DOI: 10.5061/dryad.fttdz08w9
title: MHC class II genotype-by-pathogen genotype interaction for infection prevalence in a natural rodent-Borrelia system

description: MHC genes are extraordinarily polymorphic in most taxa. Host-pathogen
 coevolution driven by negative frequency-dependent selection (NFDS) is one
 of the main hypotheses for the maintenance of such immunogenetic
 variation. Here we test a critical but rarely tested assumption of this
 hypothesis—that MHC alleles affect resistance/susceptibility to a pathogen
 in a strain-specific way, i.e. that there is a host genotype-by-pathogen
 genotype interaction. In a field study of bank voles naturally infected
 with the tick-transmitted bacterium Borrelia afzelii, we tested for MHC
 class II (DQB) genotype-by-B. afzelii strain interactions for infection
 prevalence between ten DQB alleles and seven strains. One allele (DQB*37)
 showed an interaction, such that voles carrying DQB*37 had higher
 prevalence of two strains and lower prevalence of one strain than
 individuals without the allele. These findings were corroborated by
 analyses of strain composition of infections, which revealed an effect of
 DQB*37 in the form of lower b diversity among infections in voles carrying
 the allele. Taken together, these results provide rare support at the
 molecular genetic level for a key assumption of models of antagonistic
 coevolution through NFDS.
description: <strong>Field
 sampling</strong> Animals for this study were trapped at Kalvs
 mosse, a damp deciduous wood (ca 24 ha) at Revingehed in southern Sweden
 (55°42’N, 13°29’E), in May-October 2006-2014. Animals were trapped with
 live traps (Ugglan special, GrahnAB, Sweden) baited with grains and apple
 or carrot. From each individual we took a skin biopsy
 (Ø 2 mm) from the ear for
 DNA extraction. We also recorded body mass to the nearest 0.1 g using a
 Pesola spring balance. During 2007-2008, we collected longitudinal data by
 trapping bank voles about every 6 weeks during May-October and tagging
 each individual with a transponder (Trovan ID-100 Unique) subcutaneously
 implanted on the back, which allowed identification of each individual
 upon recapture. <strong>DQB and ospC
 sequencing</strong> Skin biopsies were stored in 70% ethanol until
 DNA extraction using the protocol of (Laird et al. 1991). <em>B.
 afzelii</em>-infected bank voles were identified by real-time
 PCR of flaB
 (Råberg
 2012). To determine which
 ospC strains an infected vole carried we used 454
 amplicon pyrosequencing, as described in Strandh and Råberg
 (2015). The ospC data set used in the present study is the same
 as in Råberg et al.
 (2017).
 <em>B.
 afzelii</em>-infected voles were genotyped at
 <em>DQB
 </em>by amplifying
 205 out of 272bp in exon 2 using the primers MyglDQBfw and MyglDQBrv
 (Scherman et al.
 2014), followed by
 amplicon sequencing. Exon 2 contains the majority of the peptide binding
 residues and is the most polymorphic exon in this gene
 (Scherman et al.
 2014). Two different
 sequencing methods were used: 300 bp paired-end Illumina MiSeq sequencing
 (N=265 in the final data set) and 454 pyrosequencing (N=36 in the final
 data set; a subset of the data from Scherman et al. (2021). Libraries were prepared and the data filtered
 as described in Scherman
 et al. (2021). The
 concordance between Illumina MiSeq sequencing and 454 pyrosequencing of
 MHC is high (Razali et al.
 2017). The reproducibility
 (number of <em>DQB
 </em>alleles
 detected in all replicates from an individual/total number of
 <em>DQB
 </em>alleles
 detected in that individual) was in all cases 100% for both Illumina MiSeq
 sequencing (samples from 34 longitudinally sampled voles; 2-4
 samples/vole) and 454 pyrosequencing (13 technical duplicates;
 Scherman et al.
 2021). Laird, P., Zijderveld, A., Linders, K. &
 Rudnicki, M. (1991). Simplified mammalian DNA isolation procedure. Nucleic
 Acids Res., 19, 4293. Råberg, L. (2012). Infection intensity and
 infectivity of the tick-borne pathogen Borrelia afzelii.
 J. Evol.
 Biol.,
 25. Råberg, L., Hagström, Å., Andersson, M., Bartkova,
 S., Scherman, K., Strandh, M., et al. (2017). Evolution of antigenic diversity in the
 tick-transmitted bacterium Borrelia afzelii: a role for host
 specialization? J. Evol. Biol., 30, 1034–1041.
 Razali, H., O’Connor, E.,
 Drews, A., Burke, T. & Westerdahl, H. (2017). A quantitative and
 qualitative comparison of illumina MiSeq and 454 amplicon sequencing for
 genotyping the highly polymorphic major histocompatibility complex (MHC)
 in a non-model species. BMC Res. Notes, 10, 346.
 Scherman, K., Råberg, L.
 & Westerdahl, H. (2014). Positive selection on MHC class II DRB
 and DQB genes in the bank vole (Myodes glareolus). J. Mol. Evol.,
 78. Scherman, K., Råberg, L. & Westerdahl,
 H. (2021). Borrelia Infection in Bank Voles Myodes glareolus Is Associated
 With Specific DQB Haplotypes Which Affect Allelic Divergence Within
 Individuals. Front. Immunol., 12, 703025.
 Strandh, M. & Råberg,
 L. (2015). Within-host competition between Borrelia afzelii ospC strains
 in wild hosts as revealed by massively parallel amplicon sequencing.
 Philos. Trans. R. Soc. London. B, 370, 20140293.