Microsporidia-cypovirus interactions during simultaneous infection of the tree defoliator Dendrolimus sibiricus (Lepidoptera: Lasiocampidae).

The Siberian moth, Dendrolimus sibiricus is a dangerous forest defoliator, the number one pest of boreal forests in Asia. Search for effective and ecologically friendly control measures drives attention to microbial pathogens. Viruses and microsporidia are obligate intracellular parasites widespread in insect populations causing either chronic or acute infections. Interactions of these pathogens vary from antagonistic to synergistic. The goal of the work was to test a recently discovered cytoplasmatic polyhedrosis virus (cypovirus) strain DsCPV-1 isolated from D.sibiricus, combined with a microsporidium, against D. sibiricus, by feeding the inoculum (viral polyhedral and microsporidian spores). Three different microsporidian parasites of lepidopterans were tested against D. sibiricus as monoinfection: Nosema bombycis from silkworm, N. pyrausta from corn borer, and Tubulinosema loxostegi from beet webworm. Nosema bombycis was the most virulent, with a median lethal time of 7 days in the first and second instars treated with 100,000 and 1 million spores/larva, respectively. Nosema bombycis (dose 100,000 spores/larva) was chosen to test it as mixed infection in combination with an extremely low dose of DsCPV-1 (1 polyhedron/larva) against two races of D. sibiricus second instar larvae (the fir-feeding race and the larch-feeding race). The mixed infection demonstrated the most prominent negative effect on larval lethal time and weight for the both tested races. Mixed infections showed a synergistic effect for the fir-feeding larvae but additive effect only for the larch feeding larvae. Both pathogens co-developed successfully in the larvae with equal ratio of producing inoculum. The combination of these entomopathogens is therefore promising for forest protection against the Siberian moth and could be the way to significantly decrease the amount of pathogens applied in field.

A general and efficient representation of ancestral recombination graphs.

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. However, this approach is out of step with some modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalizes these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.

The Impact of a Cypovirus on Parental and Filial Generations of Lymantria dispar L.

Recently, we found that the spongy moth Lymantria dispar L. is susceptible to infection by a Dendrolimus sibiricus cytoplasmic polyhedrosis virus (DsCPV-1). In the present study, we evaluated the pathogenicity of DsCPV-1 against L. dispar larvae and its impact on surviving insects after the infection. Offspring of virally challenged insects were tested for susceptibility to a stress factor (starvation). In addition, we used light microscopy and quantitative polymerase chain reaction (qPCR) to test the ability of DsCPV-1 to be transmitted vertically. We found insect mortality of the L. dispar parents following the infection was positively associated with DsCPV-1 dose. DsCPV-1 was lethal to second-instar L. dispar larvae with a 50% lethal dose (LD50) of 1687 occlusion bodies per larva. No vertical transmission of DsCPV-1 to offspring larvae was detected, while the majority of insect deaths among offspring larvae were caused by microsporidia (Vairimorpha lymantriae), which was harbored by the parents. The offspring of virally challenged parents exhibited a higher number of detected microsporidia compared to the control. Our findings suggest that the application of DsCPV-1 is effective in controlling pests in terms of transgenerational impact following virus exposure.

A general and efficient representation of ancestral recombination graphs.

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). New developments have made it possible to infer ARGs at scale, enabling many new applications in population and statistical genetics. This rapid progress, however, has led to a substantial gap opening between theory and practice. Standard mathematical formalisms, based on exhaustively detailing the "events" that occur in the history of a sample, are insufficient to describe the outputs of current methods. Moreover, we argue that the underlying assumption that all events can be known and precisely estimated is fundamentally unsuited to the realities of modern, population-scale datasets. We propose an alternative mathematical formulation that encompasses the outputs of recent methods and can capture the full richness of modern large-scale datasets. By defining this ARG encoding in terms of specific genomes and their intervals of genetic inheritance, we avoid the need to exhaustively list (and estimate) all events. The effects of multiple events can be aggregated in different ways, providing a natural way to express many forms of approximate and partial knowledge about the recombinant ancestry of a sample.

Recoverability of ancestral recombination graph topologies.

Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem, as this relies on mutations having occurred on the correct lineages in order to detect the recombination and resolve the ordering of coalescence events in the local trees. We investigate the probability of reconstructing the true topology of ancestral recombination graphs (ARGs) under the coalescent with recombination and gene conversion. We explore how sample size and mutation rate affect the inherent uncertainty in reconstructed ARGs, which sheds light on the theoretical limitations of ARG reconstruction methods. We illustrate our results using estimates of evolutionary rates for several organisms; in particular, we find that for parameter values that are realistic for SARS-CoV-2, the probability of reconstructing genealogies that are close to the truth is low.

Laboratory Cultivation of Vairimorpha (Nosema) ceranae (Microsporidia: Nosematidae) in Artificially Infected Worker Bees.

Nosemosis type C is a dangerous and widespread disease of the adult European honey bee Apis mellifera and is caused by the spore-forming intracellular parasite Vairimorpha (Nosema) ceranae. The search for new ways of therapy for this disease is complicated due to the seasonal availability of V. ceranae-infected insects as well as the lack of a developed system for the pathogen's cultivation. By carrying out trials which used different infectious dosages of the parasite, spore storage protocols, host age, and incubation temperatures, we present a simple, safe, and efficient method of V. ceranae propagation in artificially infected worker bees in the laboratory. The method is based on feeding the groups of adult worker bees with microsporidian spores and insect maintenance in plastic bottles at 33 °C. The source of the spores originated from the cadavers of infected insects from the previous round of cultivation, in which the infective spores persist for up to six months. An analysis of five independent cultivation rounds involving more than 2500 bees showed that the proposed protocol exploiting the dosage of one million spores per bee yielded over 60 million V. ceranae spores per bee, and most of the spore samples can be isolated from living insects.

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction.

The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination.

Susceptibility of the Gypsy Moth Lymantria dispar (Lepidoptera: Erebidae) to Nosema pyrausta (Microsporidia: Nosematidae).

The gypsy moth, Lymantria dispar, is a notorious forest defoliator, and various pathogens are known to act as natural regulators of its population density. As a widespread herbivore with a broad range of inhabited areas and host plants, it is potentially exposed to parasitic microorganisms from other insect hosts. In the present paper, we determined the susceptibility of gypsy moth larvae to the microsporidium Nosema pyrausta from the European corn borer, Ostrinia nubilalis. Gypsy moth samples from two localities of Western Siberia were used. N. pyrausta developed infections in the salivary gland and adipose tissue of gypsy moth prepupae and pupae, forming spore masses after 30 days of alimentary exposure to the second instar larvae. Among the experimental groups, the infection levels ranged from 0 to 9.5%. Effects of a covert baculovirus infection, phenylthiourea pretreatment and feeding insects on an artificial diet versus natural foliage were not significant in terms of microsporidia prevalence levels. Thus, L. dispar showed a low level of susceptibility to a non-specific microsporidium. It can be referred to as a resistant model host and not an appropriate substitute host for laboratory propagation of the microsporidium.

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation.

MOTIVATION: The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG, which implements a parsimony-based greedy heuristic algorithm for finding plausible genealogical histories (ancestral recombination graphs) that are minimal or near-minimal in the number of posited recombination and mutation events. RESULTS: Given an input dataset of aligned sequences, KwARG outputs a list of possible candidate solutions, each comprising a list of mutation and recombination events that could have generated the dataset; the relative proportion of recombinations and recurrent mutations in a solution can be controlled via specifying a set of 'cost' parameters. We demonstrate that the algorithm performs well when compared against existing methods. AVAILABILITY AND IMPLEMENTATION: The software is available at https://github.com/a-ignatieva/kwarg. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A characterisation of the reconstructed birth-death process through time rescaling.

The dynamics of a population exhibiting exponential growth can be modelled as a birth-death process, which naturally captures the stochastic variation in population size over time. In this article, we consider a supercritical birth-death process, started at a random time in the past, and conditioned to have n sampled individuals at the present. The genealogy of individuals sampled at the present time is then described by the reversed reconstructed process (RRP), which traces the ancestry of the sample backwards from the present. We show that a simple, analytic, time rescaling of the RRP provides a straightforward way to derive its inter-event times. The same rescaling characterises other distributions underlying this process, obtained elsewhere in the literature via more cumbersome calculations. We also consider the case of incomplete sampling of the population, in which each leaf of the genealogy is retained with an independent Bernoulli trial with probability ψ, and we show that corresponding results for Bernoulli-sampled RRPs can be derived using time rescaling, for any values of the underlying parameters. A central result is the derivation of a scaling limit as ψ approaches 0, corresponding to the underlying population growing to infinity, using the time rescaling formalism. We show that in this setting, after a linear time rescaling, the event times are the order statistics of n logistic random variables with mode log(1∕ψ); moreover, we show that the inter-event times are approximately exponentially distributed.

Hexokinase as a versatile molecular genetic marker for Microsporidia.

Hexokinase (HK) is a core glycolytic enzyme of Microsporidia which regulates host cell metabolic processes. The goal of the present study was to test for the utility of HK for molecular phylogenetics, species identification and molecular detection of microsporidia in infected insects. HK sequence-based reconstructions were essentially similar to those based upon largest subunit RNA polymerase (RPB1) gene sequences, as well as previously published rRNA gene and genome-based trees. Comparing HK sequences allowed clear differentiation of closely related taxa, such as Nosema bombycis and Nosema pyrausta. In Nosema ceranae, unique SNPs were found for an isolate from wild colonies of the Burzyan dark honey bee as compared with the isolates from domesticated European honey bee. Similarly, in Encephalitozoon cuniculi, HK was as effective as RPB1 for discrimination of isolates belonging to different ITS genotypes. Amplification using species-specific primers flanking short fragments at the 3'-end of HK gene showed the presence of infection in insect tissues infected with N. pyrausta, Nosema ceranae and Paranosema (Antonospora) locustae. For the latter parasite species, HK expression was also demonstrated at early stages of infection using total mRNA extracts of locust larvae. These results indicate the suitability of HK as a novel tool for molecular genetic studies of Microsporidia.

Infection of Chorthippus loratus (Orthoptera: Acrididae) with Liebermannia sp. (Microsporidia) in South-Western Russia.

Chorthippus loratus collected in Krasnodar Territory in 2017 was infected at 15% rate with a microsporidium possessing ovocylindrical binucleate spores, 2.6 × 1.2 µm in size. SSU RNA gene typing (Genbank accession # MH396491) showed its allocation to the genus Liebermannia. Degenerate primers based upon largest subunit RNA polymerase II (RPB1) sequences of closest relatives allowed amplifying the respective gene fragment of Liebermannia sp. (# MH396492). The present finding indicates worldwide distribution of the Liebermannia genus and parasitism in hosts with nonoverlapping geographic ranges (representing Neotropical versus Palearctic fauna), while previous observations were restricted to Acridoidea endemic for South America.

Greater wax moth Galleria mellonella (Lepidoptera: Pyralidae) as a resistant model host for Nosema pyrausta (Microsporidia: Nosematidae).

Galleria mellonella fed 3 million Nosema pyrausta spores per larva showed 0 and 5% infestation rate at 30 °C and 24 °C, respectively. N. pyrausta virulence did not increase after passage through G. mellonella for three generations. When larvae were pretreated with phenylthiourea, Bacillus thuringiensis or combination of both, infection rates were 11%, 15% and 22%, respectively. Injection of untreated and potassium hydroxide-primed spores resulted in approximately 10% and 50% infection, respectively. G. mellonella is resistant to high dosages of N. pyrausta spores, serving as a prospective model of insect resistance to microsporidia, while host immunosuppression and/or spore activation increases success of the pathogen.

Natural infection of the beet webworm Loxostege sticticalis L. (Lepidoptera: Crambidae) with three Microsporidia and host switching in Nosema ceranae.

Three species of Microsporidia were identified from a population of the beet webworm Loxostege sticticalis at prevalence rates of 35, 4, and 3%. The most prevalent parasite (Tubulinosema sp.) was similar to Tubulinosema acridophagus (99.8% ssrDNA sequence similarity) and was also isolated from the parasitoid Lydella thompsoni (Diptera, Tachinidae) that emerged from the beet webworms. In laboratory assays, spores of this Tubulinosema sp. showed an infection rate of up to 80% for both L. sticticalis and Galleria mellonella larvae. The spores were viable after 12 months of storage in dried infected cadavers. The second most prevalent parasite was closely related to Nosema furnacalis and Nosema granulosis (98.7% similarity). Fresh spores showed a 50% infection rate under laboratory conditions. The third most abundant parasite was identified as the honeybee pathogen Nosema ceranae (100% ssrDNA and 95-100% IGS similarity). In the laboratory, fresh spores of N. ceranae isolated from beet webworm and honey bee were infective to L. sticticalis larvae at the rates of 5 and 2%, respectively.

Ultrastructure and molecular phylogeny of Anisofilariata chironomi g.n. sp.n. (Microsporidia: Terresporidia) from Chironomus plumosus L. (Diptera: Chironomidae).

Larvae of Chironomus plumosus, collected in North-Western Russia in September 2008, were infected with a microsporidium possessing broadly oval uninucleate spores in sporophorous vesicles. Sporogony and spore ultrastructure of this microsporidium differed from that of known microsporidian species, suggesting establishment of a new species, Anisofilariata chironomi, being a type species of a new genus. Sporogony di-, tetra-, octo-, and 16-sporoblastic. Fixed and stained spores are 4.7-6.8 x 3.4-5.4 microm in size, the spore measurements varying depending upon the number of spores in the sporophorous vesicle. The polaroplast is bipartite, with anterior and posterior parts composed of very thin and thick lamellae, respectively, and occupies the major volume of the spore. The polar filament is anisofilar, with two broad proximal and 10-13 narrow distal coils arranged in 2-4 layers. The sporophorous vesicle is bounded by a thin membrane and contains multiple tubular structures. Small subunit ribosomal DNA phylogeny showed basal position of the new microsporidium to a cluster uniting microsporidia infecting ciliates (Euplotespora binucleata), microcrustaceans (Glugoides intestinalis, Mrazekia macrocyclopis), lepidopteran insects (Cystosporogenes spp., Endoreticulatus spp.) and human (Vittaforma corneae), nested within Clade IV sensu Vossbrinck and Debrunner-Vossbrinck (2005 Folia Parasitol 52:131-142). No close phylogenetic relationships were found between A. chironomi and microsporidia from other dipteran hosts.