Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

Moncla, Louise H.; Black, Allison; DeBolt, Chase; Lang, Misty; Graff, Nicholas R.; Pérez-Osorio, Ailyn C.; Müller, Nicola F.; Haselow, Dirk; Lindquist, Scott; Bedford, Trevor

doi:10.7554/elife.66448

Cited by 17 publications

(8 citation statements)

References 70 publications

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“…To query whether iSNVs ever became dominant in tips sampled downstream, we used a transmission metric developed previously [ 58 ]. Using the tree JSON output from the Nextstrain pipeline [ 54 ], we traversed the tree from root to tip.…”

Section: Methodsmentioning

confidence: 99%

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

et al. 2021

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The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.

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Section: Methodsmentioning

confidence: 99%

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

et al. 2021

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“…We have written the analysis code with the intention that it should be paired with a Nextstrain build [17], which will create the necessary alignment and metadata files as well as a phylogenetic tree, which is not necessary for the analysis but is a useful companion for the interpretation of the results. Of the pathogens considered in this manuscript, we used builds produced and maintained by the Nextstrain team for influenza A and B (https://github.com/nextstrain/seasonal-flu, created as part of [35]), measles (https://github.com/nextstrain/measles), mumps (https://github.com/nextstrain/mumps, created as part of [33]), dengue (https:// github.com/nextstrain/dengue, created as part of [4]), and enterovirus D68 (https: //github.com/nextstrain/enterovirus_d68, created as part of [20]). For the influenza A and B viruses, we tweaked the builds to contain sequences from any date, rather than limiting the tree to isolates sampled within the past 12 years.…”

Section: Input Data For the Estimation Of Rate Of Adaptationmentioning

confidence: 99%

An Atlas of Adaptive Evolution in Endemic Human Viruses

Kistler

Bedford

2023

Preprint

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Through antigenic evolution, viruses like seasonal influenza evade recognition by neutralizing antibodies elicited by previous infection or vaccination. This means that a person with antibodies well-tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. It is not fully understood which of the many endemic human viruses evolve in this fashion. To expand that knowledge, we assess adaptive evolution across the viral genome in 28 endemic viruses, spanning a wide range of viral families and transmission modes. We find that surface proteins consistently show the highest rates of adaptation, and estimate that ten viruses in this panel undergo antigenic evolution to selectively fix mutations that enable the virus to escape recognition by prior immunity. We compare overall rates of amino acid substitution between these antigenically-evolving viruses and SARS-CoV-2, showing that SARS-CoV-2 viruses are accumulating protein-coding changes at substantially faster rates than these endemic viruses.

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“…Perhaps owing to this, mumps outbreaks have occurred worldwide over the past decades, mainly in vaccinated adolescents and young adults. These outbreaks often occurred in close contact settings (schools, households, parties), and were mostly caused by genotypes that are different from the vaccine genotype [5, 6, 7, 8, 9, 10, 11, 12, 13]. For instance, the current vaccine used in the Netherlands contains the Jeryl-Lynn strain (genotype A), and is genetically distant from the recent outbreak strains (genotypes D and G) [14, 15].…”

Section: Introductionmentioning

confidence: 99%

Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology

van Boven,

Backer,

Veldhuijzen

et al. 2023

Preprint

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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 serological data from outbreaks of mumps virus genotype G among college students in the Netherlands over the period 2009-2012. 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 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 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.HighlightsWe use paired pre- and post-outbreak serological data to estimate mumps infection rates in college students.We use a two-component mixture model to provide individual estimates of infection for each participant.The estimated population infection attack rate is higher than reported earlier (9.5% vs 4.2%).The estimated individual probability of infection increases with decreasing pre-outbreak antibody concentrations, from 12% in the lowest to 5.6% in the highest quartile.

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Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

Cited by 17 publications

References 70 publications

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

An Atlas of Adaptive Evolution in Endemic Human Viruses

Estimation of the infection attack rate of mumps in an outbreak among college students using paired serology

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