) of respiratory viruses from rapid antigen tests (RAT-WGS) is a novel approach to expanding genomic surveillance of respiratory infections. To date however, there are limited data on the genomic stability of these viruses on RATs. In this study, we investigated the effect of storage conditions and nucleic acid preservatives on the ability to enhance stability and improve recovery of respiratory virus genomes from RATs. METHODS A mixture of common respiratory viruses was used to inoculate RATs at different environmental temperatures (4°C, 20°C and 36°C), with two preservative reagents (RNALater and DNA/RNA shield) Nucleic acid was extracted from RATs at two different timepoints (72 h and seven days) and subject to real-time multiplex respiratory PCR to detect a range of respiratory viruses. WGS was performed using target-enrichment with the TWIST Comprehensive Viral Research Panel. Defined metrics from an automated in-house bioinformatic pipeline were used to assess and compare viral genome recovery under different conditions. RESULTS Nucleic acid degradation (indicated by relative change in PCR cycle threshold and WGS-based metrics) was most notable at 20 °C and 36 °C. Storage in either RNALater or DNA / RNA shield improved genome recovery for respiratory viruses across all temperature conditions, although this was most pronounced for RNALater. Subtyping of Influenza viruses demonstrated the applicability of RAT-WGS in downstream genomic epidemiological surveillance. CONCLUSIONS Under simulated conditions, RAT-WGS demonstrated that (i) viral genomes were generally stable at 4°C at 72 h and 1 week, (ii) RNALater has a more significant preservation of nucleic acids compared to DNA/RNA Shield and (iii) genome recovery can be achieved using a sequencing depth of 500,000 reads per sample in RNALater, across all respiratory viruses and conditions.
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Affiliation(s)
- G Butel-Simoes
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - E Steinig
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - I Savic
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - M Zhanduisenov
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - G Papadakis
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - T Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - J Moselen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - L Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - D A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - C K Lim
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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15
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Gallego-García P, Estévez-Gómez N, De Chiara L, Alvariño P, Juiz-González PM, Torres-Beceiro I, Poza M, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Aja-Macaya P, Ladra S, Moreno-Flores A, Gude-González MJ, Coira A, Aguilera A, Costa-Alcalde JJ, Trastoy R, Barbeito-Castiñeiras G, García-Souto D, Tubio JMC, Trigo-Daporta M, Camacho-Zamora P, Costa JG, González-Domínguez M, Canoura-Fernández L, Glez-Peña D, Pérez-Castro S, Cabrera JJ, Daviña-Núñez C, Godoy-Diz M, Treinta-Álvarez AB, Veiga MI, Sousa JC, Osório NS, Comas I, González-Candelas F, Hong SL, Bollen N, Dellicour S, Baele G, Suchard MA, Lemey P, Agulla A, Bou G, Alonso-García P, Pérez-Del-Molino ML, García-Campello M, Paz-Vidal I, Regueiro B, Posada D. Dispersal history of SARS-CoV-2 in Galicia, Spain. J Med Virol 2024; 96:e29773. [PMID: 38940448 DOI: 10.1002/jmv.29773] [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: 03/25/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron-BA.1 variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOVIGAL Consortium and from the GISAID database, along with mobility information from other Spanish regions and foreign countries. Our analysis indicates that initial introductions during the Alpha phase were predominantly from other Spanish regions and France. However, as the pandemic progressed, introductions from Portugal and the United States became increasingly significant. The number of detected introductions varied from 96 and 101 for Alpha and Delta to 39 for Omicron-BA.1. Most of these introductions left a low number of descendants (<10), suggesting a limited impact on the evolution of the pandemic in Galicia. Notably, Galicia's major coastal cities emerged as critical hubs for viral transmission, highlighting their role in sustaining and spreading the virus. This research emphasizes the critical role of regional connectivity in the spread of SARS-CoV-2 and offers essential insights for enhancing public health strategies and surveillance measures.
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Affiliation(s)
- Pilar Gallego-García
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Nuria Estévez-Gómez
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, Spain
| | | | - Pedro M Juiz-González
- Servicio de Microbiología del Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Isabel Torres-Beceiro
- Servicio de Microbiología del Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Margarita Poza
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
- Microbiome and Health Group, Faculty of Sciences, University of A Coruña (UDC), A Coruña, Spain
| | - Juan A Vallejo
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
| | - Soraya Rumbo-Feal
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
| | - Kelly Conde-Pérez
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
| | - Pablo Aja-Macaya
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
| | - Susana Ladra
- Database Laboratory, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), A Coruña, Spain
| | | | | | - Amparo Coira
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - Antonio Aguilera
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - José J Costa-Alcalde
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - Rocío Trastoy
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - Gema Barbeito-Castiñeiras
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - Daniel García-Souto
- CiMUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José M C Tubio
- CiMUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physic Anthropology, Santiago de Compostela, Spain
| | - Matilde Trigo-Daporta
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Pablo Camacho-Zamora
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Juan García Costa
- Servicio de Microbiología, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Luis Canoura-Fernández
- Servicio de Microbiología, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Daniel Glez-Peña
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Sonia Pérez-Castro
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jorge J Cabrera
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Carlos Daviña-Núñez
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Montserrat Godoy-Diz
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Ana Belén Treinta-Álvarez
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Maria Isabel Veiga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
| | - João Carlos Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
| | - Iñaki Comas
- Tuberculosis Genomics Unit, BioMedicine Institute of Valencia, Spanish Research Council (CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health, Madrid, Spain
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, Valencia, Spain
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Madrid, Spain
- Joint Research Unit "Infection and Public Health", FISABIO-University of Valencia, Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Nena Bollen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, Maryland, USA
| | - Andrés Agulla
- Servicio de Microbiología del Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Germán Bou
- Microbiology Research Group, Institute of Biomedical Research (INIBIC) - Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC) - CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Edificio Sur, Hospital Universitario A Coruña, As Xubias, A Coruña, Spain
| | - Pilar Alonso-García
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - María Luisa Pérez-Del-Molino
- Department of Microbiology, Complexo Hospitalario Universitario de Santiago de Compostela. SERGAS - Microbiology Research Group, Institute of Biomedical Research (IDIS), Santiago de Compostela, Spain
| | - Marta García-Campello
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Isabel Paz-Vidal
- Servicio de Microbiología, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Benito Regueiro
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, Spain
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16
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Phumiphanjarphak W, Aiewsakun P. Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling. BMC Bioinformatics 2024; 25:222. [PMID: 38914932 PMCID: PMC11197340 DOI: 10.1186/s12859-024-05846-y] [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: 08/08/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a promising solution to this problem by providing an unbiased overview of the microbial community, enabling detection of any viruses without prior target selection. However, a major challenge in utilising metagenomic next-generation sequencing for virome investigation is that data analysis can be highly complex, involving numerous data processing steps. RESULTS Here, we present Entourage to address this challenge. Entourage enables short-read sequence assembly, viral sequence search with or without reference virus targets using contig-based approaches, and intrasample sequence variation quantification. Several workflows are implemented in Entourage to facilitate end-to-end virus sequence detection analysis through a single command line, from read cleaning, sequence assembly, to virus sequence searching. The results generated are comprehensive, allowing for thorough quality control, reliability assessment, and interpretation. We illustrate Entourage's utility as a streamlined workflow for virus detection by employing it to comprehensively search for target virus sequences and beyond in raw sequence read data generated from HeLa cell culture samples spiked with viruses. Furthermore, we showcase its flexibility and performance on a real-world dataset by analysing a preassembled Tara Oceans dataset. Overall, our results show that Entourage performs well even with low virus sequencing depth in single digits, and it can be used to discover novel viruses effectively. Additionally, by using sequence data generated from a patient with chronic SARS-CoV-2 infection, we demonstrate Entourage's capability to quantify virus intrasample genetic variations, and generate publication-quality figures illustrating the results. CONCLUSIONS Entourage is an all-in-one, versatile, and streamlined bioinformatics software for virome investigation, developed with a focus on ease of use. Entourage is available at https://codeberg.org/CENMIG/Entourage under the MIT license.
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Affiliation(s)
- Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, 272 Rama VI Road, Bangkok, 10400, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, 272 Rama VI Road, Bangkok, 10400, Thailand.
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
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17
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Coldbeck-Shackley RC, Adamson PJ, Whybrow D, Selway CA, Papanicolas LE, Turra M, Leong LEX. Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance. J Clin Virol 2024; 174:105709. [PMID: 38924832 DOI: 10.1016/j.jcv.2024.105709] [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: 03/11/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis. METHODS We implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis. RESULTS Optimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone. CONCLUSIONS These findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.
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Affiliation(s)
| | - Penelope J Adamson
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Daryn Whybrow
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Caitlin A Selway
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lito E Papanicolas
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Mark Turra
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia
| | - Lex E X Leong
- Microbiology and Infectious Diseases, SA Pathology, Adelaide 5000 Australia; UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000 Australia
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18
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Ereqat S, Alikhan NF, Al-Jawabreh A, Matthews M, Al-Jawabreh A, de Oliveira Martins L, Trotter AJ, Al-Kaila M, Page AJ, Pallen MJ, Nasereddin A. Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine. Pathogens 2024; 13:521. [PMID: 38921818 PMCID: PMC11206313 DOI: 10.3390/pathogens13060521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima's D, Fu-Li's F, and Fu-Li's D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright's F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.
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Affiliation(s)
- Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
| | - Nabil-Fareed Alikhan
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Amer Al-Jawabreh
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Arab American University, Jenin P.O. Box 240, Palestine
- Leishmaniases Research Unit, Jericho P5840227, Palestine
| | - Michaela Matthews
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Ahmed Al-Jawabreh
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
- Ministry of Health of the State of Palestine, Ramallah P6028100, Palestine;
| | - Leonardo de Oliveira Martins
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Mai Al-Kaila
- Ministry of Health of the State of Palestine, Ramallah P6028100, Palestine;
| | - Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (N.-F.A.); (L.d.O.M.); (A.J.T.); (A.J.P.); (M.J.P.)
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Dis, Jerusalem P.O. Box 51000, Palestine; (S.E.); (A.N.)
- Al-Quds Bard College, Al-Quds University, East Jerusalem P.O. Box 20002, Palestine
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Pena NM, Santana LC, Hunter JR, Blum VF, Vergara T, Gouvea C, Leal E, Bellei N, Schechter M, Diaz RS. T cell-mediated Immune response and correlates of inflammation and their relationship with COVID-19 clinical severity: not an intuitive guess. BMC Infect Dis 2024; 24:612. [PMID: 38902613 PMCID: PMC11191252 DOI: 10.1186/s12879-024-09490-y] [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: 05/01/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Predictors of the outcome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remain to be fully determined. We evaluated selected viral characteristics and immunological responses that might predict and/or correlate to the clinical outcome of COVID-19. METHODS For individuals developing divergent clinical outcomes, the magnitude and breadth of T cell-mediated responses were measured within 36 h of symptom onset. Peripheral Blood Mononuclear Cells (PBMCs) were subjected to in vitro stimulation with SARS-CoV-2-based peptides. In addition, SARS-CoV-2 sequences were generated by metagenome, and HLA typing was performed using Luminex technology. FINDINGS CD4+ T cell activation was negatively correlated with SARS-CoV-2 basal viral load in patients with severe COVID-19 (p = 0·043). The overall cellular immune response, as inferred by the IFN-γ signal, was higher at baseline for patients who progressed to mild disease compared to patients who progressed to severe disease (p = 0·0044). Subjects with milder disease developed higher T cell responses for MHC class I and II-restricted peptides (p = 0·033). INTERPRETATION Mounting specific cellular immune responses in the first days after symptom onset, as inferred by IFN-γ magnitude in the ELISPOT assay, may efficiently favor a positive outcome. In contrast, progression to severe COVID-19 was accompanied by stronger cellular immune responses, higher CD4 + T cell activation, and a higher number of in silico predicted high-affinity class I HLA alleles.
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Affiliation(s)
- Nathalia Mantovani Pena
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
- Weill Cornell Medicine, New York, United States of America
| | - Luiz Claudio Santana
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - James R Hunter
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Vinicius Fontanesi Blum
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Tania Vergara
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
- Oncohiv, Rio de Janeiro, Brazil
| | - Celso Gouvea
- Centro de Hematologia e Hemoterapia do Ceará, Fortaleza, CE, Brazil
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil
| | - Nancy Bellei
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
| | - Mauro Schechter
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Sobhie Diaz
- Infectious Diseases Division, Federal University of São Paulo (UNIFESP), Pedro de Toledo, 669, Vila Clementino, Sao Paulo, SP, 04039-032, Brazil.
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Djuicy DD, Omah IF, Parker E, Tomkins-Tinch CH, Otieno JR, Yifomnjou MHM, Essengue LLM, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-ewe OO, Ogunsanya OA, Olono A, Eromon P, Yonga MGW, Essima GD, Touoyem IP, Mounchili LJM, Eyangoh SI, Esso L, Nguidjol IME, Metomb SF, Chebo C, Agwe SM, Mossi HM, Bilounga CN, Etoundi AGM, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, O’Toole Á, Magee A, Zeller M, Gangavarapu K, Varilly P, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Ihekweazu C, Jide I, Adetifa I, Njoum R, Happi CT. Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309115. [PMID: 38947021 PMCID: PMC11213044 DOI: 10.1101/2024.06.18.24309115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Nigeria and Cameroon reported their first mpox cases in over three decades in 2017 and 2018 respectively. The outbreak in Nigeria is recognised as an ongoing human epidemic. However, owing to sparse surveillance and genomic data, it is not known whether the increase in cases in Cameroon is driven by zoonotic or sustained human transmission. Notably, the frequency of zoonotic transmission remains unknown in both Cameroon and Nigeria. To address these uncertainties, we investigated the zoonotic transmission dynamics of the mpox virus (MPXV) in Cameroon and Nigeria, with a particular focus on the border regions. We show that in these regions mpox cases are still driven by zoonotic transmission of a newly identified Clade IIb.1. We identify two distinct zoonotic lineages that circulate across the Nigeria-Cameroon border, with evidence of recent and historic cross border dissemination. Our findings support that the complex cross-border forest ecosystems likely hosts shared animal populations that drive cross-border viral spread, which is likely where extant Clade IIb originated. We identify that the closest zoonotic outgroup to the human epidemic circulated in southern Nigeria in October 2013. We also show that the zoonotic precursor lineage circulated in an animal population in southern Nigeria for more than 45 years. This supports findings that southern Nigeria was the origin of the human epidemic. Our study highlights the ongoing MPXV zoonotic transmission in Cameroon and Nigeria, underscoring the continuous risk of MPXV (re)emergence.
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Affiliation(s)
- Delia Doreen Djuicy
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | - Ifeanyi F. Omah
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Edyth Parker
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | | | | | - Akeemat Opeyemi Ayinla
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Muhammad I. Ahmed
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oludayo O. Ope-ewe
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola Akinola Ogunsanya
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Alhaji Olono
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena Eromon
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Gael Dieudonné Essima
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | | | | | - Sara Irene Eyangoh
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | - Linda Esso
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Inès Mandah Emah Nguidjol
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Steve Franck Metomb
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Cornelius Chebo
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Samuel Mbah Agwe
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Hans Makembe Mossi
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | - Chanceline Ndongo Bilounga
- Department for the Control of Disease, Epidemics and Pandemics, Ministry of Public Health, Yaounde, Cameroon
| | | | - Olusola Akanbi
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Abiodun Egwuenu
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | | | - Chimaobi Chukwu
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Kabiru Suleiman
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Afolabi Akinpelu
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Adama Ahmad
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | | | - Richard Ojedele
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Victor Oripenaye
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Kenneth Ikeata
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | | | | | - Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Andrew Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick Varilly
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention (Africa CDC),Addis Ababa, Ethiopia
| | | | - Yenew Kebede Tebeje
- Africa Centres for Disease Control and Prevention (Africa CDC),Addis Ababa, Ethiopia
| | - Onikepe Folarin
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Pardis Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Idriss Jide
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Ifedayo Adetifa
- Nigeria Centre for Disease Control and Prevention., Abuja, Nigeria
| | - Richard Njoum
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115, USA
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21
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Parker E, Omah IF, Varilly P, Magee A, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-ewe OO, Ogunsanya OA, Olono A, Eromon P, Tomkins-Tinch CH, Otieno JR, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, Djuicy DD, Essengue LLM, Yifomnjou MHM, Zeller M, Gangavarapu K, O’Toole Á, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Njoum R, Ihekweazu C, Jide I, Adetifa I, Happi CT. Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309104. [PMID: 38947052 PMCID: PMC11213064 DOI: 10.1101/2024.06.18.24309104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Five years before the 2022-2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus' (MPXV) emergence. Here we generated 112 MPXV genomes from Nigeria from 2021-2023. We identify the closest zoonotic outgroup to the human epidemic in southern Nigeria, and estimate that the lineage transmitting from human-to-human emerged around July 2014, circulating cryptically until detected in September 2017. The epidemic originated in Southern Nigeria, particularly Rivers State, which also acted as a persistent and dominant source of viral dissemination to other states. We show that APOBEC3 activity increased MPXV's evolutionary rate twenty-fold during human-to-human transmission. We also show how Delphy, a tool for near-real-time Bayesian phylogenetics, can aid rapid outbreak analytics. Our study sheds light on MPXV's establishment in West Africa before the 2022-2023 global outbreak and highlights the need for improved pathogen surveillance and response.
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Affiliation(s)
- Edyth Parker
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ifeanyi F. Omah
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
- Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Patrick Varilly
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Magee
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Akeemat Opeyemi Ayinla
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Muhammad I. Ahmed
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oludayo O. Ope-ewe
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola Akinola Ogunsanya
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Alhaji Olono
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena Eromon
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Olusola Akanbi
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Abiodun Egwuenu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | - Chimaobi Chukwu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Kabiru Suleiman
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Afolabi Akinpelu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Adama Ahmad
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | - Richard Ojedele
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Victor Oripenaye
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Kenneth Ikeata
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | | | | | - Delia Doreen Djuicy
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | | | | | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia
| | | | - Yenew Kebede Tebeje
- Africa Centres for Disease Control and Prevention, P.O. Box 3243, Addis Ababa, Ethiopia
| | - Onikepe Folarin
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Pardis Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, UK
| | - Richard Njoum
- Virology Service, Centre Pasteur du Cameroun, 451 Rue 2005, Yaounde 2, P.O. Box 1274
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Idriss Jide
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ifedayo Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA 02115
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22
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Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, Brooke CB. Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin. Virus Evol 2024; 10:veae046. [PMID: 38915760 PMCID: PMC11196192 DOI: 10.1093/ve/veae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
The antigenic evolution of the influenza A virus hemagglutinin (HA) gene poses a major challenge for the development of vaccines capable of eliciting long-term protection. Prior efforts to understand the mechanisms that govern viral antigenic evolution mainly focus on HA in isolation, ignoring the fact that HA must act in concert with the viral neuraminidase (NA) during replication and spread. Numerous studies have demonstrated that the degree to which the receptor-binding avidity of HA and receptor-cleaving activity of NA are balanced with each other influences overall viral fitness. We recently showed that changes in NA activity can significantly alter the mutational fitness landscape of HA in the context of a lab-adapted virus strain. Here, we test whether natural variation in relative NA activity can influence the evolutionary potential of HA in the context of the seasonal H1N1 lineage (pdmH1N1) that has circulated in humans since the 2009 pandemic. We observed substantial variation in the relative activities of NA proteins encoded by a panel of H1N1 vaccine strains isolated between 2009 and 2019. We comprehensively assessed the effect of NA background on the HA mutational fitness landscape in the circulating pdmH1N1 lineage using deep mutational scanning and observed pronounced epistasis between NA and residues in or near the receptor-binding site of HA. To determine whether NA variation could influence the antigenic evolution of HA, we performed neutralizing antibody selection experiments using a panel of monoclonal antibodies targeting different HA epitopes. We found that the specific antibody escape profiles of HA were highly contingent upon NA background. Overall, our results indicate that natural variation in NA activity plays a significant role in governing the evolutionary potential of HA in the currently circulating pdmH1N1 lineage.
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Affiliation(s)
- Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - William K Reiser
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kyle Heimburger
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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23
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Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade L, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308523. [PMID: 38946967 PMCID: PMC11213110 DOI: 10.1101/2024.06.14.24308523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n=15). All patients received remdesivir and some also received nirmatrelvir-ritonavir or monoclonal antibodies. Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient treated with remdesivir and nirmatrelvir-ritonavir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Ruchi Rani
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Wei Wang
- Systems Genomics Section, NIH/NIAID/DIR/LPD
| | - Jingmei Hsu
- Department of Medicine, Weill Cornell Medicine
| | | | | | | | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | | | | | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine
- Department of Population Health Science, Weill Cornell Medicine
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24
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Meade PS, Bandawane P, Bushfield K, Hoxie I, Azcona KR, Burgos D, Choudhury S, Diaby A, Diallo M, Gaynor K, Huang A, Kante K, Khan SN, Kim W, Ajayi PK, Roubidoux E, Nelson S, McMahon R, Albrecht RA, Krammer F, Marizzi C. Detection of clade 2.3.4.4b highly pathogenic H5N1 influenza virus in New York City. J Virol 2024; 98:e0062624. [PMID: 38747601 PMCID: PMC11237497 DOI: 10.1128/jvi.00626-24] [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: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/28/2024] Open
Abstract
Highly pathogenic avian influenza viruses of the H5N1 clade 2.3.4.4b were detected in North America in the winter of 2021/2022. These viruses have spread across the Americas, causing morbidity and mortality in both wild and domestic birds as well as some mammalian species, including cattle. Many surveillance programs for wildlife as well as commercial poultry operations have detected these viruses. In this study, we conducted surveillance of avian species in the urban environment in New York City. We detected highly pathogenic H5N1 viruses in six samples from four different bird species and performed whole-genome sequencing. Sequencing analysis showed the presence of multiple different genotypes. Our work highlights that the interface between animals and humans that may give rise to zoonotic infections or even pandemics is not limited to rural environments and commercial poultry operations but extends into the heart of our urban centers.IMPORTANCEWhile surveillance programs for avian influenza viruses are often focused on migratory routes and their associated stop-over locations or commercial poultry operations, many bird species-including migratory birds-frequent or live in urban green spaces and wetlands. This brings them into contact with a highly dense population of humans and pets, providing an extensive urban animal-human interface in which the general public may have little awareness of circulating infectious diseases. This study focuses on virus surveillance of this interface, combined with culturally responsive science education and community outreach.
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Affiliation(s)
- Philip S. Meade
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pooja Bandawane
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kaitlyn Bushfield
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Irene Hoxie
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karla R. Azcona
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Daneidy Burgos
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Sadia Choudhury
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Adama Diaby
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Mariama Diallo
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Kailani Gaynor
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Aaron Huang
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Kadiatou Kante
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - Shehryar N. Khan
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | - William Kim
- New York City Virus Hunters Program, BioBus, New York, New York, USA
| | | | - Ericka Roubidoux
- Department of Host Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sasha Nelson
- Animal Care Centers of New York, New York, New York, USA
| | | | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Christine Marizzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- New York City Virus Hunters Program, BioBus, New York, New York, USA
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25
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da Silva AF, da Silva Neto AM, Aksenen C, Jeronimo P, Dezordi F, Almeida S, Costa H, Salvato R, Campos TD, Wallau G, of the Fiocruz Genomic Network OB. ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance. NAR Genom Bioinform 2024; 6:lqae056. [PMID: 38800829 PMCID: PMC11127631 DOI: 10.1093/nargab/lqae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned ViralFlow into a general-purpose reference-based genome assembler for all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. ViralFlow v1.0 runs on a broad range of computational infrastructures, from laptop computers to high-performance computing (HPC) environments, and generates standard and well-formatted outputs suited for both public health reporting and scientific problem-solving. ViralFlow v1.0 is available at: https://viralflow.github.io/index-en.html.
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Affiliation(s)
- Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Antonio Marinho da Silva Neto
- Data Analysis and Engineering, Genomic Surveillance Unit, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | | | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | | | - Hudson Marques Paula Costa
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Richard Steiner Salvato
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, Rio Grande do Sul 90450-190, Brazil
| | - Tulio de Lima Campos
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
| | - Gabriel da Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Pernambuco 50670-420, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, D-20359 Hamburg, Germany
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26
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Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024; 20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.
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Affiliation(s)
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Syed A. Rahman
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isaiah G. L. Bicar
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Sullivan Gregory
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Grant D. Brown
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
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27
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Hikmat H, Le Targa L, Boschi C, Py J, Bedotto M, Morand A, Cassir N, Aherfi S, La Scola B, Colson P. Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022. J Med Virol 2024; 96:e29706. [PMID: 38888111 DOI: 10.1002/jmv.29706] [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: 02/07/2024] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024]
Abstract
The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.
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Affiliation(s)
- Houmadi Hikmat
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Lorlane Le Targa
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Biosellal, Lyon, France
| | - Celine Boschi
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Justine Py
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Marielle Bedotto
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Aurélie Morand
- Service d'Accueil des Urgences Pédiatriques, Hôpital Nord, AP-HM, Marseille, France
- Service de Pédiatrie Générale, Hôpital Timone, AP-HM, Marseille, France
| | - Nadim Cassir
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Sarah Aherfi
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Bernard La Scola
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Philippe Colson
- Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Universite, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
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28
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Xu X, Deng Y, Ding J, Tang Q, Lin Y, Zheng X, Zhang T. High-resolution and real-time wastewater viral surveillance by Nanopore sequencing. WATER RESEARCH 2024; 256:121623. [PMID: 38657304 DOI: 10.1016/j.watres.2024.121623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Wastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Qinling Tang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Yunqi Lin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region; School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
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29
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Jimenez-Vasquez V, Vargas-Herrera N, Bárcena-Flores L, Hurtado V, Padilla-Rojas C, Araujo-Castillo RV. Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022. Genomics Inform 2024; 22:5. [PMID: 38907313 PMCID: PMC11184951 DOI: 10.1186/s44342-024-00006-3] [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: 07/31/2023] [Accepted: 03/04/2024] [Indexed: 06/23/2024] Open
Abstract
During the third year of the pandemic in Peru, the persistent transmission of SARS-CoV-2 led to the appearance of more transmissible and immune-evasive Omicron sublineages; in that context, the National Genomic Surveillance of SARS-CoV-2 performed by the Peruvian National Institute of Health detected spike mutations in the circulating Omicron BA.5.1.25 sublineage which was later designated as DJ.1 and increased during the fourth COVID-19 wave, this eventually branched into new sublineages. The introduction, emergence, and timing of the most recent common ancestor (tMRCA) of BA.5.1.25 and its descendants (DJ.1, DJ.1.1, DJ.1.2, and DJ.1.3) were investigated in this paper as well as the time lags between their emergence and identification by the Peruvian National Institute of Health. Our findings show that ongoing genomic surveillance of SARS-CoV-2 is critical for understanding its phylogenetic evolution and the emergence of novel variations.
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Affiliation(s)
- Victor Jimenez-Vasquez
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru
| | - Natalia Vargas-Herrera
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru.
| | - Luis Bárcena-Flores
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru
| | - Verónica Hurtado
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru
| | - Carlos Padilla-Rojas
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru
| | - Roger V Araujo-Castillo
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Capac Yupanqui 1400-Jesus Maria, Lima, Peru
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30
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Spilsberg B, Leithaug M, Christiansen DH, Dahl MM, Petersen PE, Lagesen K, Fiskebeck EMLZ, Moldal T, Boye M. Development and application of a whole genome amplicon sequencing method for infectious salmon anemia virus (ISAV). Front Microbiol 2024; 15:1392607. [PMID: 38873156 PMCID: PMC11169708 DOI: 10.3389/fmicb.2024.1392607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
Infectious salmon anemia (ISA) is an infectious disease primarily affecting farmed Atlantic salmon, Salmo salar, which is caused by the ISA virus (ISAV). ISAV belongs to the Orthomyxoviridae family. The disease is a serious condition resulting in reduced fish welfare and high mortality. In this study, we designed an amplicon-based sequencing protocol for whole genome sequencing of ISAV. The method consists of 80 ISAV-specific primers that cover 92% of the virus genome and was designed to be used on an Illumina MiSeq platform. The sequencing accuracy was investigated by comparing sequences with previously published Sanger sequences. The sequences obtained were nearly identical to those obtained by Sanger sequencing, thus demonstrating that sequences produced by this amplicon sequencing protocol had an acceptable accuracy. The amplicon-based sequencing method was used to obtain the whole genome sequence of 12 different ISAV isolates from a small local epidemic in the northern part of Norway. Analysis of the whole genome sequences revealed that segment reassortment took place between some of the isolates and could identify which segments that had been reassorted.
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Affiliation(s)
- Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Magnus Leithaug
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | | | - Maria Marjunardóttir Dahl
- National Reference Laboratory for Fish and Animal Diseases, Faroese Food and Veterinary Authority, Torshavn, Faroe Islands
| | - Petra Elisabeth Petersen
- National Reference Laboratory for Fish and Animal Diseases, Faroese Food and Veterinary Authority, Torshavn, Faroe Islands
| | - Karin Lagesen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Ås, Norway
| | | | - Torfinn Moldal
- Department of Aquatic Animal Health and Welfare, Norwegian Veterinary Institute, Ås, Norway
| | - Mette Boye
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
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31
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Paremskaia AI, Volchkov PY, Deviatkin AA. IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data. Viruses 2024; 16:873. [PMID: 38932165 PMCID: PMC11209090 DOI: 10.3390/v16060873] [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: 03/18/2024] [Revised: 04/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed.
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Affiliation(s)
- Anastasiia Iu. Paremskaia
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
| | - Pavel Yu. Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The MCSC Named after A. S. Loginov, 111123 Moscow, Russia
| | - Andrei A. Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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32
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Liu Y, Sapoval N, Gallego-García P, Tomás L, Posada D, Treangen TJ, Stadler LB. Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nat Commun 2024; 15:4545. [PMID: 38806450 PMCID: PMC11133379 DOI: 10.1038/s41467-024-48334-w] [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: 11/15/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.
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Affiliation(s)
- Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA.
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA.
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33
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Silva T, Oliveira E, Oliveira A, Menezes A, Jeremias WDJ, Grenfell RF, Monte-Neto RLD, Pascoal-Xavier MA, Campos MA, Fernandes G, Alves P. Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants. Braz J Microbiol 2024:10.1007/s42770-024-01387-x. [PMID: 38802687 DOI: 10.1007/s42770-024-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Since the emergence of SARS-CoV-2 in December 2019, more than 12,000 mutations in the virus have been identified. These could cause changes in viral characteristics and directly impact global public health. The emergence of variants is a great concern due to the chance of increased transmissibility and infectivity. Sequencing for surveillance and monitoring circulating strains is extremely necessary as the early identification of new variants allows public health agencies to make faster and more effective decisions to contain the spread of the virus. In the present study, we identified circulating variants in samples collected in Belo Horizonte, Brazil, and detected a recombinant lineage using the Sanger method. The identification of lineages was done through gene amplification of SARS-CoV-2 by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). By using these specific fragments, we were able to differentiate one variant of interest and five circulating variants of concern. We were also able to detect recombinants. Randomly selected samples were sequenced by either Sanger or Next Generation Sequencing (NGS). Our findings validate the effectiveness of Sanger sequencing as a powerful tool for monitoring variants. It is easy to perform and allows the analysis of a larger number of samples in countries that cannot afford NGS.
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Affiliation(s)
- Thaís Silva
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Eneida Oliveira
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Alana Oliveira
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - André Menezes
- Secretaria Municipal de Saúde, 2336, Afonso Pena Avenue, Belo Horizonte, Minas Gerais, 30130-007, Brazil
| | - Wander de Jesus Jeremias
- Department of Pharmacy, Federal University of Ouro Preto (UFOP), 27, Nine Street, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Rafaella Fq Grenfell
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Rubens Lima do Monte-Neto
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Marcelo A Pascoal-Xavier
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
- Department of Anatomic Pathology, College of Medicine, Federal University of Minas Gerais, 6627, Presidente Antônio Carlos Avenue, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marco A Campos
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Gabriel Fernandes
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil
| | - Pedro Alves
- Instituto René Rachou, Fundação Oswaldo Cruz, 1715, Augusto de Lima Avenue, Belo Horizonte, Minas Gerais, 30190-002, Brazil.
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Suljič A, Zorec TM, Zakotnik S, Vlaj D, Kogoj R, Knap N, Petrovec M, Poljak M, Avšič-Županc T, Korva M. Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing. Brief Bioinform 2024; 25:bbae263. [PMID: 38833323 PMCID: PMC11149657 DOI: 10.1093/bib/bbae263] [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: 11/07/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.
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Affiliation(s)
- Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Tomaž Mark Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Doroteja Vlaj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
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Velasco JM, Valderama MT, Diones PC, Leonardia S, Alcantara S, Joonlasak K, Chinnawirotpisan P, Manasatienkij W, Klungthong C, Arellano ER, Osia CM, Magistrado-Payot J, Fajardo P, Navarro FC, Wuertz KM, Farmer A. Outbreak of influenza and SARS-CoV-2 at the Armed Forces of the Philippines Health Service Education and Training Center, September 25-October 10, 2023. MSMR 2024; 31:9-15. [PMID: 38847656 PMCID: PMC11189823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
In the last week of September 2023, a surge of influenza-like illness was observed among students of the Armed Forces of the Philippines (AFP) Health Service Education and Training Center, where 48 (27 males and 21 females; age in years: mean 33, range 27-41) of 247 military students at the Center presented with respiratory symptoms. Between September 25 and October 10, 2023, all 48 symptomatic students were evaluated with real-time reverse transcription polymerase chain reaction and sequencing for both influenza and SARS-CoV-2. Thirteen (27%) students were found positive for influenza A/H3 only, 6 (13%) for SARS-CoV-2 only, and 4 (8%) were co-infected with influenza A/H3 and SARS-CoV-2. Seventeen influenza A/ H3N2 viruses belonged to the same clade, 3C.2a1b.2a.2a.3a, and 4 SARSCoV-2 sequences belonged to the JE1.1 lineage, indicating a common source outbreak for both. The influenza A/H3N2 circulating virus belonged to a different clade than the vaccine strain for 2023 (3C.2a1b.2a.2a). Only 4 students had received the influenza vaccine for 2023. In response, the AFP Surgeon General issued a memorandum to all military health institutions on October 19, 2023 that mandated influenza vaccination as a prerequisite for enrollment of students at all education and training centers, along with implementation of non-pharmaceutical interventions and early notification and testing of students exhibiting influenza-like-illness.
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Affiliation(s)
- John Mark Velasco
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of the Philippines Manila, Ermita
| | - Maria Theresa Valderama
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Paula Corazon Diones
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Susie Leonardia
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Simon Alcantara
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Khajohn Joonlasak
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Piyawan Chinnawirotpisan
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Errol Roy Arellano
- V. Luna Medical Center, AFP Health Service Command, Quezon City, Philippines
| | - Carrol Mae Osia
- Public Health Service Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Joy Magistrado-Payot
- Office of the Surgeon General, Camp General Emilio Aguinaldo, Quezon City, Philippines
| | - Paul Fajardo
- Public Health Service Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Fatima Claire Navarro
- Office of the Surgeon General, Camp General Emilio Aguinaldo, Quezon City, Philippines
| | - Kathryn McGuckin Wuertz
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Aaron Farmer
- Walter Reed Army Institute of Research-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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Iglesias-Caballero M, Mas V, Vázquez-Morón S, Vázquez M, Camarero-Serrano S, Cano O, Palomo C, Ruano MJ, Cano-Gómez C, Infantes-Lorenzo JA, Campoy A, Agüero M, Pozo F, Casas I. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. Int J Mol Sci 2024; 25:5499. [PMID: 38791536 PMCID: PMC11122236 DOI: 10.3390/ijms25105499] [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: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.
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Affiliation(s)
- María Iglesias-Caballero
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Vicente Mas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sonia Vázquez-Morón
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mónica Vázquez
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sara Camarero-Serrano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Olga Cano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Concepción Palomo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - María José Ruano
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Cristina Cano-Gómez
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - José Antonio Infantes-Lorenzo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Albert Campoy
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Montserrat Agüero
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Francisco Pozo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Inmaculada Casas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Tang MHE, Bennedbaek M, Gunalan V, Qvesel AG, Thorsen TH, Larsen NB, Rasmussen LD, Krogsgaard LW, Rasmussen M, Stegger M, Alexandersen S. Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants. Heliyon 2024; 10:e29703. [PMID: 38694057 PMCID: PMC11061675 DOI: 10.1016/j.heliyon.2024.e29703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/03/2024] Open
Abstract
Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5'-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5'-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.
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Affiliation(s)
- Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbaek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Theis Hass Thorsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Western Australia, Australia
| | - Soren Alexandersen
- Division of Diagnostic Preparedness, Statens Serum Institut, Copenhagen, Denmark
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
- Deakin University, School of Medicine, Waurn Ponds, Geelong, Australia
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Kogoj R, Grašek M, Suljič A, Zakotnik S, Vlaj D, Kotnik Koman K, Fafangel M, Petrovec M, Avšič-Županc T, Korva M. Sequencing analysis of SARS-CoV-2 cases in Slovenian long-term care facilities to support outbreak control. Front Public Health 2024; 12:1406777. [PMID: 38813418 PMCID: PMC11133669 DOI: 10.3389/fpubh.2024.1406777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Residents of long-term care facilities (LTCFs) are at high risk of morbidity and mortality due to COVID-19, especially when new variants of concern (VOC) emerge. To provide intradisciplinary data in order to tailor public health interventions during future epidemics, available epidemiologic and genomic data from Slovenian LTCFs during the initial phases of the COVID-19 pandemic was analyzed. Methods The first part of the study included SARS-CoV-2 reverse-transcription Real-Time PCR (rtRT-PCR) positive LTCF residents, from 21 facilities with COVID-19 outbreaks occurring in October 2020. The second part of the study included SARS-CoV-2 rtRT-PCR positive LTCF residents and staff between January and April 2021, when VOC Alpha emerged in Slovenia. Next-generation sequencing (NGS) was used to acquire SARS-CoV-2 genomes, and lineage determination. In-depth phylogenetic and mutational profile analysis were performed and coupled with available field epidemiological data to assess the dynamics of SARS-CoV-2 introduction and transmission. Results 370/498 SARS-CoV-2 positive residents as well as 558/699 SARS-CoV-2 positive residents and 301/358 staff were successfully sequenced in the first and second part of the study, respectively. In October 2020, COVID-19 outbreaks in the 21 LTCFs were caused by intra-facility transmission as well as multiple independent SARS-CoV-2 introductions. The Alpha variant was confirmed in the first LTCF resident approximately 1.5 months after the first Alpha case was identified in Slovenia. The data also showed a slower replacement of existing variants by Alpha in residents compared to staff and the general population. Discussion Multiple SARS CoV-2 introductions as well as intra-facility spreading impacted disease transmission in Slovenian LTCFs. Timely implementation of control measures aimed at limiting new introductions while controlling in-facility transmission are of paramount importance, especially as new VOCs emerge. Sequencing, in conjunction with epidemiological data, can facilitate the determination of the need for future improvements in control measures to protect LTCF residents from COVID-19 or other respiratory infections.
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Affiliation(s)
- Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manja Grašek
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Doroteja Vlaj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Kotnik Koman
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Fafangel
- Communicable Diseases Center, National Institute of Public Health, Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Misa Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Kantor RS, Jiang M. Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8161-8168. [PMID: 38691513 PMCID: PMC11097388 DOI: 10.1021/acs.est.4c02638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.
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Affiliation(s)
- Rose S. Kantor
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Minxi Jiang
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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40
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Vogels CBF, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog KS, Fauver JR, Morrison AM, Michael SF, Grubaugh ND. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024; 25:433. [PMID: 38693476 PMCID: PMC11062901 DOI: 10.1186/s12864-024-10350-x] [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: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. RESULTS We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. CONCLUSIONS DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.
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Affiliation(s)
- Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Emma Taylor-Salmon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Dennis Dijk
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Timothy Locksmith
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Yibo Dong
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Namratha Tarigopula
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Omer Tekin
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sarah Schmedes
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Charles Panzera
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Julieta Vergara
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Edgar Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Kaylee S Herzog
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph R Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrea M Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, USA.
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41
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Paull JS, Petros BA, Brock-Fisher TM, Jalbert SA, Selser VM, Messer KS, Dobbins ST, DeRuff KC, Deng D, Springer M, Sabeti PC. Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study. THE LANCET. MICROBE 2024; 5:e468-e477. [PMID: 38621394 PMCID: PMC11322816 DOI: 10.1016/s2666-5247(23)00399-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 04/17/2024]
Abstract
BACKGROUND Sequencing of SARS-CoV-2 from rapid diagnostic tests (RDTs) can bolster viral genomic surveillance efforts; however, approaches to maximise and standardise pathogen genome recovery from RDTs remain underdeveloped. We aimed to systematically optimise the elution of genetic material from RDT components and to evaluate the efficacy of RDT sequencing for outbreak investigation. METHODS In this laboratory and cohort-based study we seeded RDTs with inactivated SARS-CoV-2 to optimise the elution of genomic material from RDT lateral flow strips. We measured the effect of changes in buffer type, time in buffer, and rotation on PCR cycle threshold (Ct) value. We recruited individuals older than 18 years residing in the greater Boston area, MA, USA, from July 18 to Nov 5, 2022, via email advertising to students and staff at Harvard University, MA, USA, and via broad social media advertising. All individuals recruited were within 5 days of a positive diagnostic test for SARS-CoV-2; no other relevant exclusion criteria were applied. Each individual completed two RDTs and one PCR swab. On Dec 29, 2022, we also collected RDTs from a convenience sample of individuals who were positive for SARS-CoV-2 and associated with an outbreak at a senior housing facility in MA, USA. We extracted all returned PCR swabs and RDT components (ie, swab, strip, or buffer); samples with a Ct of less than 40 were subject to amplicon sequencing. We compared the efficacy of elution and sequencing across RDT brands and components and used RDT-derived sequences to infer transmission links within the outbreak at the senior housing facility. We conducted metagenomic sequencing of negative RDTs from symptomatic individuals living in the senior housing facility. FINDINGS Neither elution duration of greater than 10 min nor rotation during elution impacted viral titres. Elution in Buffer AVL (Ct=31·4) and Tris-EDTA Buffer (Ct=30·8) were equivalent (p=0·34); AVL outperformed elution in lysis buffer and 50% lysis buffer (Ct=40·0, p=0·0029 for both) as well as Universal Viral Transport Medium (Ct=36·7, p=0·079). Performance of RDT strips was poorer than that of matched PCR swabs (mean Ct difference 10·2 [SD 4·3], p<0·0001); however, RDT swabs performed similarly to PCR swabs (mean Ct difference 4·1 [5·2], p=0·055). No RDT brand significantly outperformed another. Across sample types, viral load predicted the viral genome assembly length. We assembled greater than 80% complete genomes from 12 of 17 RDT-derived swabs, three of 18 strips, and four of 11 residual buffers. We generated outbreak-associated SARS-CoV-2 genomes using both amplicon and metagenomic sequencing and identified multiple introductions of the virus that resulted in downstream transmission. INTERPRETATION RDT-derived swabs are a reasonable alternative to PCR swabs for viral genomic surveillance and outbreak investigation. RDT-derived lateral flow strips yield accurate, but significantly fewer, viral reads than matched PCR swabs. Metagenomic sequencing of negative RDTs can identify viruses that might underlie patient symptoms. FUNDING The National Science Foundation, the Hertz Foundation, the National Institute of General Medical Sciences, Harvard Medical School, the Howard Hughes Medical Institute, the US Centers for Disease Control and Prevention, the Broad Institute and the National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Brittany A Petros
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA; Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA.
| | - Taylor M Brock-Fisher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | - Davy Deng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA.
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Igari H, Sakao S, Ishige T, Saito K, Murata S, Yahaba M, Taniguchi T, Suganami A, Matsushita K, Tamura Y, Suzuki T, Ido E. Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19. Nat Commun 2024; 15:3604. [PMID: 38684722 PMCID: PMC11058237 DOI: 10.1038/s41467-024-47941-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Numerous SARS-CoV-2 variant strains with altered characteristics have emerged since the onset of the COVID-19 pandemic. Remdesivir (RDV), a ribonucleotide analogue inhibitor of viral RNA polymerase, has become a valuable therapeutic agent. However, immunosuppressed hosts may respond inadequately to RDV and develop chronic persistent infections. A patient with respiratory failure caused by interstitial pneumonia, who had undergone transplantation of the left lung, developed COVID-19 caused by Omicron BA.5 strain with persistent chronic viral shedding, showing viral fusogenicity. Genome-wide sequencing analyses revealed the occurrence of several viral mutations after RDV treatment, followed by dynamic changes in the viral populations. The C799F mutation in nsp12 was found to play a pivotal role in conferring RDV resistance, preventing RDV-triphosphate from entering the active site of RNA-dependent RNA polymerase. The occurrence of diverse mutations is a characteristic of SARS-CoV-2, which mutates frequently. Herein, we describe the clinical case of an immunosuppressed host in whom inadequate treatment resulted in highly diverse SARS-CoV-2 mutations that threatened the patient's health due to the development of drug-resistant variants.
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Affiliation(s)
- Hidetoshi Igari
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan.
- COVID-19 Vaccine Center, Chiba University Hospital, Chiba, Chiba, Japan.
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan.
| | - Seiichiro Sakao
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Pulmonary Medicine, School of Medicine, International University of Health and Welfare, Narita, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan.
| | - Kengo Saito
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Shota Murata
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Misuzu Yahaba
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
| | - Toshibumi Taniguchi
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan
| | - Akiko Suganami
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Yutaka Tamura
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Takuji Suzuki
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba, Chiba, Japan
| | - Eiji Ido
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
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Daviña-Núñez C, Pérez S, Cabrera-Alvargonzález JJ, Rincón-Quintero A, Treinta-Álvarez A, Godoy-Diz M, Suárez-Luque S, Regueiro-García B. Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern. PLoS One 2024; 19:e0289188. [PMID: 38683803 PMCID: PMC11057745 DOI: 10.1371/journal.pone.0289188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
To control the SARS-CoV-2 pandemic, healthcare systems have focused on ramping up their capacity for epidemiological surveillance through viral whole genome sequencing. In this paper, we tested the performance of two protocols of SARS-CoV-2 nucleic acid enrichment, an amplicon enrichment using different versions of the ARTIC primer panel and a hybrid-capture method using KAPA RNA Hypercap. We focused on the challenge of the Omicron variant sequencing, the advantages of automated library preparation and the influence of the bioinformatic analysis in the final consensus sequence. All 94 samples were sequenced using Illumina iSeq 100 and analysed with two bioinformatic pipelines: a custom-made pipeline and an Illumina-owned pipeline. We were unsuccessful in sequencing six samples using the capture enrichment due to low reads. On the other hand, amplicon dropout and mispriming caused the loss of mutation G21987A and the erroneous addition of mutation T15521A respectively using amplicon enrichment. Overall, we found high sequence agreement regardless of method of enrichment, bioinformatic pipeline or the use of automation for library preparation in eight different SARS-CoV-2 variants. Automation and the use of a simple app for bioinformatic analysis can simplify the genotyping process, making it available for more diagnostic facilities and increasing global vigilance.
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Affiliation(s)
- Carlos Daviña-Núñez
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain
- Universidade de Vigo, Vigo, Spain
| | - Sonia Pérez
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Jorge Julio Cabrera-Alvargonzález
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Anniris Rincón-Quintero
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Ana Treinta-Álvarez
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Montse Godoy-Diz
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Silvia Suárez-Luque
- Dirección Xeral de Saúde Pública, Xunta de Galicia, Consellería de Sanidade, Santiago de Compostela, A Coruña, Spain
| | - Benito Regueiro-García
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain
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44
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Duchen D, Clipman SJ, Vergara C, Thio CL, Thomas DL, Duggal P, Wojcik GL. A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction. PLoS One 2024; 19:e0301069. [PMID: 38669259 PMCID: PMC11051683 DOI: 10.1371/journal.pone.0301069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/09/2024] [Indexed: 04/28/2024] Open
Abstract
Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Center for Biomedical Data Science, Yale School of Medicine, New Haven, CT, United States of America
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Chloe L. Thio
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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46
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Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nat Commun 2024; 15:3508. [PMID: 38664380 PMCID: PMC11045810 DOI: 10.1038/s41467-024-47774-8] [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: 11/11/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.
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Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Andrew Hagy
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | | | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Jorge L Muñoz-Jordán
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gilberto A Santiago
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Melanie Spillane
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Bureau for Global Health, United States Agency for International Development, Arlington, VA, USA
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert Paulino-Ramírez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Sayira Mueses
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Armando Peguero
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Francesca F Norman
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, CIBER de Enfermedades Infecciosas, IRYCIS, Hospital Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan-Carlos Galán
- Microbiology Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Section of Infectious Diseases, Boston University School of Medicine, Center for Emerging Infectious Disease Policy and Research, Boston University, and National Emerging Infectious Disease Laboratory, Boston, MA, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA.
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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47
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Sobel Leonard A, Mendoza L, McFarland AG, Marques AD, Everett JK, Moncla L, Bushman FD, Odom John AR, Hensley SE. Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status. Virus Evol 2024; 10:veae034. [PMID: 38859985 PMCID: PMC11163376 DOI: 10.1093/ve/veae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at antigenic sites. Because of antigenic drift, influenza vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite the high levels of viral diversity observed across populations, most human studies reveal limited intrahost diversity, leaving the origin of population-level viral diversity unclear. Previous studies show host characteristics, such as immunity, might affect within-host viral evolution. Here we investigate influenza A viral diversity in children aged between 6 months and 18 years. Influenza virus evolution in children is less well characterized than in adults, yet may be associated with higher levels of viral diversity given the lower level of pre-existing immunity and longer durations of infection in children. We obtained influenza isolates from banked influenza A-positive nasopharyngeal swabs collected at the Children's Hospital of Philadelphia during the 2017-18 influenza season. Using next-generation sequencing, we evaluated the population of influenza viruses present in each sample. We characterized within-host viral diversity using the number and frequency of intrahost single-nucleotide variants (iSNVs) detected in each sample. We related viral diversity to clinical metadata, including subjects' age, vaccination status, and comorbid conditions, as well as sample metadata such as virus strain and cycle threshold. Consistent with previous studies, most samples contained low levels of diversity with no clear association between the subjects' age, vaccine status, or health status. Further, there was no enrichment of iSNVs near known antigenic sites. Taken together, these findings are consistent with previous observations that the majority of intrahost influenza virus infection is characterized by low viral diversity without evidence of diversifying selection.
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Affiliation(s)
- Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Lydia Mendoza
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Alexander G McFarland
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Andrew D Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - John K Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Louise Moncla
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce St., Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA
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48
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Merkt S, Ali S, Gudina EK, Adissu W, Gize A, Muenchhoff M, Graf A, Krebs S, Elsbernd K, Kisch R, Betizazu SS, Fantahun B, Bekele D, Rubio-Acero R, Gashaw M, Girma E, Yilma D, Zeynudin A, Paunovic I, Hoelscher M, Blum H, Hasenauer J, Kroidl A, Wieser A. Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity. Nat Commun 2024; 15:3463. [PMID: 38658564 PMCID: PMC11043357 DOI: 10.1038/s41467-024-47556-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Under-reporting of COVID-19 and the limited information about circulating SARS-CoV-2 variants remain major challenges for many African countries. We analyzed SARS-CoV-2 infection dynamics in Addis Ababa and Jimma, Ethiopia, focusing on reinfection, immunity, and vaccination effects. We conducted an antibody serology study spanning August 2020 to July 2022 with five rounds of data collection across a population of 4723, sequenced PCR-test positive samples, used available test positivity rates, and constructed two mathematical models integrating this data. A multivariant model explores variant dynamics identifying wildtype, alpha, delta, and omicron BA.4/5 as key variants in the study population, and cross-immunity between variants, revealing risk reductions between 24% and 69%. An antibody-level model predicts slow decay leading to sustained high antibody levels. Retrospectively, increased early vaccination might have substantially reduced infections during the delta and omicron waves in the considered group of individuals, though further vaccination now seems less impactful.
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Affiliation(s)
- Simon Merkt
- Life and Medical Sciences (LIMES), University of Bonn, Bonn, Germany
| | - Solomon Ali
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Esayas Kebede Gudina
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Wondimagegn Adissu
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Addisu Gize
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
- CIH LMU Center for International Health, LMU Munich, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Kira Elsbernd
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rebecca Kisch
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | | | - Bereket Fantahun
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
| | - Mulatu Gashaw
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Eyob Girma
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Daniel Yilma
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Ahmed Zeynudin
- Jimma University Clinical Trial Unit, Jimma University Institute of Health, Jimma, Ethiopia
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany
| | - Michael Hoelscher
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany
- Unit Global Health, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES), University of Bonn, Bonn, Germany.
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
- Center for Mathematics, Technische Universität München, Garching, Germany.
| | - Arne Kroidl
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
| | - Andreas Wieser
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
- Immunology, Infection and Pandemic Research IIP, Fraunhofer ITMP, Munich, Germany.
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany.
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49
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Monzón S, Varona S, Negredo A, Vidal-Freire S, Patiño-Galindo JA, Ferressini-Gerpe N, Zaballos A, Orviz E, Ayerdi O, Muñoz-Gómez A, Delgado-Iribarren A, Estrada V, García C, Molero F, Sánchez-Mora P, Torres M, Vázquez A, Galán JC, Torres I, Causse Del Río M, Merino-Diaz L, López M, Galar A, Cardeñoso L, Gutiérrez A, Loras C, Escribano I, Alvarez-Argüelles ME, Del Río L, Simón M, Meléndez MA, Camacho J, Herrero L, Jiménez P, Navarro-Rico ML, Jado I, Giannetti E, Kuhn JH, Sanchez-Lockhart M, Di Paola N, Kugelman JR, Guerra S, García-Sastre A, Cuesta I, Sánchez-Seco MP, Palacios G. Monkeypox virus genomic accordion strategies. Nat Commun 2024; 15:3059. [PMID: 38637500 PMCID: PMC11026394 DOI: 10.1038/s41467-024-46949-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. Person-to-person transmission appears higher than for clade I or subclade IIa MPXV, possibly caused by genomic changes in subclade IIb MPXV. Key genomic changes could occur in the genome's low-complexity regions (LCRs), which are challenging to sequence and are often dismissed as uninformative. Here, using a combination of highly sensitive techniques, we determine a high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This reveals significant variation in short tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of single-nucleotide polymorphisms (SNPs) and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs), including OPG153, OPG204, and OPG208, could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. We posit that genomic studies focusing on phenotypic MPXV differences should consider LCR variability.
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Affiliation(s)
- Sara Monzón
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Sarai Varona
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Universidad Nacional de Educación a Distancia (UNED), 2832, Madrid, Spain
| | - Anabel Negredo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Santiago Vidal-Freire
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Angel Zaballos
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Oskar Ayerdi
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Ana Muñoz-Gómez
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | | | - Vicente Estrada
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Cristina García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Francisca Molero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Patricia Sánchez-Mora
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Montserrat Torres
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ana Vázquez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan-Carlos Galán
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Ignacio Torres
- Servicio de Microbiología, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, 46010, Valencia, Spain
| | - Manuel Causse Del Río
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, 14004, Córdoba, Spain
| | - Laura Merino-Diaz
- Unidad Clínico de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013, Sevilla, Spain
| | - Marcos López
- Servicio de Microbiología y Parasitología, Hospital Universitario Puerta de Hierro Majadahonda, 28222, Madrid, Spain
| | - Alicia Galar
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, 28007, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiología, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, 28006, Madrid, Spain
| | - Almudena Gutiérrez
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Cristina Loras
- Servicio de Microbiología, Hospital General y Universitario, 13005, Ciudad Real, Spain
| | - Isabel Escribano
- Servicio de Microbiología, Hospital General Universitario Dr. Balmis, 03010, Alicante, Spain
| | | | | | - María Simón
- Servicio de Microbiología, Hospital Central de la Defensa "Gómez Ulla", 28947, Madrid, Spain
| | - María Angeles Meléndez
- Servicio de Microbiología y Parasitología, Hospital Universitario 12 de Octubre, 28041, Madrid, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Laura Herrero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Jiménez
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Luisa Navarro-Rico
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel Jado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Elaina Giannetti
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
| | - Mariano Sanchez-Lockhart
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Nicholas Di Paola
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Jeffrey R Kugelman
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Susana Guerra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departmento de Medicina Preventiva, Salud Publica y Microbiología, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Isabel Cuesta
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maripaz P Sánchez-Seco
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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50
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Žuštra A, Leonard VR, Holland LA, Hu JC, Mu T, Holland SC, Wu LI, Begnel ER, Ojee E, Chohan BH, Richardson BA, Kinuthia J, Wamalwa D, Slyker J, Lehman DA, Gantt S, Lim ES. Longitudinal dynamics of the nasopharyngal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their infants. RESEARCH SQUARE 2024:rs.3.rs-4257641. [PMID: 38699359 PMCID: PMC11065085 DOI: 10.21203/rs.3.rs-4257641/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest and of clinical relevance. The impact of SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019 (COVID-19) pandemic, on the nasopharyngeal microbiome, particularly among individuals living with HIV, is not fully characterized. Here we describe the nasopharyngeal microbiome before, during and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their infants (18 HIV-exposed, uninfected and 18 HIV-unexposed, uninfected), followed between September 2021 through March 2022. We show using genomic epidemiology that mother and infant dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. Additionally, we used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and infants infected with SARS-CoV-2, 6 infants negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint matched SARS-CoV-2 negative mothers and infants. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- and long-term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and infants had significantly different microbiome composition and bacterial load (p-values <.0001). However, in both mothers and infants, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV-exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.
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