Etienne Loire

Arthropod-borne viruses or arboviruses alternate between vertebrates and arthropods, facing distinct selection pressures in each host. Surprisingly, mechanisms facilitating host alternation remain unstudied. Here, we investigate two phenomena potentially facilitating host alternation in bluetongue virus (BTV): adaptive mutations and genome formula variation (GFV; i.e., differences in segment copy numbers). First, we searched for mutations indicative of host adaptation in cattle, sheep, and midges infected during an epizootic. No mutation was fixed in all samples of a given host. Thus, adaptive mutations may not be a major mechanism facilitating host alternation in the studied epizootic. Second, we investigated the relationship between GFV and a proxy of viral fitness, namely, head infection in midges. We analyzed the genome formula (GF) in Culicoides imicola midges, either with or without head infection 10 days after oral inoculation. GFs differed between dissemination groups, suggesting a correlation between GF and head infection. Finally, we investigated the mechanisms underlying GF generation. Currently, two scenarios have been proposed: random generation followed by selection or directed generation through molecular mechanisms. To limit the influence of selection, we analyzed the GF after a single replication cycle in cell culture. GFs converged toward specific values across replicates. Moreover, GFs differed between arthropod and vertebrate cells. Thus, GF generation does not seem purely stochastic and is probably influenced by host-specific mechanisms. Overall, our findings highlight GFV as a mechanism potentially facilitating host alternation of BTV, and they do not strongly support an involvement of mutations in the same phenomenon. IMPORTANCE: Arthropod-borne viruses are major public health concerns worldwide. These viruses follow a complex cycle involving an alternation between arthropods and vertebrates. Surprisingly, little is known about the mechanisms that could facilitate this alternation. Understanding such mechanisms could aid the development of antiviral strategies. Here, using bluetongue virus as a model, we investigated two potential mechanisms facilitating alternation. These mechanisms are adaptive mutations and genome formula variation (GFV). We found limited evidence for host-specific parallel mutations in natural populations from a single epizootic. In contrast, we observed a potential link between GFV and viral fitness. Moreover, our results suggest that molecular mechanisms generate host-specific genome formulas from the first round of cell infection.

To improve and rationalize the detection of carbapenemase-producing Enterobacterales (CPE) in rectal swabs in a high-prevalence and resource-constrained setting, addressing surveillance challenges typically encountered in laboratories with limited resources. A point prevalence survey (PPS) was conducted on 15 August 2022, in a provincial children’s hospital in northern Vietnam. Rectal swab samples of all admitted children were collected and plated on a selective medium for carbapenem-resistant Enterobacterales (CRE). Species identification and antimicrobial susceptibility testing (AST) were performed by MALDI-TOF, and VITEK2 XL and interpreted according to CLSI breakpoints (2022). Carbapenemases were detected by the carbapenem inactivation method (CIM) and quantitative real-time PCR (qRT-PCR). Rectal swab samples were obtained from 376 patients. Of 178 isolates growing on the CRE screening agar, 140 isolates were confirmed as Enterobacterales of which 118 (84.3%) isolates were resistant to meropenem and/or ertapenem. CIM and PCR showed that 90/118 (76.3%) were carbapenemase producers. Overall, 83/367 (22.6%) were colonized by CPE. Klebsiella pneumoniae, Escherichia coli and Enterobacter cloacae complex were the most common CPE detected, with NDM as the predominant carbapenemase (78/90; 86.7%). Phenotypic resistance to meropenem was the best predictor of CPE production (sensitivity 85.6%, specificity 100%) compared with ertapenem resistance (95.6% sensitivity, 36% specificity). CIM was 100% concordant with PCR in detecting carbapenemases. These findings underscore the effectiveness of meropenem resistance as a robust indicator of the production of carbapenemases and the reliability of the CIM method to detect such carbapenemases in resource-limited settings where the performance of molecular methods is not possible.

ESBL-producing Escherichia coli (ESBL-Ec) is considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human and environment compartments. There is likelihood of ESBL-Ec animal–human transmission but proof of cross-compartment transmission is still unclear. To characterize ESBL-Ec genetic similarity in various compartments (humans, animals and environment) from a rural area of Madagascar. We collected ESBL-Ec isolates prospectively from humans, animals and the environment (water) between April and October 2018. These isolates were subject to WGS and analysed with cutting-edge phylogenomic methods to characterize population genetic structure and infer putative transmission events among compartments. Of the 1454 samples collected, 512 tested positive for ESBL-Ec. We successfully sequenced 510 samples, and a phylogenomic tree based on 179 365 SNPs was produced. Phylogenetic distances between and amongst compartments were indistinguishable, and 104 clusters of recent transmission events between compartments were highlighted. Amongst a large diversity of ESBL-Ec genotypes, no lineage host specificity was observed, indicating the regular occurrence of ESBL-Ec transfer among compartments in rural Madagascar. Our findings stress the importance of using a phylogenomic approach on ESBL-Ec samples in various putative compartments to obtain a clear baseline of AMR transmissions in rural settings, where one wants to identify risk factors associated with transmission or to measure the effect of ‘One Health’ interventions in low- and middle-income countries.

A bstract: Deciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polygenic architectures. In this study, we developed a population genomics approach coupled with functional predictions to address the evolution and genetic basis of olfactory-based assortative mate preferences in the house mouse, suspected to have evolved as a response to selection against hybridisation. We used whole genome resequencing data and the C2 statistic of the program B ay P ass , which contrasts allele frequencies corrected for population structure, to characterize genetic differentiation between sets of populations with strong contrast in behaviour (expressing or not assortative mate preferences) and we identified some regions of the genome showing the expected significant and consistent association with behavioural divergence. A series of Olfactory and Vomeronasal Receptor genes, among the most differentiated genomic regions and in line with functional predictions, stand out as the prime candidates underlying this olfactory-based behavioural divergence. These genes form large gene clusters in the genome, with two main candidate clusters extending up to 1.8 Mb. Variant analyses indicate a potential dual role of regulatory and protein-coding changes in the evolution of choosiness. This study shows that combining expectations on the genomic patterns of divergence with functional expectations represents a promising route to unravelling the genetic architecture of complex trait variation and provides novel insights into the role of olfactory and vomeronasal receptors in mammal adaptation and speciation.

The variation in viral gene frequencies remains a largely unexplored aspect of within-host genetics. This phenomenon is often considered to be specific to multipartite viruses. Multipartite viruses have segmented genomes, but in contrast to segmented viruses, their segments are each encapsidated alone in a virion. A main hypothesis explaining the evolution of multipartism is that, compared to segmented viruses, it facilitates the regulation of segment abundancy, and the genes the segments carry, within a host. These differences in gene frequencies could allow for expression regulation. Here, we show that wild populations of a segmented virus, bluetongue virus (BTV), also present unequal segment frequencies. BTV cycles between ruminants and Culicoides biting midges. As expected from a role in expression regulation, segment frequencies tended to show specific values that differed between ruminants and midges. Our results expand previous knowledge on gene frequency variation and call for studies on its role and conservation beyond multipartite viruses.

Background: Arthropod borne virus infections are the cause of severe emerging diseases. Among the diseases due to arboviruses, dengue (DEN) and Rift Valley fever (RVF) are in the top ten in the list of diseases responsible of severe human cases worldwide. Understanding the effects of viral infection on gene expression in competent vectors is a challenge for the development of early diagnostic tools and may enable researchers and policy makers to better anticipate outbreaks in the next future. Methods: In this study, alterations in gene expression across the entire Aedes aegypti genome during infection with DENV and RVFV were investigated in vitro at two time points of infection, the early phase (24 h) and the late phase (6 days) of infection using the RNA sequencing approach Results: A total of 10 upregulated genes that share a similar expression profile during infection with both viruses at early and late phases of infection were identified. Family B and D clip-domain serine proteases (CLIP) were clearly overrepresented as well as C-type lectins and transferrin. Conclusions: Our data highlight the presence of 10 viral genes upregulated in Ae. aegypti during infection. They may also be targeted in the case of the development of broad-spectrum anti-viral diagnostic tools focusing the mosquito vectors rather than the mammalian hosts as they may predict the emergence of outbreaks.

We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also available via a web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

Peste des Petits Ruminants (PPR) is a highly infectious disease caused by a virus of the Morbillivirus genus. The current PPR eradication effort relies mainly on the implementation of massive vaccination campaigns. One of the most widely used PPR vaccines is the Nigeria 75/1 strain obtained after attenuation by 75 serial passages of the wild type isolate in cell cultures. Here we use high throughput deep sequencing of the historical passages that led to the Nigeria 75/1 attenuated strain to understand the evolution of PPRV attenuation and to assess the risk of reversal in different cell types. Comparison of the consensus sequences of the wild type and vaccine strains showed that only 18 fixed mutations separate the two strains. At the earliest attenuation passage at our disposal (passage 47), 12 out of the 18 mutations were already present at a frequency of 100%. Low-frequency variants were identified along the genome in all passages. Sequencing of passages after the vaccine strain showed evidence of genetic drift during cell passages, especially in cells expressing the SLAM receptor targeted by PPRV. However, 15 out of the 18 mutations related to attenuation remained fixed in the population. In vitro experiments suggest that one mutation in the leader region of the PPRV genome affects virus replication. Our results suggest that only a few mutations can have a serious impact on the pathogenicity of PPRV. Risk of reversion to virulence of the attenuated PPRV strain Nigeria 75/1 during serial passages in cell cultures seems low but limiting the number of passages during vaccine production is recommended.