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van Boven M, Backer JA, Veldhuijzen I, Gomme J, van Binnendijk R, Kaaijk P. Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology. Epidemics 2024; 46:100751. [PMID: 38442537 DOI: 10.1016/j.epidem.2024.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/07/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Mumps virus is a highly transmissible pathogen that is effectively controlled in countries with high vaccination coverage. Nevertheless, outbreaks have occurred worldwide over the past decades in vaccinated populations. Here we analyse an outbreak of mumps virus genotype G among college students in the Netherlands over the period 2009-2012 using paired serological data. To identify infections in the presence of preexisting antibodies we compared mumps specific serum IgG concentrations in two consecutive samples (n=746), whereby the first sample was taken when students started their study prior to the outbreaks, and the second sample was taken 2-5 years later. We fit a binary mixture model to the data. The two mixing distributions represent uninfected and infected classes. Throughout we assume that the infection probability increases with the ratio of antibody concentrations of the second to first sample. The estimated infection attack rate in this study is higher than reported earlier (0.095 versus 0.042). The analyses yield probabilistic classifications of participants, which are mostly quite precise owing to the high intraclass correlation of samples in uninfected participants (0.85, 95%CrI: 0.82-0.87). The estimated probability of infection increases with decreasing antibody concentration in the pre-outbreak sample, such that the probability of infection is 0.12 (95%CrI: 0.10-0.13) for the lowest quartile of the pre-outbreak samples and 0.056 (95%CrI: 0.044-0.068) for the highest quartile. We discuss the implications of these insights for the design of booster vaccination strategies.
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Affiliation(s)
- Michiel van Boven
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Jantien A Backer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Irene Veldhuijzen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Justin Gomme
- Department of Epidemiology and Social Medicine, University of Antwerp, Antwerp, Belgium; NHS Scotland, Edinburgh, Scotland, United Kingdom
| | - Rob van Binnendijk
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Patricia Kaaijk
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Gavilán AM, Perán-Ramos P, Sanz JC, García-Comas L, Pérez-Abeledo M, Castellanos AM, Berciano JM, López-Perea N, Masa-Calles J, Echevarría JE, Fernández-García A. Investigating Local Patterns of Mumps Virus Circulation, Using a Combination of Molecular Tools. Viruses 2023; 15:2420. [PMID: 38140661 PMCID: PMC10747990 DOI: 10.3390/v15122420] [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: 11/08/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Mumps is a vaccine-preventable disease caused by the mumps virus (MuV). However, MuV has re-emerged in many countries with high vaccine coverage. The World Health Organization (WHO) recommends molecular surveillance based on sequencing of the small hydrophobic (SH) gene. Additionally, the combined use of SH and non-coding regions (NCR) has been described in different studies, proving to be a useful complement marker to discriminate general patterns of circulation at national and international levels. The aim of this work is to test local-level usefulness of the combination of SH and MF-NCR sequencing in tracing hidden transmission clusters and chains during the last epidemic wave (2015-2020) in Spain. A database with 903 cases from the Autonomous Community of Madrid was generated by the integration of microbiological and epidemiological data. Of these, 453 representative cases were genotyped. Eight different SH variants and thirty-four SH haplotypes were detected. Local MuV circulation showed the same temporal pattern previously described at a national level. Only two of the thirteen previously identified outbreaks were caused by more than one variant/haplotype. Geographical representation of SH variants allowed the identification of several previously undetected clusters, which were analysed phylogenetically by the combination of SH and MF-NCR, in a total of 90 cases. MF-NCR was not able to improve the discrimination of geographical clusters based on SH sequencing, showing limited resolution for outbreak investigations.
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Affiliation(s)
- Ana M. Gavilán
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - Paula Perán-Ramos
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
| | - Juan Carlos Sanz
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Laboratorio Regional de Salud Pública de la Comunidad de Madrid, 28055 Madrid, Spain;
| | - Luis García-Comas
- Servicio de Epidemiología, Consejería de Sanidad de la Comunidad de Madrid, 28009 Madrid, Spain;
| | - Marta Pérez-Abeledo
- Laboratorio Regional de Salud Pública de la Comunidad de Madrid, 28055 Madrid, Spain;
| | - Ana M. Castellanos
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - José M. Berciano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
| | - Noemí López-Perea
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Medicina Preventiva y Salud Pública, Universidad Autónoma de Madrid/IdiPAZ, 28049 Madrid, Spain
| | - Josefa Masa-Calles
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Juan E. Echevarría
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
| | - Aurora Fernández-García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029 Madrid, Spain; (A.M.G.); (J.M.B.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.C.S.); (N.L.-P.); (J.M.-C.)
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3
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Gokhale DV, Brett TS, He B, King AA, Rohani P. Disentangling the causes of mumps reemergence in the United States. Proc Natl Acad Sci U S A 2023; 120:e2207595120. [PMID: 36623178 PMCID: PMC9934068 DOI: 10.1073/pnas.2207595120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/19/2022] [Indexed: 01/11/2023] Open
Abstract
Over the past two decades, multiple countries with high vaccine coverage have experienced resurgent outbreaks of mumps. Worryingly, in these countries, a high proportion of cases have been among those who have completed the recommended vaccination schedule, raising alarm about the effectiveness of existing vaccines. Two putative mechanisms of vaccine failure have been proposed as driving observed trends: 1) gradual waning of vaccine-derived immunity (necessitating additional booster doses) and 2) the introduction of novel viral genotypes capable of evading vaccinal immunity. Focusing on the United States, we conduct statistical likelihood-based hypothesis testing using a mechanistic transmission model on age-structured epidemiological, demographic, and vaccine uptake time series data. We find that the data are most consistent with the waning hypothesis and estimate that 32.8% (32%, 33.5%) of individuals lose vaccine-derived immunity by age 18 y. Furthermore, we show using our transmission model how waning vaccine immunity reproduces qualitative and quantitatively consistent features of epidemiological data, namely 1) the shift in mumps incidence toward older individuals, 2) the recent recurrence of mumps outbreaks, and 3) the high proportion of mumps cases among previously vaccinated individuals.
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Affiliation(s)
- Deven V. Gokhale
- Odum School of Ecology, University of Georgia, Athens, GA30602
- Center of Ecology of Infectious Diseases, Athens, GA30602
- Center for Influenza Disease & Emergence Research, Athens, GA30602
| | - Tobias S. Brett
- Odum School of Ecology, University of Georgia, Athens, GA30602
- Center of Ecology of Infectious Diseases, Athens, GA30602
- Center for Influenza Disease & Emergence Research, Athens, GA30602
| | - Biao He
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA30602
| | - Aaron A. King
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI48109
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI48109
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA30602
- Center of Ecology of Infectious Diseases, Athens, GA30602
- Center for Influenza Disease & Emergence Research, Athens, GA30602
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4
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Improved Immunogenicity of the Inactivated F Genotype Mumps Vaccine against Diverse Circulating Mumps Viruses in Mice. Vaccines (Basel) 2023; 11:vaccines11010106. [PMID: 36679951 PMCID: PMC9862704 DOI: 10.3390/vaccines11010106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Mumps is an acute infectious disease caused by the mumps virus (MuV). Despite high global vaccination coverage, mumps outbreaks continue to occur, even in vaccinated populations. Therefore, we aimed to identify candidate vaccines that can induce an immunogenic response against diverse MuV genotypes with greater efficacy than the currently available options. Vaccine candidates were sourced using formalin-inactivated viral strains. The inactivated vaccines were administered to BALB/c mice (through a primer and booster dose administered after a three-week interval). We tested the neutralizing antibodies of the candidate vaccines against various MuV genotypes to determine their overall efficacy. The formalin-inactivated F genotype vaccine was found to have higher cross-neutralizing titers against genotypes F, H, and G as well as significant Th1 cytokines responses, IFN-γ, TNF-α, and IL-2 than the Jeryl Lynn (JL) vaccine. Our findings suggest that the inactivated F genotype mumps vaccine has higher immunogenicity than the JL vaccine against diverse circulating MuVs.
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Kidokoro M, Shiino T, Yamaguchi T, Nariai E, Kodama H, Nakata K, Sano T, Gotou K, Kisu T, Maruyama T, Kuba Y, Sakata W, Higashi T, Kiyota N, Sakai T, Yahiro S, Nagita A, Watanabe K, Hirokawa C, Hamabata H, Fujii Y, Yamamoto M, Yokoi H, Sakamoto M, Saito H, Shibata C, Inada M, Fujitani M, Minagawa H, Ito M, Shima A, Murano K, Katoh H, Kato F, Takeda M, Suga S. Nationwide and long-term molecular epidemiologic studies of mumps viruses that circulated in Japan between 1986 and 2017. Front Microbiol 2022; 13:728831. [PMID: 36386684 PMCID: PMC9650061 DOI: 10.3389/fmicb.2022.728831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
In Japan, major mumps outbreaks still occur every 4–5 years because of low mumps vaccine coverage (30–40%) owing to the voluntary immunization program. Herein, to prepare for a regular immunization program, we aimed to reveal the nationwide and long-term molecular epidemiological trends of the mumps virus (MuV) in Japan. Additionally, we performed whole-genome sequencing (WGS) using next-generation sequencing to assess results from conventional genotyping using MuV sequences of the small-hydrophobic (SH) gene. We analyzed 1,064 SH gene sequences from mumps clinical samples and MuV isolates collected from 25 prefectures from 1986 to 2017. The results showed that six genotypes, namely B (110), F (1), G (900), H (3), J (41), and L (9) were identified, and the dominant genotypes changed every decade in Japan since the 1980s. Genotype G has been exclusively circulating since the early 2000s. Seven clades were identified for genotype G using SH sequence-based classification. To verify the results, we performed WGS on 77 representative isolates of genotype G using NGS and phylogenetically analyzed them. Five clades were identified with high bootstrap values and designated as Japanese clade (JPC)-1, -2, -3, -4, -5. JPC-1 and -3 accounted for over 80% of the total genotype G isolates (68.3 and 13.8%, respectively). Of these, JPC-2 and -5, were newly identified clades in Japan through this study. This is the first report describing the nationwide and long-term molecular epidemiology of MuV in Japan. The results provide information about Japanese domestic genotypes, which is essential for evaluating the mumps elimination progress in Japan after the forthcoming introduction of the mumps vaccine into Japan’s regular immunization program. Furthermore, the study shows that WGS analysis using NGS is more accurate than results obtained from conventional SH sequence-based classification and is a powerful tool for accurate molecular epidemiology studies.
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Affiliation(s)
- Minoru Kidokoro
- Department of Quality Assurance, Radiation Safety, and Information Management, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Minoru Kidokoro,
| | - Teiichiro Shiino
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomohiro Yamaguchi
- Public Hygiene Division, Gifu Prefectural Tono Region Public Health Center, Tajimi, Japan
| | - Eri Nariai
- Department of Health and Food Safety, Ishikawa Prefectural Institute of Public Health and Environmental Science, Kanazawa, Japan
| | - Hiroe Kodama
- Department of Health and Food Safety, Ishikawa Prefectural Institute of Public Health and Environmental Science, Kanazawa, Japan
| | - Keiko Nakata
- Division of Virology, Osaka Institute of Public Health, Osaka, Japan
| | - Takako Sano
- Division of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Japan
| | - Keiko Gotou
- Division of Virology, Ibaraki Prefectural Institute of Public Health, Mito, Ibaraki, Japan
| | - Tomoko Kisu
- Virus Research Center, Clinical Research Division, Sendai National Hospital, Sendai, Japan
| | - Tomomi Maruyama
- Department of Infectious Diseases, Gifu Prefectural Research Institute for Health and Environmental Sciences, Kakamigahara, Japan
| | - Yumani Kuba
- Department of Medical Microbiology and zoology, Okinawa Prefectural Institute of Health and Environment, Uruma, Japan
| | - Wakako Sakata
- Kitakyushu City Institute of Health and Environmental Sciences, Kitakyushu, Japan
| | - Teruaki Higashi
- Kitakyushu City Institute of Health and Environmental Sciences, Kitakyushu, Japan
| | - Naoko Kiyota
- Department of Microbiology, Kumamoto Prefectural Institute of Public-Health and Environmental Science, Uto, Japan
| | - Takashi Sakai
- Department of Microbiology, Kumamoto Prefectural Institute of Public-Health and Environmental Science, Uto, Japan
| | - Shunsuke Yahiro
- Department of Microbiology, Kumamoto Prefectural Institute of Public-Health and Environmental Science, Uto, Japan
| | - Akira Nagita
- Department of Pediatrics, Mizushima Central Hospital, Kurashiki, Japan
| | - Kaori Watanabe
- Virology Section, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
| | - Chika Hirokawa
- Virology Section, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Japan
| | | | - Yoshiki Fujii
- Division of Biological Science, Hiroshima City Institute of Public Health, Hiroshima, Japan
| | - Miwako Yamamoto
- Division of Biological Science, Hiroshima City Institute of Public Health, Hiroshima, Japan
| | - Hajime Yokoi
- Health Science Division, Chiba City Institute of Health and Environment, Chiba, Japan
| | - Misako Sakamoto
- Health Science Division, Chiba City Institute of Health and Environment, Chiba, Japan
| | - Hiroyuki Saito
- Department of Microbiology, Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Chihiro Shibata
- Department of Microbiology, Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Machi Inada
- Virology and Epidemiology Division, Nara Prefecture Institute of Health, Sakurai, Japan
| | - Misako Fujitani
- Virology and Epidemiology Division, Nara Prefecture Institute of Health, Sakurai, Japan
| | - Hiroko Minagawa
- Laboratory of Virology, Aichi Prefectural Institute of Public Health, Nagoya, Japan
| | - Miyabi Ito
- Laboratory of Virology, Aichi Prefectural Institute of Public Health, Nagoya, Japan
| | - Akari Shima
- Microbiology Division, Saga Prefectural Institute of Public Health and Pharmaceutical Research, Saga, Japan
| | - Keiko Murano
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Katoh
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiro Kato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shigeru Suga
- Department of Pediatrics, National Hospital Organization Mie National Hospital, Tsu, Japan
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Frost JR, Shaikh S, Severini A. Exploring the Mumps Virus Glycoproteins: A Review. Viruses 2022; 14:v14061335. [PMID: 35746805 PMCID: PMC9229384 DOI: 10.3390/v14061335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
The resurgence of mumps in vaccinated adult populations has raised concerns about possible waning vaccine immunity or a potential lack of protection to the circulating strain. A number of individual studies have investigated if there are amino acid variations between the circulating wild-type strains and vaccine strains. In these studies, the HN and F mumps surface glycoproteins have been of interest, because of their role in viral infection, and because the HN protein is the target of neutralizing antibodies. Here, we summarize the single nucleotide variants and their potential effect that have been identified between mumps genotypes in the HN and F proteins.
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Affiliation(s)
- Jasmine Rae Frost
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (J.R.F.); (S.S.)
| | - Saba Shaikh
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (J.R.F.); (S.S.)
| | - Alberto Severini
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (J.R.F.); (S.S.)
- JC Wilt Infectious Diseases Research Centre, NMLB, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
- Correspondence: ; Tel.: +1-204-789-6022; Fax: +1-204-318-2222
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7
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Forgione RE, Di Carluccio C, Milanesi F, Kubota M, Fabregat Nieto F, Molinaro A, Hashiguchi T, Francesconi O, Marchetti R, Silipo A. Characterization of Natural and Synthetic Sialoglycans Targeting the Hemagglutinin-Neuraminidase of Mumps Virus. Front Chem 2021; 9:711346. [PMID: 34778199 PMCID: PMC8578797 DOI: 10.3389/fchem.2021.711346] [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: 05/18/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The inhibition of surface viral glycoproteins offers great potential to hamper the attachment of viruses to the host cells surface and the spreading of viral infection. Mumps virus (MuV) is the etiological agent of the mumps infectious disease and causes a wide spectrum of mild to severe symptoms due to the inflammation of the salivary glands. Here we focus our attention on the hemagglutinin-neuraminidase (HN) isolated from MuV SBL-1 strain. We describe the molecular features of host sialoglycans recognition by HN protein by means of NMR, fluorescence assays and computational studies. Furthermore, we also describe the synthesis of a N-acetylneuraminic acid-derived thiotrisaccharide targeting the viral protein, and the corresponding 3D-complex. Our results provide the basis to improve the design and synthesis of potent viral hemagglutinin-neuraminidase inhibitors.
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Affiliation(s)
- Rosa Ester Forgione
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
| | - Francesco Milanesi
- Department of Chemistry "Ugo Schiff" and INSTM, University of Florence Polo Scientifico e Tecnologico, Florence, Italy.,Magnetic Resonance Center CERM, Sesto Fiorentino, Italy
| | - Marie Kubota
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka, Japan
| | - Ferran Fabregat Nieto
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff" and INSTM, University of Florence Polo Scientifico e Tecnologico, Florence, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, Complesso Universitario Monte Sant'Angelo, University of Naples Federico II, Naples, Italy
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8
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Streamlined Whole Genome Sequencing of Mumps for High Resolution Outbreak Analysis. J Clin Microbiol 2021; 60:e0084121. [PMID: 34757832 DOI: 10.1128/jcm.00841-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since 2015, the United States has experienced a resurgence in the number of mumps cases and outbreaks in fully vaccinated populations. These outbreaks have occurred predominantly in close quarter settings such as camps, colleges and detention centers. Phylogenetic analysis of 758 mumps positive samples from outbreaks across the United States, identified 743 (98%) as genotype G based on sequence analysis of the mumps small hydrophobic (SH) gene. Additionally, SH sequences in the genotype G samples showed almost no sequence diversity, with 675 (91%) of them having identical sequences or only one nucleotide difference. This uniformity of circulating genotype and strain created complications for epidemiologic investigations and necessitated the development of a system for rapidly generating mumps whole genome sequences for more detailed analysis. In this study, we report a novel and streamlined assay for whole genome sequencing (WGS) of mumps virus genotype G. The WGS procedure successfully generated 318 high-quality WGS sequences on nucleic acid from genotype G-positive respiratory samples collected during several mumps outbreaks in the United States between 2016-2019. Sequencing was performed by a rapid and highly sensitive custom Ion AmpliSeq mumps genotype G panel, with sample preparation performed on an Ion Chef and sequencing on an Ion S5. The WGS data generated by the AmpliSeq panel provided enhanced genomic resolution for epidemiological outbreak investigations. Translation and protein sequence analysis also identified several potentially important epitope changes in the circulating mumps genotype G strains compared to the Jeryl-Lynn strain (JL5) used in vaccines in the United States which could explain the current level of vaccine escapes.
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9
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Abstract
On 16–17 January 2020, four suspected mumps cases were reported to the local Public Health Authorities with an epidemiological link to a local school and football club. Of 18 suspected cases identified, 14 were included in this study. Laboratory results confirmed mumps virus as the cause and further sequencing identified genotype G. Our findings highlight that even with a high MMR vaccine coverage, mumps outbreaks in children and young adults can occur. Since most of the cases had documented immunity for mumps, we hypothesise that waning immunity or discordant mumps virus strains are likely explanations for this outbreak.
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10
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Won H, Kim AR, Yoo JS, Chung GT, Kang HJ, Kim SJ, Kim SS, Lee JW. Cross-neutralization between vaccine and circulating wild-type mumps viruses in Korea. Vaccine 2021; 39:1870-1876. [PMID: 33642163 DOI: 10.1016/j.vaccine.2021.01.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Mumps is a contagious disease caused by the mumps virus. It can be prevented using mumps vaccines, administered as a measles-mumps-rubella (MMR) vaccine. For first and second dose immunization, children aged 12-15 months and 4-6 years have been administered this vaccine since 1997 in Korea. Nevertheless, mumps outbreaks still occur in vaccinated populations worldwide. Hence, immunity against these diseases may be attenuated, or there are antigenic differences between currently available vaccine strains and circulating wild-type viruses. After the introduction of national immunization programs in Korea, mumps cases became sporadic. Viral genotypes F, H, and I have emerged since 1998 whereas the vaccine strains belong to genotype A. Here, we compared the amino acid sequences of the haemagglutinin-neuraminidase (HN) gene from wild-type viruses and the mumps vaccine and measured the cross-neutralization titers between them. We selected the F, H, and I wild-type mumps strains circulating in Korea from 1998 to 2016 and analyzed changes in the amino acid sequence of the protein encoded by the HN gene. We measured mumps virus-specific IgG and rapid focus reduction neutralization test (FRNT) titers in Korean isolates and sera obtained from 50 children aged 1-2 years who had been administered a single dose of MMR vaccine. Analysis of the HN protein sequences disclosed no changes in the glycosylation sites but did reveal 4-5 differences between the Korean isolates and the genotype A vaccine strain in terms of the neutralizing epitope sites on their HN proteins. Post-vaccination FRNT titers were significantly lower against genotypes F, H, and I than they were against genotype A. This finding highlights the possibility of a recurrence of mumps outbreaks in vaccinated populations depending on the degree of genetic conservation of the HN gene. Further research into this issue is needed to prevent the resurgence of mumps.
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Affiliation(s)
- Hyeran Won
- Division of Vaccine Research, Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Ah-Ra Kim
- Division of Vaccine Research, Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Jung-Sik Yoo
- Division of Vaccine Research, Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Gyung Tae Chung
- Division of Vaccine Research, Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Hae Ji Kang
- Division of Viral Disease, Center for Laboratory Control of Infectious Disease, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Su Jin Kim
- Division of Viral Disease, Center for Laboratory Control of Infectious Disease, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - Sung Soon Kim
- Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea
| | - June-Woo Lee
- Division of Vaccine Research, Korea National Research Institute of Health, Korea Centers for Disease Control and Prevention, CheongJu, Chungcheongbuk-do, Republic of Korea.
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11
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Ma J, Wang P, Tang J, Zheng L, Li S, Huo Y. Epidemiological and Phylogenetic Analysis of Mumps Virus Isolated from 2016 to 2019 in Henan Province, China. Jpn J Infect Dis 2020; 74:187-192. [PMID: 33132301 DOI: 10.7883/yoken.jjid.2020.649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Routine vaccination has proven to be highly effective in reducing the incidence of mumps. However, sporadic cases and/or mumps outbreaks have been reported in children and adolescents younger than 15 years of age, particularly among those aged 5-9 years. To explore the characteristics of such outbreaks in the Henan Province, clinical data of patients infected with mumps virus (MuV) were collected, and the isolated strains were phylogenetically analyzed. Of the total 426 samples analyzed, MuV RNA targeting the small hydrophobic (SH) gene was detected in 153 samples. MuV-positive cases in age groups <5 years, 5-9 years, 10-15 years, 16-19 years, and ≥20 years accounted for 1%, 17%, 12%, 2%, and 4% of the total number of cases, respectively. Phylogenetic analysis based on the SH gene sequences indicated that all of the isolated strains were of genotype F, and isolates in the same subcluster and with identical SH gene sequences tended to be derived from the same community or municipalities when analyzed alongside epidemiological data. In conclusion, the incidence of mumps in the Henan Province was high. The data provided in this study might promote further research in the clarification of the specific causes of mumps outbreaks, which can facilitate the implementation of effective prevention and control measures.
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Affiliation(s)
- Jie Ma
- The Sixth People's Hospital of Zhengzhou, China
| | | | - Jing Tang
- The Sixth People's Hospital of Zhengzhou, China
| | - Lijun Zheng
- The Sixth People's Hospital of Zhengzhou, China
| | - Sanjing Li
- The Sixth People's Hospital of Zhengzhou, China
| | - Yuqi Huo
- The Sixth People's Hospital of Zhengzhou, China
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12
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Siañez-Estrada LI, Rivera-Benítez JF, Rosas-Murrieta NH, Reyes-Leyva J, Santos-López G, Herrera-Camacho I. Immunoinformatics approach for predicting epitopes in HN and F proteins of Porcine rubulavirus. PLoS One 2020; 15:e0239785. [PMID: 32976525 PMCID: PMC7518572 DOI: 10.1371/journal.pone.0239785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
Porcine rubulavirus (PRV), which belongs to the family Paramyxoviridae, causes blue eye disease in pigs, characterized by encephalitis and reproductive failure in newborn and adult pigs, respectively. There is no effective treatment against PRV and no information on the effectiveness of the available vaccines. Continuous outbreaks have occurred in Mexico since the early 1980s, which have caused serious economic losses to pig producers. Vaccination can be used to control this disease. Searching for effective antigen candidates against PRV, we first sequenced the PAC1 F protein, then we used various immunoinformatics tools to predict antigenic determinants of B-cells and T-cells against the two glycoproteins of the virus (HN and F proteins). Finally, we used AutoDock Vina to determine the binding energies. We obtained the F gene sequence of a PRV strain collected in the early 1990s in Mexico and compared its amino acid profile with previous and more recent strains, obtaining an identity similarity of 97.78 to 99.26%. For the F proteins, seven linear B-cell epitopes, six conformational B-cell epitopes and twenty-nine T-cell MHC class I epitopes were predicted. For the HN proteins, sixteen linear B-cell epitopes, seven conformational B-cell epitopes and thirty-four T-cell MHC class I epitopes were predicted. The ATRSETDYY and AAYTTTTCF epitopes of the HN protein might be important for neutralizing the viral infection. We determined the in silico binding energy between the predicted epitopes on the F and HN proteins and swine MHC-I molecules. The binding energy of these epitopes ranged from -5.8 to -7.8 kcal/mol. The present study aimed to assess the use of HN and F proteins as antigens, either as recombinant proteins or as a series of peptides that could activate different responses of the immune system. This may help identify relevant immunogens, saving time and costs in the development of new vaccines or diagnostic tools.
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Affiliation(s)
- Luis I. Siañez-Estrada
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Ciudad de México, México
| | - Nora H. Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Julio Reyes-Leyva
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - Gerardo Santos-López
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - Irma Herrera-Camacho
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
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13
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Bizzoca ME, Campisi G, Lo Muzio L. Covid-19 Pandemic: What Changes for Dentists and Oral Medicine Experts? A Narrative Review and Novel Approaches to Infection Containment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E3793. [PMID: 32471083 PMCID: PMC7312076 DOI: 10.3390/ijerph17113793] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/20/2020] [Accepted: 05/23/2020] [Indexed: 12/22/2022]
Abstract
The authors performed a narrative review on Severe Acute Respiratory Syndrome- CoronaVirus-2 ( SARS-CoV-2) and all infectious agents with the primary endpoints to illustrate the most accepted models of safety protocols in dentistry and oral medicine, and to propose an easy view of the problem and a comparison (pre- vs post-COVID19) for the most common dental procedures. The outcome is forecast to help dentists to individuate for a given procedure the differences in terms of safety protocols to avoid infectious contagion (by SARS-CoV-2 and others dangerous agents). An investigation was performed on the online databases Pubmed and Scopus using a combination of free words and Medical Subject Headings (MESH) terms: "dentist" OR "oral health" AND "COVID-19" OR "SARS-CoV-2" OR "coronavirus-19". After a brief excursus on all infectious agents transmittable at the dental chair, the authors described all the personal protective equipment (PPE) actually on the market and their indications, and on the basis of the literature, they compared (before and after COVID-19 onset) the correct safety procedures for each dental practice studied, underlining the danger of underestimating, in general, dental cross-infections. The authors have highlighted the importance of knowing exactly the risk of infections in the dental practice, and to modulate correctly the use of PPE, in order to invest adequate financial resources and to avoid exposing both the dental team and patients to preventable risks.
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Affiliation(s)
- Maria Eleonora Bizzoca
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy;
| | - Giuseppina Campisi
- Department of Surgical, Oncological and Oral Sciences (Di.Chir.On.S.), University of Palermo, 90121 Palermo, Italy;
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy;
- C.I.N.B.O. (Consorzio Interuniversitario Nazionale per la Bio-Oncologia), 66100 Chieti, Italy
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14
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Brett TS, Rohani P. Dynamical footprints enable detection of disease emergence. PLoS Biol 2020; 18:e3000697. [PMID: 32433658 PMCID: PMC7239390 DOI: 10.1371/journal.pbio.3000697] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/23/2020] [Indexed: 12/21/2022] Open
Abstract
Developing methods for anticipating the emergence or reemergence of infectious diseases is both important and timely; however, traditional model-based approaches are stymied by uncertainty surrounding the underlying drivers. Here, we demonstrate an operational, mechanism-agnostic detection algorithm for disease (re-)emergence based on early warning signals (EWSs) derived from the theory of critical slowing down. Specifically, we used computer simulations to train a supervised learning algorithm to detect the dynamical footprints of (re-)emergence present in epidemiological data. Our algorithm was then challenged to forecast the slowly manifesting, spatially replicated reemergence of mumps in England in the mid-2000s and pertussis post-1980 in the United States. Our method successfully anticipated mumps reemergence 4 years in advance, during which time mitigation efforts could have been implemented. From 1980 onwards, our model identified resurgent states with increasing accuracy, leading to reliable classification starting in 1992. Additionally, we successfully applied the detection algorithm to 2 vector-transmitted case studies, namely, outbreaks of dengue serotypes in Puerto Rico and a rapidly unfolding outbreak of plague in 2017 in Madagascar. Taken together, these findings illustrate the power of theoretically informed machine learning techniques to develop early warning systems for the (re-)emergence of infectious diseases.
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Affiliation(s)
- Tobias S. Brett
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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15
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Brett T, Ajelli M, Liu QH, Krauland MG, Grefenstette JJ, van Panhuis WG, Vespignani A, Drake JM, Rohani P. Detecting critical slowing down in high-dimensional epidemiological systems. PLoS Comput Biol 2020; 16:e1007679. [PMID: 32150536 PMCID: PMC7082051 DOI: 10.1371/journal.pcbi.1007679] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 03/19/2020] [Accepted: 01/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite medical advances, the emergence and re-emergence of infectious diseases continue to pose a public health threat. Low-dimensional epidemiological models predict that epidemic transitions are preceded by the phenomenon of critical slowing down (CSD). This has raised the possibility of anticipating disease (re-)emergence using CSD-based early-warning signals (EWS), which are statistical moments estimated from time series data. For EWS to be useful at detecting future (re-)emergence, CSD needs to be a generic (model-independent) feature of epidemiological dynamics irrespective of system complexity. Currently, it is unclear whether the predictions of CSD-derived from simple, low-dimensional systems-pertain to real systems, which are high-dimensional. To assess the generality of CSD, we carried out a simulation study of a hierarchy of models, with increasing structural complexity and dimensionality, for a measles-like infectious disease. Our five models included: i) a nonseasonal homogeneous Susceptible-Exposed-Infectious-Recovered (SEIR) model, ii) a homogeneous SEIR model with seasonality in transmission, iii) an age-structured SEIR model, iv) a multiplex network-based model (Mplex) and v) an agent-based simulator (FRED). All models were parameterised to have a herd-immunity immunization threshold of around 90% coverage, and underwent a linear decrease in vaccine uptake, from 92% to 70% over 15 years. We found evidence of CSD prior to disease re-emergence in all models. We also evaluated the performance of seven EWS: the autocorrelation, coefficient of variation, index of dispersion, kurtosis, mean, skewness, variance. Performance was scored using the Area Under the ROC Curve (AUC) statistic. The best performing EWS were the mean and variance, with AUC > 0.75 one year before the estimated transition time. These two, along with the autocorrelation and index of dispersion, are promising candidate EWS for detecting disease emergence.
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Affiliation(s)
- Tobias Brett
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Marco Ajelli
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, Massachusetts, United States of America
- Bruno Kessler Foundation, Trento, Italy
| | - Quan-Hui Liu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, Massachusetts, United States of America
- College of Computer Science, Sichuan University, Chengdu, China
| | - Mary G. Krauland
- University of Pittsburgh, Department of Health Policy and Management, Pittsburgh, Pennsylvania, United States of America
| | - John J. Grefenstette
- University of Pittsburgh, Department of Health Policy and Management, Pittsburgh, Pennsylvania, United States of America
| | - Willem G. van Panhuis
- University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh, Department of Biomedical Informatics, Pittsburgh, Pennsylvania, United States of America
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, Massachusetts, United States of America
- ISI Foundation, Turin, Italy
| | - John M. Drake
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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16
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Mumps: an Update on Outbreaks, Vaccine Efficacy, and Genomic Diversity. Clin Microbiol Rev 2020; 33:33/2/e00151-19. [PMID: 32102901 DOI: 10.1128/cmr.00151-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mumps is an acute viral infection characterized by inflammation of the parotid and other salivary glands. Persons with mumps are infectious from 2 days before through 5 days after parotitis onset, and transmission is through respiratory droplets. Despite the success of mumps vaccination programs in the United States and parts of Europe, a recent increase in outbreaks of mumps virus infections among fully vaccinated populations has been reported. Although the effectiveness of the mumps virus component of the measles-mumps-rubella (MMR) vaccine is suboptimal, a range of contributing factors has led to these outbreaks occurring in high-vaccination-coverage settings, including the intensity of exposure, the possibility of vaccine strain mismatch, delayed implementation of control measures due to the timeliness of reporting, a lack of use of appropriate laboratory tests (such as reverse transcription-PCR), and time since last vaccination. The resurgence of mumps virus infections among previously vaccinated individuals over the past decade has prompted discussions about new strategies to mitigate the risk of future outbreaks. The decision to implement a third dose of the MMR vaccine in response to an outbreak should be considered in discussions with local public health agencies. Traditional public health measures, including the isolation of infectious persons, timely contact tracing, and effective communication and awareness education for the public and medical community, should remain key interventions for outbreak control. Maintaining high mumps vaccination coverage remains key to U.S. and global efforts to reduce disease incidence and rates of complications.
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17
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Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PC. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biol 2020; 18:e3000611. [PMID: 32045407 PMCID: PMC7012397 DOI: 10.1371/journal.pbio.3000611] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/03/2020] [Indexed: 01/24/2023] Open
Abstract
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.
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Affiliation(s)
- Shirlee Wohl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Hayden C. Metsky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Meagan Burns
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joseph A. Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Bridget Chak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Lydia A. Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christian B. Matranga
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bettina Bankamp
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott Hennigan
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Brandon Sabina
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Elizabeth H. Byrne
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Rebecca J. McNall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rickey R. Shah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Soheyla Gharib
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Fitzgerald
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Paul Barreira
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Stephen Fleming
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Susan Lett
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Paul A. Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lawrence C. Madoff
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nathan L. Yozwiak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Bronwyn L. MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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18
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Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, Haselow D, Mason W, Nookaew I, Ussery D, Jun SR. Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 75:103965. [PMID: 31319177 PMCID: PMC6832845 DOI: 10.1016/j.meegid.2019.103965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 11/22/2022]
Abstract
In 2016, a year-long large-scale mumps outbreak occurred in Arkansas among a highly-vaccinated population. A total of 2954 mumps cases were identified during this outbreak. The majority of cases (1676 (57%)) were school-aged children (5-17 years), 1536 (92%) of these children had completed the mumps vaccination schedule. To weigh the possibility that the mumps virus evaded vaccine-induced immunity in the affected Arkansas population, we established a pipeline for genomic characterization of the outbreak strains. Our pipeline produces whole-genome sequences along with phylogenetic analysis of the outbreak mumps virus strains. We collected buccal swab samples of patients who tested positive for the mumps virus during the 2016 Arkansas outbreak, and used the portable Oxford Nanopore Technology to sequence the extracted strains. Our pipeline identified the genotype of the Arkansas mumps strains as genotype G and presented a genome-based phylogenetic tree with superior resolution to a standard small hydrophobic (SH) gene-based tree. We phylogenetically compared the Arkansas whole-genome sequences to all publicly available mumps strains. While these analyses show that the Arkansas mumps strains are evolutionarily distinct from the vaccine strains, we observed no correlation between vaccination history and phylogenetic grouping. Furthermore, we predicted potential B-cell epitopes encoded by the Arkansas mumps strains using a random forest prediction model trained on antibody-antigen protein structures. Over half of the predicted epitopes of the Jeryl-Lynn vaccine strains in the Hemagglutinin-Neuraminidase (HN) surface glycoprotein (a major target of neutralizing antibodies) region are missing in the Arkansas mumps strains. In-silico analyses of potential epitopes may indicate that the Arkansas mumps strains display antigens with reduced immunogenicity, which may contribute to reduced vaccine effectiveness. However, our in-silico findings should be assessed by robust experiments such as cross neutralization assays. Metadata analysis showed that vaccination history had no effect on the evolution of the Arkansas mumps strains during this outbreak. We conclude that the driving force behind the spread of the mumps virus in the 2016 Arkansas outbreak remains undetermined.
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Affiliation(s)
- Duah Alkam
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Preecha Patumcharoenpol
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Michael Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Dirk Haselow
- Arkansas Department of Health, 4815 W Markham St, Little Rock, AR 72205, USA.
| | - William Mason
- Arkansas Department of Health, 4815 W Markham St, Little Rock, AR 72205, USA.
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - David Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR 72205, USA.
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19
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Vermeire T, Barbezange C, Francart A, Hamouda A, Litzroth A, Hutse V, Martens L, Vandermarliere E, Van Gucht S. Sera from different age cohorts in Belgium show limited cross-neutralization between the mumps vaccine and outbreak strains. Clin Microbiol Infect 2019; 25:907.e1-907.e6. [DOI: 10.1016/j.cmi.2018.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/05/2018] [Accepted: 11/10/2018] [Indexed: 11/30/2022]
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