Host Range Expansion Research Articles

The episodic resurgence of highly pathogenic avian influenza H5 virus.

Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, increasingly causing mass mortality in wild birds and poultry and incidental infections in mammals1-3. However, the ecological and virological properties that underscore future mitigation strategies still remain unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the origins of resurgent HPAI H5 and reveal significant shifts in virus ecology and evolution. Outbreak data show key resurgent events in 2016-2017 and 2020-2021, contributing to the emergence and panzootic spread of H5N1 in 2021-2022. Genomic analysis reveals that the 2016-2017 epizootics originated in Asia, where HPAI H5 reservoirs are endemic. In 2020-2021, 2.3.4.4b H5N8 viruses emerged in African poultry, featuring mutations altering HA structure and receptor binding. In 2021-2022, a new H5N1 virus evolved through reassortment in wild birds in Europe, undergoing further reassortment with low-pathogenic avian influenza in wild and domestic birds during global dissemination. These results highlight a shift in the HPAI H5 epicentre beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential. As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic-bird-wild-bird interface. Elimination strategies in domestic birds therefore remain a high priority to limit future epizootics.

Bottom‐up effects shift top‐down community structure of the parasitoid guild that attacks Asphondylia borrichiae (Diptera: Cecidomyiidae) on Borrichia frutescens (Asteraceae)

Abstract Asphondylia borrichiae induces galls at the apical meristems of its host plant, Borrichia frutescens, and the larvae develop and pupate within the gall. During development, immature stages of the midge are attacked by four species of parasitic wasps; two of these parasitoids, Galeopsomyia haemon and Torymus umbilicatus, are the most common members of the guild, and both are hyperparasitic. In the current study, plots of B. frutescens were randomly assigned to control (unmanipulated), salted or fertilised in a long‐term press experiment. Although plots initially exhibited no differences in stem length, gall and flower densities, after 3 months, they began to exhibit significant differences, suggesting stress (salted plots) and vigour (fertilised plots). Galls produced on plants from fertilised plots were approximately 20% and 31% larger than those from control and salted plots, respectively. Larger gall diameter in fertilised plots resulted in a shift of the parasitoid community towards the largest parasitoid, T. umgbilicatus, whereas smaller galls produced in salted plots became biased towards the smallest, but gregarious, G. haemon; interestingly, this pattern held for T. umbilicatus across treatments, and the effect for G. haemon was not significant when all treatments were combined. This study suggests that abiotic factors that alter host plant characteristics, such as gall diameter, affect the composition of the parasitoid guild that attacks A. borrichiae, which has implications for the acquisition of enemy‐free space during host range expansion of the midge.

Host Range Expansion of Nest-Parasitic Moths Pyralis regalis and Hypsopygia mauritialis in Social Wasp Nests: New Findings and Implications for Biological Control

Parasitic moths are common in social wasp (Hymenoptera) nests, attacking many species of Polistinae and a few species of Vespinae. In the Republic of Korea, two moth species are known to parasitize the brood of Polistes rothneyi koreanus: Pyralis regalis (Pyralidae) and Anatrachyntis japonica (Cosmopterigidae). Although previously reported elsewhere, a novel case of parasitization was recently documented in the Republic of Korea, in which Hypsopygia mauritialis (Pyralidae) was identified in the nests of social wasps. Pyralis regalis is the most common parasitic moth in the Republic of Korea, feeding on the nests of 11 species of social wasps, mostly the Korean Vespa species. To that list of hosts, we add a species of Dolichovespula and two species of Polistes. Parasitism of Vespa velutina nigrithorax, an invasive alien hornet, by both P. regalis and H. mauritialis, was observed for the first time. However, their potential to control invasive alien hornets is expected to be low. This study provides new insights into the diversity of nest-parasitic moths in social wasp nests and their hosts in the Republic of Korea, and highlights the potential for these moths to impact pest populations.

Changes in parasite species distributions could be driven by host range expansions: the case of hybridisation between two Australian reptile ticks

Anthropogenic stressors such as climate change and diminishing habitats cause widespread disturbances in species distributions for a variety of taxa. Range shifts and hybridisation following secondary contact become of particular importance when it comes to parasites such as ticks, as they are dependent on their host distributions and can carry numerous harmful pathogens. We aimed to determine if two parapatric reptile tick species, Amblyomma albolimbatum and A. limbatum, hybridise at their parapatric boundary by comparing morphological and genomic variation using single nucleotide polymorphisms. Our results show that both tick species were genomically distinct, but hybridisation has occurred. We found a hybrid and an A. limbatum outside of their previously known range, suggesting there could have been a shift in tick distribution. What were thought to be hybrids due to intermediate morphological traits were not hybrids but morphological variants of the parental species. This information suggests more distinctive morphological features are needed for identifying these tick species and that novel environmental conditions and a broadening of tick niche due to hybridisation could increase host exposure to different pathogens.

Female ticks (Ixodes scapularis) infected with Borrelia burgdorferi have increased overwintering survival, with implications for tick population growth.

The tick, Ixodes scapularis, vectors pathogens such as Borrelia burgdorferi, the bacterium that causes Lyme disease. Over the last few decades I. scapularis has expanded its range, introducing a novel health threat into these areas. Warming temperatures appear to be one cause of its range expansion to the north. However, other factors are also involved. We show that unfed adult female ticks infected with B. burgdorferi have greater overwintering survival than uninfected female ticks. Locally collected adult female ticks were placed in individual microcosms and allowed to overwinter in both forest and dune grass environments. In the spring we collected the ticks and tested both dead and living ticks for B. burgdorferi DNA. Infected ticks had greater overwintering survival compared with uninfected ticks every winter for three consecutive winters in both forest and dune grass environments. We discuss the most plausible explanations for this result. The increased winter survival of adult female ticks could enhance tick population growth. Our results suggest that, in addition to climate change, B. burgdorferi infection itself may be promoting the northern range expansion of I. scapularis. Our study highlights how pathogens could work synergistically with climate change to promote host range expansion.

First Report on Detection and Complete Genomic Analysis of a Novel CRESS DNA Virus from Sea Turtles.

To date, only a handful of viruses have been identified in sea turtles. Although eukaryotic circular Rep (replication initiation protein)-encoding single-stranded DNA (CRESS DNA) viruses have been reported from a wide variety of terrestrial species, and some of these viruses have been associated with clinical conditions in certain animals, limited information is available on CRESS DNA viruses from marine life. The present study aimed to investigate the presence of CRESS DNA viruses in sea turtles. In the present study, two (samples T3 and T33) of the 34 cloacal samples from 31 sea turtles (found in ocean waters around the Caribbean Islands of St. Kitts and Nevis) tested positive for CRESS DNA viruses by a pan-rep nested PCR assay. The partial Rep sequence of T3 shared 75.78% of a deduced amino acid (aa) identity with that of a CRESS DNA virus (classified under family Circoviridae) from a mollusk. On the other hand, the complete genome (2428 bp) of T33 was determined by an inverse nested PCR assay. The genomic organization of T33 mirrored those of type II CRESS DNA viral genomes of cycloviruses, characterized by the putative "origin of replication" in the 5'-intergenic region, and the putative Capsid (Cap)- and Rep-encoding open reading frame on the virion-sense- and antisense-strand, respectively. The putative Rep (322 aa) of T33 retained the conserved "HUH endonuclease" and the "super 3 family helicase" domains and shared pairwise aa identities of ~57% with unclassified CRESS DNA viruses from benthic sediment and mollusks. Phylogenetically, the T33 Rep formed a distinct branch within an isolated cluster of unclassified CRESS DNA viruses. The putative Cap (370 aa) of T33 shared maximum pairwise aa identity of 30.51% with an unclassified CRESS DNA virus from a capybara. Except for a blood sample from T33 that tested negative for CRESS DNA viruses, other tissue samples were not available from the sea turtles. Therefore, we could not establish whether the T3 and T33 viral strains infected the sea turtles or were of dietary origin. To our knowledge, this is the first report on the detection of CRESS DNA viruses from sea turtles, adding yet another animal species to the rapidly expanding host range of these viruses. Complete genome analysis of T33 identified a novel, unclassified CRESS DNA virus, providing insights into the high genetic diversity between viruses within the phylum Cressdnaviricota. Considering that sea turtles are an at-risk species, extensive studies on virus discovery, surveillance, and pathogenesis in these marine animals are of the utmost importance.

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range.

Investigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after requiring relatively few mutations. There is significant interest in describing how the virus interacts with mice as they are well adapted to human environments, are used widely as infection models and can be infected. Structural and binding data of the mouse ACE2 receptor with the Spike protein of newly identified SARS-CoV-2 variants are needed to better understand the impact of immune system evading mutations present in variants of concern (VOC). Previous studies have developed mouse-adapted variants and identified residues critical for binding to heterologous ACE2 receptors. Here we report the cryo-EM structures of mouse ACE2 bound to trimeric Spike ectodomains of four different VOC: Beta, Omicron BA.1, Omicron BA.2.12.1 and Omicron BA.4/5. These variants represent the oldest to the newest variants known to bind the mouse ACE2 receptor. Our high-resolution structural data complemented with bio-layer interferometry (BLI) binding assays reveal a requirement for a combination of mutations in the Spike protein that enable binding to the mouse ACE2 receptor.

Evolution of Immune Evasion and Host Range Expansion by the SARS-CoV-2 B.1.1.529 (Omicron) Variant.

Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.529 (Omicron) has rapidly become the dominant strain, with an unprecedented number of mutations within its spike gene. However, it remains unknown whether these variants have alterations in their entry efficiency, host tropism, and sensitivity to neutralizing antibodies and entry inhibitors. In this study, we found that Omicron spike has evolved to escape neutralization by three-dose inactivated-vaccine-elicited immunity but remains sensitive to an angiotensin-converting enzyme 2 (ACE2) decoy receptor. Moreover, Omicron spike could use human ACE2 with a slightly increased efficiency while gaining a significantly increased binding affinity for a mouse ACE2 ortholog, which exhibits limited binding with wild-type (WT) spike. Furthermore, Omicron could infect wild-type C57BL/6 mice and cause histopathological changes in the lungs. Collectively, our results reveal that evasion of neutralization by vaccine-elicited antibodies and enhanced human and mouse ACE2 receptor engagement may contribute to the expanded host range and rapid spread of the Omicron variant. IMPORTANCE The recently emerged SARS-CoV-2 Omicron variant with numerous mutations in the spike protein has rapidly become the dominant strain, thereby raising concerns about the effectiveness of vaccines. Here, we found that the Omicron variant exhibits a reduced sensitivity to serum neutralizing activity induced by a three-dose inactivated vaccine but remains sensitive to entry inhibitors or an ACE2-Ig decoy receptor. Compared with the ancestor strain isolated in early 2020, the spike protein of Omicron utilizes the human ACE2 receptor with enhanced efficiency while gaining the ability to utilize mouse ACE2 for cell entry. Moreover, Omicron could infect wild-type mice and cause pathological changes in the lungs. These results reveal that antibody evasion, enhanced human ACE2 utilization, and an expanded host range may contribute to its rapid spread.

Trematode fauna of fish inhabiting reservoirs of the European part of Russia

The purpose of the research is an ecological and faunal analysis of trematodes in fish inhabiting reservoirs of the European part of Russia.Materials and methods. Helminthological studies were conducted in 23 reservoirs of the European part of Russia from 2011 to 2021. The fish aged two to seven years were analyzed by methods generally accepted in ichthyoparasitology.Results and discussion. Twelve fish species from families Cyprinidae, Percidae, Esocidae and Odontobutidae were found to be infected with 29 trematode species from 14 genera which were represented by 68.9% of metacercariae. Most trematodes had a wide specificity: Tylodelphys clavata was found in 9 fish species; Diplostomum spathaceum and Paracoenogonimus ovatus in 7 species and Apophallus muehlingi in 6 species. The expanded host range for T. podicipina was observed. A. muehlingi, which is an alien species for the Volga-Caspian fisheries basin was identified in most reservoirs. Trematodes by their prevalence in reservoirs are divided into background (5 species), common (6), rare (8) and very rare (10) trematodes. Trematode fauna of fish in reservoirs included 6 to 16 species. The highest species diversity was detected in the Belgorod (16 species), Yakhroma (13 species), Uglich and Chelnav (12 species), Pestovsk and Pyalovsk (11 species) reservoirs. Fifteen trematode species were found in the perch; 12, in the bream and roach; 9, in the pike perch; 8, in the pike and rudd; 6, in the ruff and white bream; 4, in the Volga pikeperch and crucian carp; 3, in the tench; and 1, in the Amur sleeper. The formed foci of trematode infections were observed, namely, postodiplostomosis and ichthyocotylurosis infection. Three trematode species, Pseudoamphistomum truncatum, A. muehlingi and Rossicotrema donicum, were detected that pose a real and potential danger to human health and warm-blooded animals.

First Report of Macruropyxis fraxini Causing Rust Disease on Microstegium vimineum in China.

Stiltgrass (Microstegium vimineum (Trin.) A. Camus) is an annual Poaceae weed with a broad native range throughout East Asia. Stiltgrass is an invasive grass that is distributed in more than 15 provinces in China, posing a major threat to native biodiversity and restoration efforts in introduced areas. Stiltgrass often forms dense near-monocultures in forest understories and riparian areas where it disrupts forest succession, nitrogen cycling, and alters native communities (Stricker et al. 2016). In August 2018, M. vimineum with rust disease were observed near the roadside (26.759482 °E, 114.283519 °N) in Jinggangshan City, Jiangxi Province, China. Diseased plants were observed at a 2 × 10 m shady location with lesions on leaves and stems, disease incidence was over 90% (n=100). Sixty disease samples were collected to confirm the pathogen. Early symptoms on the upper leaf surfaces consisted of rust pustules, which were circular, subcircular to irregular, orange to dark-orange, crust-like, and granular. At later stages, lesions coalesced, spreading all over the plant, causing severe defoliation. Uredinia were predominantly formed on the upper surface of leaves and young stems but rarely also found on the abaxial leaf surface, exposed, yellow to yellow-orange, and 0.2-0.5 mm in diameter, occasionally reaching 0.9-1 mm, surrounded by purple lesions (n=30) (Olympus SZX7). Telia were predominantly formed on the lower surface of leaves, stems, exposed, chestnut-brown to dark-brown. Urediospores were nearly spherical, oval or obovate, light yellow, 18-23 μm × 20-26 μm, cell wall is about 2-2.5 μm (n=200) (ZEISS AXIO Imager. M2). Teliospores were ellipsoid, 37-55 μm × 25-36 μm, 2-celled, inner wall brown, 4-5.5 µm thick, outer wall hyaline, smooth, germ pores 2-4 per cell; pedicels were hyaline, composed of cell walls with loss of cytoplasm, 4.5-6.5 µm wide, and up to 160 µm long (n=200) (ZEISS AXIO Imager. M2). Pycniospores, aeciospores and basidiospores were not observed in this study. The telial morphology features were consistent with those reported of M. fraxini, but uredinial stages were not observed in these studies (Azbukina 1974; Jung et al. 2020). Genomic DNA was extracted from a representative specimen (JGS-1) and was characterized by PCR amplification and sequencing of 28S rDNA using the primer pair NS1 and NS4 (Aime 2006). The 1094-bp sequence (Genbank: ON739170) shared 99.18% nucleotide identity with M. fraxini (Genbank: KP858144). The internal transcribed spacer (ITS) region was sequenced by rust fungal primer pairs ITS4rust and ITS5u (Pfunder et al. 2001). The 564-bp sequence (Genbank: ON739169) shared 99.12% nucleotide identity with M. fraxini (Genbank: KP858145), which was consistent with the morphological features observed. To complete Koch's postulates, plants were inoculated by brushing a urediniospore suspension (1 ×105 spores/ml) onto the leaves, placed in a plant growth chamber (25℃, 8 h/d of dark, 30℃, 16 h/d of light, 8000 lux of light intensity, RH ≥ 90%). Urediniospores were formed on the leaf surface 7 to 10 days after inoculation, and all infected plants showed symptoms similar to those observed in the field, along with spores, whereas the control plants remained symptomless. Host range tests showed that rice, wheat, barley, sorghum, maize, cotton, peanut and rape were resistant to M. fraxini but soybean and peas were susceptible. More research is needed to determine whether this pathogen can be a biocontrol agent for stiltgrass, such as exploring the potential impact of this rust pathogen, expanding host range tests, and finding its alternate hosts. To the best of our knowledge, this is the first report of rust disease on stiltgrass caused by M. fraxini in China.

Late Cenozoic history and the role of Beringia in assembling a Holarctic cestode species complex

The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refugial isolation that structured diversity across the Holarctic. We use a large multi-locus nuclear DNA sequence dataset to robustly resolve relationships within the cestode genus Arostrilepis (Cyclophyllidea: Hymenolepididae), a widespread parasite of predominantly arvicoline rodents (voles, lemmings). Using this phylogeny, we confirm that several Asian Arostrilepis lineages colonized North America during up to four distinct glacial periods in association with different rodent hosts, consistent with taxon-pulse dynamics. A previously inferred westward dispersal across the land bridge is rejected. We also refine interpretations of past host colonization, providing evidence for several distinct episodes of expanding host range, which probably contributed to diversification by Arostrilepis. Finally, Arostrilepis is shown to be paraphyletic with respect to Hymenandrya thomomyis, a parasite of pocket gophers, confirming that ancient Arostrilepis species colonized new host lineages upon arriving in North America.

Long-term and rapid evolution in powdery mildew fungi.

The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.

Canine distemper virus N protein induces autophagy to facilitate viral replication

BackgroundCanine distemper virus (CDV) is one of the most contagious and lethal viruses known to the Canidae, with a very broad and expanding host range. Autophagy serves as a fundamental stabilizing response against pathogens, but some viruses have been able to evade or exploit it for their replication. However, the effect of autophagy mechanisms on CDV infection is still unclear.ResultsIn the present study, autophagy was induced in CDV-infected Vero cells as demonstrated by elevated LC3-II levels and aggregation of green fluorescent protein (GFP)-LC3 spots. Furthermore, CDV promoted the complete autophagic process, which could be determined by the degradation of p62, co-localization of LC3 with lysosomes, GFP degradation, and accumulation of LC3-II and p62 due to the lysosomal protease inhibitor E64d. In addition, the use of Rapamycin to promote autophagy promoted CDV replication, and the inhibition of autophagy by Wortmannin, Chloroquine and siRNA-ATG5 inhibited CDV replication, revealing that CDV-induced autophagy facilitated virus replication. We also found that UV-inactivated CDV still induced autophagy, and that nucleocapsid (N) protein was able to induce complete autophagy in an mTOR-dependent manner.ConclusionsThis study for the first time revealed that CDV N protein induced complete autophagy to facilitate viral replication.

Major Emerging Fungal Diseases of Reptiles and Amphibians

Emerging infectious diseases (EIDs) are caused by pathogens that have undergone recent changes in terms of geographic spread, increasing incidence, or expanding host range. In this narrative review, we describe three important fungal EIDs with keratin trophism that are relevant to reptile and amphibian conservation and veterinary practice. Nannizziopsis spp. have been mainly described in saurians; infection results in thickened, discolored skin crusting, with eventual progression to deep tissues. Previously only reported in captive populations, it was first described in wild animals in Australia in 2020. Ophidiomyces ophidiicola (formely O. ophiodiicola) is only known to infect snakes; clinical signs include ulcerating lesions in the cranial, ventral, and pericloacal regions. It has been associated with mortality events in wild populations in North America. Batrachochytrium spp. cause ulceration, hyperkeratosis, and erythema in amphibians. They are a major cause of catastrophic amphibian declines worldwide. In general, infection and clinical course are determined by host-related characteristics (e.g., nutritional, metabolic, and immune status), pathogens (e.g., virulence and environmental survival), and environment (e.g., temperature, hygrometry, and water quality). The animal trade is thought to be an important cause of worldwide spread, with global modifications in temperature, hygrometry, and water quality further affecting fungal pathogenicity and host immune response.

Plant Microbiome: An Ocean of Possibilities for Improving Disease Resistance in Plants.

Plant diseases pose a serious threat to crop production and the agricultural economy across the globe. Currently, chemical pesticides are frequently employed to combat these infections, which cause environmental toxicity and the emergence of resistant pathogens. Moreover, the genetic manipulation of plant defense pathways and the breeding of resistant genes has attained limited success due to the rapid evolution of pathogen virulence and resistance, together with host range expansion. Additionally, due to climate change and global warming, the occurrence of multiple stresses during disease outbreak has further impacted overall crop growth and productivity, posing a serious threat to food security. In this regard, harnessing the plant beneficial microbiome and its products can provide novel avenues for disease resistance in addition to boosting agricultural output, soil fertility and environmental sustainability. In plant-beneficial microbiome interactions, induced systemic resistance (ISR) has emerged as a key mechanism by which a beneficial microbiome primes the entire plant system for better defense against a wide range of phytopathogens and pests. In this review, we provide the recent developments on the role of plant beneficial microbiomes in disease resistance. We also highlight knowledge gaps and discuss how the plant immune system distinguishes pathogens and beneficial microbiota. Furthermore, we provide an overview on how immune signature hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), shape plant beneficial microbiome. We also discuss the importance of various high-throughput tools and their integration with synthetic biology to design tailored microbial communities for disease resistance. Finally, we conclude by highlighting important themes that need future attention in order to fill the knowledge gaps regarding the plant immune system and plant-beneficial-microbiome-mediated disease resistance.

Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8

BackgroundNarrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins.ResultsHere, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life.ConclusionOur data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors.C6jK379NdrHSnsPFKmaHkVVideo

Haemosporidians in Non-Passerine Birds of Colombia: An Overview of the Last 20 Years of Research

The Neotropics are highly diverse in avian species. Neotropical countries contribute a large part of the estimated diversity of haemosporidian parasites reported for the planet’s tropical zones. However, sampling is limited and biased, illustrated by only 30% of the genetic records (barcodes) from non-passerines, most of them not linked to a nominal species. This paper aimed to perform the molecular and morphological characterization of the haemosporidians that infect non-passerine birds from Colombia deposited in the biological collection named “Grupo de Estudio Relación Parásito Hospedero (GERPH)”. We analyzed 1239 samples from twelve biomes and two animal care facilities. Phylogenetic relationships using barcodes and mitochondrial genomes were estimated. In addition, the reports of haemosporidian infections in non-passerine birds from the Neotropics recorded after 1978 were summarized. We reported the presence of thirteen morphological haemosporidian species, four potential new species deposited in GERPH, a host range expansion for two Plasmodium species, and a barcode sequence for Haemoproteus caprimulgi. We confirmed the species associated with 56 molecular lineages reported in other neotropical countries at the genus level. Thus, biological collections and curated databases such as MalAvi are essential to support integrative approaches demanded in modern taxonomy.

Multistep diversification in spatiotemporal bacterial-phage coevolution

The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.

Genetic Diversity and Expanded Host Range of J Paramyxovirus Detected in Wild Small Mammals in China

J paramyxovirus (JPV) is a rodent-borne Jeilongvirus isolated from moribund mice (Mus musculus) with hemorrhagic lung lesions trapped in the 1972 in northern Queensland, Australia. The JPV antibodies have been detected in wild mice, wild rats, pigs, and human populations in Australia. Here, by next-generation sequencing (NGS), we detected JPV from M. musculus in Shandong Province of China. Molecular detection of JPV was performed to survey to survey the infection among 66 species of wild small mammals collected from six eco-climate regions in China by applying JPV specific RT-PCR and sequencing. Altogether, 21 out of 3070 (0.68%) wild small mammals of four species were positive for JPV, including 5.26% (1/19) of Microtus fortis, 3.76% (17/452) of M. musculus, 1.67% (1/60) of Apodemus peninsulae, and 0.48% (2/421) of Apodemus agrarius, which captured three eco-climate regions of China (northeastern China, northern China, and Inner Mongolia-Xinjiang). Sequence analysis revealed the currently identified JPV was clustered with other 14 Jeilongvirus members, and shared 80.2% and 89.2% identity with Australia's JPV partial RNA polymerase (L) and glycoprotein (G) genes, respectively. Phylogenetic analysis demonstrated the separation of three lineages of the current JPV sequences. Our results show three new hosts (A. agrarius, A. peninsulae, and M. fortis) for JPV, most of which were widely distributed in China, and highlight the potential zoonotic transmission of JPV in humans. The detection of JPV in wild small mammals in China broaden the viral diversity, geographical distribution, and reservoir types of JPV. Future studies should prioritize determining the epidemiological characteristics of JPV, so that potential risks can be mitigated.

Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China.

Getah virus (GETV) mainly causes disease in livestock and may pose an epidemic risk due to its expanding host range and the potential of long-distance dispersal through animal trade. Here, we used metagenomic next-generation sequencing (mNGS) to identify GETV as the pathogen responsible for reemerging swine disease in China and subsequently estimated key epidemiological parameters using phylodynamic and spatially-explicit phylogeographic approaches. The GETV isolates were able to replicate in a variety of cell lines, including human cells, and showed high pathogenicity in a mouse model, suggesting the potential for more mammal hosts. We obtained 16 complete genomes and 79 E2 gene sequences from viral strains collected in China from 2016 to 2021 through large-scale surveillance among livestock, pets, and mosquitoes. Our phylogenetic analysis revealed that three major GETV lineages are responsible for the current epidemic in livestock in China. We identified three potential positively selected sites and mutations of interest in E2, which may impact the transmissibility and pathogenicity of the virus. Phylodynamic inference of the GETV demographic dynamics identified an association between livestock meat consumption and the evolution of viral genetic diversity. Finally, phylogeographic reconstruction of GETV dispersal indicated that the sampled lineages have preferentially circulated within areas associated with relatively higher mean annual temperature and pig population density. Our results highlight the importance of continuous surveillance of GETV among livestock in southern Chinese regions associated with relatively high temperatures. IMPORTANCE Although livestock is known to be the primary reservoir of Getah virus (GETV) in Asian countries, where identification is largely based on serology, the evolutionary history and spatial epidemiology of GETV in these regions remain largely unknown. Through our sequencing efforts, we provided robust support for lineage delineation of GETV and identified three major lineages that are responsible for the current epidemic in livestock in China. We further analyzed genomic and epidemiological data to reconstruct the recent demographic and dispersal history of GETV in domestic animals in China and to explore the impact of environmental factors on its genetic diversity and its diffusion. Notably, except for livestock meat consumption, other pig-related factors such as the evolution of live pig transport and pork production do not show a significant association with the evolution of viral genetic diversity, pointing out that further studies should investigate the potential contribution of other host species to the GETV outbreak. Our analysis of GETV demonstrates the need for wider animal species surveillance and provides a baseline for future studies of the molecular epidemiology and early warning of emerging arboviruses in China.