DOI: 10.5061/dryad.dr7sqvb54
title: Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections

description: Interactions among pathogen genotypes that vary in host specificity may
 affect overall transmission dynamics in multi-host systems. Borrelia
 burgdorferi, a bacterium that causes Lyme disease, is typically
 transmitted among wildlife by Ixodes ticks. Despite the existence of many
 alleles of B. burgdorferi’s sensu stricto outer surface protein C (ospC)
 gene, most human infections are caused by a small number of ospC alleles
 [“human infectious alleles” (HIAs)], suggesting variation in host
 specificity associated with ospC. To characterize the wildlife host
 association of B. burgdorferi’s ospC alleles, we used metagenomics to
 sequence ospC alleles from 68 infected individuals belonging to eight
 mammalian species trapped at three sites in suburban New Brunswick, New
 Jersey (USA). We found that multiple allele (“mixed”) infections were
 common. HIAs were most common in mice (Peromyscus spp.) and only one HIA
 was detected at a site where mice were rarely captured. OspC allele U was
 exclusively found in chipmunks (Tamias striatus), and although a
 significant number of different alleles were observed in chipmunks,
 including HIAs, allele U never co-occurred with other alleles in mixed
 infections. Our results suggest that allele U may be excluding other
 alleles, thereby reducing the capacity of chipmunks to act as reservoirs
 for HIAs.
description: # Diversity and host specificity of Borrelia burgdorferi's outer
 surface protein C (ospC) alleles in synanthropic mammals, with a notable
 ospC allele U absence from mixed infections
 This repository includes
 raw sequence reads, SAMtools coverage data, coverage data graphs,
 metadata, and R code that allow one to reproduce all of the analyses in
 our manuscript. ## Description of the data and file structure Raw sequence
 reads (fastq format) are presented in a tarred/compressed file called
 "221028_KLY7P_Ellis copy.tar". "Shifflett et al.
 2023_metadata.xlsx" is the main data file. There are two sheets that
 are called separately in the R code. They describe the captured animals
 and provide additional information including whether they were infected
 and what species they belong to and where and when they were captured. The
 first sheet, “Data”, lists the date of capture, the site an individual was
 captured at, the common name for the species (under “animal”), the
 scientific name for the species, the individual’s weight (in grams; blank
 cells indicate that weight was not recorded), the individual’s sex
 (M=male, F=female, juv= juvenile and unable to sex; blanks in the Sex
 column are due to an inability to determine the sex of the individuals),
 The ear-tag ID given (tags with "R" at the end represent
 recaptured individuals), recapture status (no means the animal was caught
 for the first time and yes means the animal had been previously captured),
 followed by a unique ID. The second sheet, "Infected" lists the
 individual's unique ID, *B. burgdorferi* infection status as
 determined by PCR protocol (PCR_Infected), and *B. burgdorferi* infection
 status as determined by the qPCR protocol (qPCR_Infected).  The directory
 "samtools_coverage_data" includes the SAMtools coverage data as
 txt files. These are called in the R code. This directory is
 zipped/compressed. The directory "ospC_Coverage_Rraphs" includes
 plots of the sequencing coverage for each sample. This directory is
 zipped/compressed. The file "RecaptureData.xlsx" includes
 additional information about each of the recaptured individuals that can
 be also found in the main data file. The first tab “ID” reports the
 ear-tag ID given to each captured individual followed by the individual’s
 unique ID. An “R” is added to the original ear-tag ID for each additional
 capture of the same individual; while the ear-tag ID changes for each
 capture, the individual’s ID stays the same. The following sheet
 “meta_data” includes two tables. The first table lists all the recaptured
 individuals whose *B. burgdorferi* infection status or *ospC* allele
 composition did NOT change between captures. The second table shows
 recaptured individuals who developed a *B. burgdorferi* infection between
 captures and individuals whose *ospC* allele composition changed between
 captures. Both tables list the date of capture, the site location, the
 scientific name of the species caught, the ear-tag ID, ID, *B.
 burgdorferi* infection status determined by PCR followed by qPCR (1
 representing infections, 0 representing no infection), and the ospC allele
 ID. On the second table, empty cells allow for a visual distinction
 between different capture dates. ## Code/Software The R code that conducts
 the statistical analyses in our manuscript can be found in the file
 "Rutgers's paper supplementary R code.R". This R code uses
 the SAMtools coverage txt files and the metadata file.