Periodic Reporting for period 2 - BeePath (Impact of vector-mediated transmission on the evolution and ecology of a bee virus)
Période du rapport: 2022-09-01 au 2024-02-29
As has been recently exemplified by the global Covid19 pandemic, emerging diseases can pose important risks to their hosts, while at the same time being critical test cases for understanding the evolutionary ecology of host-pathogen interactions. The origins of disease emergence generally lie in a change in host-pathogen ecology, such as increased transmission opportunities through an increase in contact, for example through habitat destruction or range expansion. Another mechanism for increasing transmission is the acquisition of novel transmission routes. Effects on both host and pathogen can be particularly drastic when transmission changes from direct to vector-borne transmission, i.e. such as transmission of malaria or viruses via mosquitoes to humans or aphids to plants, or even transmission routes that mimic vector-borne transmission, such as blood or organ donations. Compared to direct transmission, vector-borne transmission is expected to lead to increases in pathogen prevalence and virulence, that is pathogens are expected to become more widespread and cause more harm to their hosts. Despite its importance for disease prevention and control, we lack empirical and theoretical understanding of the evolutionary ecology of vector-borne transmission, and particularly of the acquisition of this transmission route. The emergence of the ectoparasitic mite Varroa destructor in honeybees provides a unique opportunity to study how a novel vector affects pathogen ecology and evolution: this mite which feeds mainly on the fat body of honeybees is a novel vector for Deformed Wing Virus (DWV), a disease linked to severe increases in individual and hive mortality. To study the fundamental evolutionary ecology of emerging vector-borne diseases, we are exploiting a unique natural experiment, the presence of Varroa-free island refugia. We test how this novel vector affects epidemiology and viral evolution, and how we might ultimately mitigate the effects of these evolving viruses on host populations. Using this system, we have already shown that the acquisition of Varroa as a viral vector in honeybees has virus-dependent knock-on effects in wild bees. With this project, we aim to elucidate how transmission dynamics change in response to a novel vector and how this affects virus evolution in the field. We then aim to dissect the drivers of these changes in evolutionary ecology in the lab, to ask, for example, which characteristics of vector-borne transmission are key in driving changes observed in the field. With this knowledge, we then aim to improve our general understanding of pathogen evolution through modelling, as well as testing whether control and mitigation strategies can help to protect the hosts of this evolving pathogen. With this body of work, we aim to deepen our knowledge of the ecological and evolutionary risk factors driving disease emergence, specifically the role of vector-borne transmission; this knowledge is crucial for human societies in preventing and mitigating emerging diseases in wildlife, agriculture and in human health. Furthermore, the honeybees and wild bees we work with are crucial pollinators of crops and wild flowering plants, key for maintaining biodiversity and human food security. We specifically aim to test strategies for mitigating the effects of evolving viruses on these communities through conservation measures, thereby promoting wild and managed pollinators that are crucial for human and environmental health.
As we aim to study how gaining vector-borne transmission affects the ecology and evolution of Deformed Wing Virus in honeybees and the wider bee community, studying field populations in 'natural laboratories' - island refugia that remain free of the virus-vectoring Varroa mite or that have already been invaded - is the basis of our project. We started our field collections in spring 2021, but had to adapt our plans to fit with the constantly changing pandemic restrictions. Nevertheless, we were able to collect samples that have allowed us not only to study evolution but also to investigate the temporal stability of these viral communities, comparing them to samples from 2015. This collection also allowed us to track the invasion of one of the remaining island refugia, the Isle d'Oeussant, by Varroa and its effects on viral composition in real time. Using transcriptomics on these samples as well as successfully preparing archival samples for RNA sequencing, we were able to see evidence of evolution in action in these populations. To achieve our aim of studying how vector-borne transmission changes transmission networks and whether it for example turns honeybees into a superspreader species, additional in-depth sampling was necessary, which we couldn't achieve under pandemic restrictions in 2021. For this reason, we returned to the islands in 2022 and conducted large-scale sampling and ecological surveys.
These two expeditions produced a large body of samples: In 2021, we collected a total of 1600 honeybees and bumblebees from 12 island and mainland sites. In 2022, focussing on in-depth sampling and ecological surveys, we collected 2900 honeybees and bumblebees from 6 islands. We have extracted RNA for viral genetics from all individuals, have screened them for prevalence of key viruses as well as measuring viral load by qPCR. To determine species and to assess population density of wild bumblebees, we have additionally extracted DNA for population genetics from 2500 bumblebees and have performed microsatellite analysis on them to determine colony numbers through genetic mark-recapture analysis.
Key results thus far are that virome composition is indeed relatively stable over time, driven primarily by host species; within honeybees, the presence of Varroa dictates virome composition and leads to a reduction in viral diversity, whereas in bumblebees, viral diversity is higher in mainland populations, i.e. populations that are larger and well-connected. We also found that in bumblebees, social organisation, in addition to population size and genetic variability, is important for disease transmission: sisters share more pathogens than unrelated individuals in wild populations. While we found overall stability in virome composition, we do find strong evidence for evolution within DWV, with a reversion of the decline in prevalence of DWV-A observed earlier with the emergence of DWV-B and crucially, evidence that recombinants between DWV-A and DWV-B may be under selection and may have arisen independently in the field.
These two expeditions produced a large body of samples: In 2021, we collected a total of 1600 honeybees and bumblebees from 12 island and mainland sites. In 2022, focussing on in-depth sampling and ecological surveys, we collected 2900 honeybees and bumblebees from 6 islands. We have extracted RNA for viral genetics from all individuals, have screened them for prevalence of key viruses as well as measuring viral load by qPCR. To determine species and to assess population density of wild bumblebees, we have additionally extracted DNA for population genetics from 2500 bumblebees and have performed microsatellite analysis on them to determine colony numbers through genetic mark-recapture analysis.
Key results thus far are that virome composition is indeed relatively stable over time, driven primarily by host species; within honeybees, the presence of Varroa dictates virome composition and leads to a reduction in viral diversity, whereas in bumblebees, viral diversity is higher in mainland populations, i.e. populations that are larger and well-connected. We also found that in bumblebees, social organisation, in addition to population size and genetic variability, is important for disease transmission: sisters share more pathogens than unrelated individuals in wild populations. While we found overall stability in virome composition, we do find strong evidence for evolution within DWV, with a reversion of the decline in prevalence of DWV-A observed earlier with the emergence of DWV-B and crucially, evidence that recombinants between DWV-A and DWV-B may be under selection and may have arisen independently in the field.
We are currently developing whole genome sequencing approaches, with the aim of sequencing entire and intact single viral genomes to study viral evolution in full detail. In parallel, we are developing methods to study mutations under selection in the field in isolated lab experiments. Expected results by the end of the project include quantifying how vector-borne transmission has changed transmission rates within and between species in the field; identifying mutations under selection by vector-borne transmission in the field, and testing these mutations in the lab, for example, elucidating whether they are evolving in response to the circumvention of host defence barriers. We also aim to further develop agent-based models on host populations, to simulate the effect of evolved viruses on host populations, and whether conservation or control strategies can mitigate these.