| Literature DB >> 31963517 |
Sten Calvelage1, Marcin Smreczak2, Anna Orłowska2, Conrad Martin Freuling3, Thomas Müller3, Christine Fehlner-Gardiner4, Susan Nadin-Davis4, Dirk Höper1, Paweł Trębas2.
Abstract
Rabies in wildlife has been successfully controlled in parts of Europe and North America using oral rabies vaccination, i.e., the distribution of baits containing live-attenuated virus strains. Occasionally, these vaccines caused vaccine virus-induced rabies cases. To elucidate the mechanisms of genetic selection and the effect of viral populations on these rabies cases, a next generation sequencing approach as well as comprehensive data analyses of the genetic diversity of Street Alabama Dufferin (SAD) and ERA vaccine virus strains and vaccine-induced rabies cases from Canada and several European countries were conducted. As a result, twelve newly generated sets of sequencing data from Canada and Poland were added to a pool of previously investigated samples. While the population-based analysis showed a segregation of viruses of ERA vaccine-induced rabies cases from those of SAD Bern original (SAD Bernorig)-derived rabies cases, the in-depth variant analysis revealed three distinct combinations of selected variants for the ERA vaccine-induced cases, suggesting the presence of multiple replication-competent haplotypes in the investigated ERA-BHK21 vaccine. Our findings demonstrate the potential of a deep sequencing approach in combination with comprehensive analyses on the consensus, population, and variant level.Entities:
Keywords: next generation sequencing; population analysis; rabies; vaccine
Mesh:
Substances:
Year: 2020 PMID: 31963517 PMCID: PMC7020022 DOI: 10.3390/v12010115
Source DB: PubMed Journal: Viruses ISSN: 1999-4915 Impact factor: 5.048
Overview of additional vaccine-induced rabies cases from Poland and the Ontario province of Canada analyzed in this study.
| Sample ID | Animal | Origin | Date of Finding | Distributed Vaccine | Reference | Sample Material | Sequencing Method | RABV Reads | Mean Depth |
|---|---|---|---|---|---|---|---|---|---|
| C/POL/2017 | Red fox | Małopolska, Poland | Dec 2017 | SAD Bern | This Study | Brain | 1 | 8286 | 170 |
| C/CAN/1992N8944 | Red fox | Carleton, Canada | 1992 | ERA | [ | Brain | 2 | 49,610 | 1138 |
| C/CAN/1992N8991 | Raccoon | Tyendinaga, Canada | 1992 | ERA | [ | Brain | 2 | 50,587 | 1092 |
| C/CAN/1994N6762-B | Cow | Gloucester, Canada | 1994 | ERA | [ | Brain | 2 | 51,225 | 1129 |
| C/CAN/1994N6762-M | Mouse | Gloucester, Canada | 1994 | ERA | [ | Brain | 2 | 50,403 | 1165 |
| C/CAN/1994N35116 | Striped skunk | Hullet, Canada | 1994 | ERA | [ | Brain | 2 | 49,319 | 1127 |
| C/CAN/1996N5367 | Red fox | Ops, Canada | 1996 | ERA | [ | Brain | 2 | 50,188 | 1090 |
| C/CAN/1998N4916 | Raccoon | Normanby, Canada | 1998 | ERA | [ | Brain | 2 | 51,239 | 1092 |
| C/CAN/1999N6567 | Red fox | Mulmur, Canada | 1999 | ERA | [ | Brain | 2 | 51,411 | 995 |
Overview of ERA and Street Alabama Dufferin (SAD) Bern vaccine batches analyzed in this study.
| Sample ID | Vaccine Strain | Batch ID | Description | Sequencing Method | RABV Reads | Mean Depth |
|---|---|---|---|---|---|---|
| B/ERA/lot16 | ERA | lot 016 | ERA-BHK21 vaccine batch from 2005 | 2 | 50,788 | 11,301 |
| B/SAD/Bern/4024 | SAD Bern | 17/61Lj (4024) | Lysvulpen vaccine batches that were distributed in the area of Małopolska in autumn 2016, spring 2017 and autumn 2017 | 1 | 51,098 | 1317 |
| B/SAD/Bern/7024 | SAD Bern | 17/76Lj (7024) | 1 | 52,001 | 1333 |
List of additional R packages used for the calculation and graphical representation of the Manhattan distances.
| R Package | Version | Description |
|---|---|---|
| ape | 5.3 | Analyses of phylogenetics and evolution |
| cluster | 2.0.8 | Extended cluster analysis |
| fpc | 2.2-3 | Flexible procedures for clustering |
| ggplot2 | 3.2.0 | Data visualizations |
| ggrepel | 0.8.1 | Non-overlapping text labels for ggplot2 |
| grid | 3.6.0 | Grid graphics package |
| phyloseq | 1.28.0 | Handling and analysis of high-throughput microbiome census data |
| vegan | 2.5-5 | Community ecology package |
Figure 1Population-based analysis of ERA-BHK21 (left) and SAD Bernorig-derived vaccine batches (B/…) (right) and viruses of their vaccine-induced rabies cases (C/…) displayed by a fitted pairwise Manhattan distances plot. Data sets of samples that were added in this study (Table 1 and Table 2) are highlighted in bold, whereas data sets of vaccine batches and their related induced rabies cases are displayed in different colors: blue—SAD B19 vaccine batches; green—SAD Bern vaccine batches, dark blue—SAD Bernorig-derived vaccine-induced rabies cases; orange—ERA-BHK21 vaccine batch; and dark orange—ERA-derived vaccine-induced rabies cases (orange/dark orange). For the ERA vaccine-induced rabies cases, three distinct combinations of single nucleotide variants were selected that originate from the progenitor ERA-BHK21 vaccine (see Section 3.2), forming groups of samples with specific differences that are represented by the colors of the respective sample names (1–3).
Figure 2Schematic illustration of all variants found for the ERA vaccine-induced rabies cases as well as nucleotide exchanges between viruses from vaccine-induced rabies cases and the ERA-BHK21 vaccine virus strain. Colored dotted lines display differences at the consensus level for viruses from vaccine-induced rabies cases that derived from selected combinations of single nucleotide variants (SNVs) found in the progenitor ERA-BHK21 vaccine virus (group 1–3; Table 4, for variant frequencies, see Table S7, Supplementary File). Nucleotide bases illustrated on the genome sequence represent spontaneous mutations found for viruses of vaccine-induced rabies cases. Each of these three groups were characterized by a unique set of differences at the consensus level (Table 4). The only exception was the sample C/CAN/1994N35116 which lacked one difference (position 3587, Table S7) and had one additional difference in close proximity that cannot be found in any of the other samples (position 3734, Table S7).
Groups of viruses from ERA vaccine-induced rabies cases showing similar patterns of nucleotide exchanges compared to the progenitor ERA-BHK21 vaccine virus strain at the consensus level.
| Samples | Host Species | Number of Group-Specific Differences | |
|---|---|---|---|
| Group 1 | C/CAN/1992N8944 | Red fox | 9 |
| C/CAN/1992N8991 | Raccoon | ||
| C/CAN/1996N5367 | Red fox | ||
| C/CAN/1996 | |||
| Group 2 | C/CAN/1994N35116 | Striped skunk | 7 |
| C/CAN/1994N6762B | Cow | ||
| C/CAN/1994N6762M | Cow (M-passage) 1 | ||
| C/CAN/1994 | |||
| C/CAN/1998N4916 | Raccoon | ||
| Group 3 | C/CAN/1991 | Striped skunk | 3 |
| C/CAN/1999N6567 | Red fox |
1 Mouse-passaged virus originating from C/CAN/1994N6762-B.
Viruses of ERA vaccine-induced rabies cases that maintained the vaccine consensus in the form of an SNV.
| Sample ID | Position * | Consensus Vaccine-Induced Case | Variant Vaccine-Induced Case (Consensus Vaccine) | Frequency of SNVs in the Vaccine-Induced Case |
|---|---|---|---|---|
| CAN/1992N8944 | 10,840 | A | G | 33.7% |
| CAN/1994N6762-M | 3085 | T | C | 31.9% |
* Nucleotide position relative to the sequence of the ERA-BHK21 vaccine batch B/ERA/lot16 full genome.
Figure 3Population-based analysis of ERA-BHK21- and SAD-Bernorig-derived vaccine strains and viruses of their vaccine-induced rabies cases in relation to selected field RABV strains (F/…).