The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain

In new epidemics after the host shift, the pathogens may experience accelerated evolution driven by novel selective pressures. When the accelerated evolution enters a positive feedback loop with the expanding epidemics, the pathogen's runaway evolution may be triggered. To test this possibility in COVID-19, we analyze the extensive databases and identify 5 major waves of strains, one replacing the previous one in 2020-2021. The mutations differ entirely between waves and the number of mutations continues to increase, from 3-4 to 21-31. The latest wave is the Delta strain which accrues 31 new mutations to become highly prevalent. Interestingly, these new mutations in Delta strain emerge in multiple stages with each stage driven by 6-12 coding mutations that form a fitness group. In short, the evolution of SARS-CoV-2 from the oldest to the youngest wave, and from the earlier to the later stages of the Delta wave, is a process of acceleration with more and more mutations. The global increase in the viral population size (M(t), at time t) and the mutation accumulation (R(t)) may have indeed triggered the runaway evolution in late 2020, leading to the highly evolved Alpha and then Delta strain. To suppress the pandemic, it is crucial to break the positive feedback loop between M(t) and R(t), neither of which has yet to be effectively dampened by late 2021. New waves beyond Delta, hence, should not be surprising.

A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles

The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this study, we present the most comprehensive phylogenetic and phylogeographic analysis, contributing to a better understanding of the origins, diversification, and the role of different host species in the evolution and diffusion of a dog-related variant endemic of South America. A total of 237 complete Nucleoprotein gene sequences were studied, corresponding to wild and domestic species, performing selection analyses, ancestral states reconstructions, and recombination analyses. This variant originated in Brazil and disseminated through Argentina and Paraguay, where a previously unknown lineage was found. A single host shift was identified in the phylogeny, from dog to the crab-eating fox (Cerdocyon thous) in the Northeast of Brazil. Although this process occurred in a background of purifying selection, there is evidence of adaptive evolution -or selection of sub-consensus sequences- in internal branches after the host shift. The interaction of domestic and wild cycles persisted after host switching, as revealed by spillover and putative recombination events.

Evolution of parasitoid host preference and performance in response to an invasive host acting as evolutionary trap

The invasion of a novel host species can create a mismatch in host choice and offspring survival (performance) when native parasitoids attempt to exploit the invasive host without being able to circumvent its resistance mechanisms. Invasive hosts can therefore act as evolutionary trap reducing parasitoids’ fitness and this may eventually lead to their extinction. Yet, escape from the trap can occur when parasitoids evolve behavioural avoidance or a physiological strategy compatible with the trap host, resulting in either host-range expansion or a complete host-shift. We developed an individual based model to investigate which conditions promote parasitoids to evolve behavioural preference that matches their performance, including host-trap avoidance, and which conditions lead to adaptations to the unsuitable hosts. One important aspect of these conditions was reduced host survival during incompatible interaction, where a failed attempt by a parasitoid resulted in host killing. This non-reproductive host mortality had a strong influence on the likelihood of establishment of novel host-parasitoid relationship. Killing unsuitable hosts can constrain adaptation under conditions which in fact promoted adaptation when parasitoids would leave the trap host unharmed and survive parasitoid attack. Moreover, our model revealed that host-search efficiency and genetic variation in host-preference play a key role in the likelihood that parasitoids will include the suboptimal host in their host range, or will evolve behavioural avoidance resulting in specialization and host-range conservation, respectively. Hence, invasive species might change the evolutionarily trajectory of native parasitoid species, which is important for predicting biocontrol ability of native parasitoids towards novel hosts.

Connecting neuromodulation, brain development, and life history timing associated with ecological speciation in Rhagoletis pomonella

Host shifts are considered a key generator of insect biodiversity, yet how insects synchronize life history timing and preference for new hosts is not well understood. Neurochemicals such as biogenic amines play key roles in both development and behavior, and therefore provide a potential source for such synchronization. Here, we correlated life history timing, brain development, and corresponding levels of 14 neurochemicals in Rhagoletis pomonella (Diptera: Tephritidae), a species undergoing ecological speciation through an ongoing host shift from hawthorn to apple fruit. We found that adult brain differentiation in both host races was initiated only after pupal diapause ended, and at this stage the titers of precursors for several neurotransmitter pathways also increased significantly. Conversely, neurotransmitter product titres generally increased at later stages up to adult fly sexual maturation. Further analysis showed that the apple host race exhibited adult brain differentiation three weeks earlier than the hawthorn host race, which correlated with significantly lower titers of several neurochemicals, particularly biogenic amines, in the earlier developing apple race as compared to the hawthorn race. We thus propose that these neurotransmitter levels could influence the differences in life history timing and host preference observed in these two races, promoting their ongoing speciation.

Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison

Coronaviruses (CoVs) are widespread and highly diversified in wildlife and domestic mammals and can emerge as zoonotic or epizootic pathogens and consequently host shift from these reservoirs, highlighting the importance of veterinary surveillance. All genera can be found in mammals, with α and β showing the highest frequency and diversification. The aims of this study were to review the literature for features of CoV surveillance in animals, to test widely used molecular protocols, and to identify the most effective one in terms of spectrum and sensitivity. We combined a literature review with analyses in silico and in vitro using viral strains and archive field samples. We found that most protocols defined as pan-coronavirus are strongly biased towards α- and β-CoVs and show medium-low sensitivity. The best results were observed using our new protocol, showing LoD 100 PFU/mL for SARS-CoV-2, 50 TCID50/mL for CaCoV, 0.39 TCID50/mL for BoCoV, and 9 ± 1 log2 ×10−5 HA for IBV. The protocol successfully confirmed the positivity for a broad range of CoVs in 30/30 field samples. Our study points out that pan-CoV surveillance in mammals could be strongly improved in sensitivity and spectrum and propose the application of a new RT-PCR assay, which is able to detect CoVs from all four genera, with an optimal sensitivity for α-, β-, and γ-.

Host phylogeny and ecological associations best explain Wolbachia host shifts in scale insects

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on earth. Wolbachia’ s success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch to new host species. Whilst much progress has been made in elucidating the phenotypes induced by Wolbachia, our understanding of Wolbachia host shifting is still very limited: we lack answers to even fundamental questions concerning Wolbachia’s routes of transfer and the importance of factors influencing host shifts. Here, we investigate the diversity and host-shift patterns of Wolbachia in scale insects, a group of arthropods with intimate associations with other insects that make them well-suited to studying host shifts. Using Illumina pooled amplicon sequencing of Wolbachia-infected scale insects and their direct associates we determined the identity of all Wolbachia strains, revealing that 32% of samples were multiply infected (with up to five distinct strains per species). We then fitted a Generalised Additive Mixed Model (GAMM) to our data to estimate the influence of factors such as the host phylogeny and the geographic distribution of each species on Wolbachia strain sharing among scale insect species. The model predicts no significant contribution of host geography but strong effects of host phylogeny, with high rates of Wolbachia sharing among closely related species and a sudden drop-off in sharing with increasing phylogenetic distance. We also detected the same Wolbachia strain in scale insects and several intimately associated species (ants, wasps, beetles, and flies). This indicates putative host shifts and potential routes of transfers via these associates and highlights the importance of ecological connectivity in Wolbachia host-shifting.

Captivity and the co-diversification of great ape microbiomes

Wild great apes harbor clades of gut bacteria that are restricted to each host species. Previous research shows the evolutionary relationships among several host-restricted clades mirror those of great-ape species. However, processes such as geographic separation, host-shift speciation, and host-filtering based on diet or gut physiology can generate host-restricted bacterial clades and mimic patterns of co-diversification across host species. To gain insight into the distribution of host-restricted taxa, we examine captive great apes living under conditions where sharing of bacterial strains is readily possible. Here, we show that increased sampling of wild and captive apes identifies additional host-restricted lineages whose relationships are not concordant with the host phylogeny. Moreover, the gut microbiomes of captive apes converge through the displacement of strains that are restricted to their wild conspecifics by human-restricted strains. We demonstrate that host-restricted and co-diversifying bacterial strains in wild apes lack persistence and fidelity in captive environments.

Plant host shift: The viability and persistence of a polyphagous non-native insect

Drosophila suzukii (Diptera: Drosophilidae) has become a pervasive pest in several countries around the world. Many studies have investigated the preference and attractiveness of potential hosts on this invasive, polyphagous drosophilid. Thus far, no studies have investigated whether a shift of fruit host could affect its ecological viability or spatiotemporal persistence. In this study, we analysed the fecundity and oviposition period jointly with the survival time of D. suzukii subject to a shift in host fruit, using a joint modelling method for longitudinal outcomes and time-until-event outcomes. The number of eggs laid by females was higher in raspberry than in strawberry and when setting adults of F1 generation underwent a first host shift. The joint modelling also suggested that insects reared on raspberry survived longer. We then combined experimental results with a two-patch dispersal model to investigate how host shift in a species that exhibits both passive and density-dependent dispersal may affect its asymptotic dynamics. In line with empirical evidence, we found that a shift in host choice can significantly affect the growth potential and fecundity of a species such as D. suzukii, which ultimately could aid such invasive populations in their ability to persist within a changing environment.