Biology subjects

Maree, F.

Publications and source records attributed to Maree, F..

3 recordsLinked to original sources

bioRxiv2023

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Author summaryFoot and mouth disease (FMD) viruses are endemic in sub-Saharan Africa. Due to the complexity of the disease epidemiology and the lack of available data, there is a need to use phylogenetic approaches to understand the role of potential hosts involved in the circulation and maintenance of the viruses. The uneven host sampling of the available sequences requires us to take advantage of the recent advances in phylogenetic reconstruction. Therefore, using two structural coalescent model approximations we estimated the circulation of FMD virus serotypes SAT1 and SAT2 between cattle, buffalo and impala populations. Our results suggest that in Africa, the impala population seems to act as an intermediate host between the cattle and buffalo populations and play a more important role in the circulation of the viruses than was previously suspected. Until now, the role of the impala population in the circulation of FMDV has been suggested, but never explicitly shown.

molecular biology↗

bioRxiv2021

Viral dynamics and immune responses to foot-and-mouth disease virus in African buffalo (Syncerus caffer).

Foot-and-mouth disease (FMD) is one of the most important livestock diseases restricting international trade. While it is clear that African buffalo (Syncerus caffer) act as the main wildlife reservoir, viral and immune response dynamics during FMD virus acute infection have not been described before in this species. We used experimental needle inoculation and contact infections with three Southern African Territories serotypes to assess clinical, virological and immunological dynamics for thirty days post infection. Clinical FMD in the needle inoculated buffaloes was mild and characterised by pyrexia. Despite the absence of generalised vesicles, all contact animals were readily infected with their respective serotypes within the first 2-9 days after being mixed with needle challenged buffaloes. Irrespective of the route of infection or serotype there were positive associations between the viral loads in blood and the induction of host innate pro-inflammatory cytokines and acute phase proteins. Viral loads in blood and tonsils were tightly correlated during the acute phase of the infection, however, viraemia significantly declined after a peak at 4 days post infection (dpi), which correlated with the presence of detectable neutralising antibodies. In contrast, infectious virus was isolated in the tonsils until the last sampling point (30 dpi) in most animals. The pattern of virus detection in serum and tonsil swabs was similar for all three serotypes in the direct challenged and contact challenged animals. We have demonstrated for the first time, that African buffalo are indeed systemically affected by FMD virus and clinical FMD in buffalo is characterized by a transient pyrexia. Despite the lack of FMD lesions, infection of African buffalo was characterised by high viral loads in blood and oropharynx, rapid and strong host innate and adaptive immune responses and high transmissibility.

zoology↗

bioRxiv2018

Within-host recombination in structural proteins of the Foot-and-Mouth Disease Virus

Although recombination is known to occur in FMDV, it is considered only a minor determinant of virus sequence diversity. This is because recombination appears to be highly suppressed at phylogenetic scales; inter-serotypic recombination events are rare; and in those a mosaic structure is present whereby recombination only occurs almost exclusively in non-structural proteins. Here we show that co-inoculation of closely related strains in buffaloes results over time in extensive within-host recombination in the genomic region coding for structural proteins. This enables us to directly estimate recombination rates for the first time. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Thanks to the features of our experimental setup, we are also able to build a high-resolution map of effective within-host recombination in the capsid-coding region. We find that the linkage disequilibrium pattern inside VP1 points to a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although those intra-host results are not immediately transportable to a phylogenetic setting, they force us to reconsider the relevance of recombination and epistasis, suggesting that they must play a major and so far underappreciated role in the molecular evolution of the virus at all time scales.\n\nAuthor summaryRecombination in the capsid-coding region of the Foot-and-Mouth Disease virus genome is highly suppressed at phylogenetic scales. However, the role of recombination in the intra-host dynamics of the virus is not known. In our experiment, a co-infection of African buffaloes with closely related FMDV strains results in a population structure of the intra-host viral swarm, allowing us to detect recombination events. For structural protein-coding sequences, the swarm dynamics is driven by extensive within-host recombination. During the acute infection phase, we infer intra-host recombination rates of 0.1 per base per year, comparable to the typical mutation rate of the virus. The recombination map reveals two linkage blocks within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between blocks. Our findings support a major role for recombination and epistasis in the intra-host evolution of FMDV.

microbiology↗