Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Mumps virus) | 110 buccal swabs from mumps positive patients in Washington | Washington StateDepartment of Health | Sequences were deposited in Genbank under accessions MT859507-MT859672. Raw reads were deposited under SRA project number PRJNA641715 | Full metadata for each sequence is available in the manuscript in Supplementary file 1a |
| Biological sample (Mumps virus) | 56 buccal swabs from mumps positive patients from other US states | Wisconsin State Lab of Hygiene | Sequences were deposited in Genbank under accessions MT859507-MT859672. Raw reads were deposited under SRA project number PRJNA641715 | Full metadata for each sequence is available in the manuscript in Supplementary file 1a |
| Biological sample (Mumps virus) | Publicly available mumps genomes | NIAID Virus Pathogen Database and Analysis Resource (ViPR) (Pickett et al., 2012) | http://www.viprbrc.org/ | |
| Sequence- based reagent | mumps_1.5 kb primers | This paper | PCR primers | Full list of PCR primer sequences is available in the Materials and methods section under ‘Viral RNA extraction, cDNA synthesis, and amplicon generation’ |
| Commercial assay or kit | QiAmp Viral RNA Mini Kit | Qiagen, Valencia, CA, USA | Cat #: 52904 | |
| Commercial assay or kit | Protoscript II First strand synthesis kit | New England Biolabs, Ipswich MD, USA | Cat #: E6560L | |
| Commercial assay or kit | Q5 Hotstart DNA polymerase | New England Biolabs, Ipswich, MD, USA | Cat #: M0493L | |
| Commercial assay or kit | Ampure XP beads | Beckman Coulter | Cat #: A63881 | |
| Commercial assay or kit | Nextera XT DNA Library Prep Kit | Illumina, San Diego, CA, USA | Cat #: FC-131–1096 | |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | RRID:SCR_016368 |
| Software, algorithm | MAFFT | Katoh et al., 2002 | https://mafft.cbrc.jp/alignment/software/ | RRID:SCR_016368 |
| Software, algorithm | TreeTime | Sagulenko et al., 2018 | https://github.com/neherlab/treetime | |
| Software, algorithm | BEAST (versions 1.8.4 and 2.6.2) | Drummond et al., 2012, Lemey et al., 2009, Bouckaert et al., 2019 | https://beast.community/ and https://www.beast2.org/ | RRID:SCR_010228 |
| Software, algorithm | IQTREE | Nguyen et al., 2015 | http://www.iqtree.org | |
| Software, algorithm | Github repo with protocols for generating mumps sequences from buccal swabs | This paper | https://github.com/blab/mumps-seq | This github repository contains documentation and protocols for all lab procedures and bioinformatics pipelines used to generate consensus genomes from mumps buccal swabs |
| Software, algorithm | Github repo with scripts used to analyze data and generate figures for this manuscript | This paper | https://github.com/blab/mumps-wa-phylodynamics | This github repository contains all of the code used to generate figures and perform the analyses described in this manuscript. This repository also contains xml files used for input for BEAST analyses and alignments and tree files used to generate and plot phylogenetic trees |