The evolutionary dynamics history of canine distemper virus through analysis of the hemagglutinin gene during 1930-2020.

Canine distemper virus (CDV) is a lethal viral disease of carnivores which is considered to be a serious threat to domestic and wild species. Despite the widespread use of vaccines, CDV still occurs in vaccinated animals and current vaccines does not guarantee complete protection. In this study, a total of 286 hemagglutinin (H) gene sequences of the virus isolated in 25 countries during 90 years (1930-2020) were analyzed by Bayesian maximum likelihood analysis to estimate the population dynamics. We identified the most recent common ancestor (TMRCA) of the virus in 1868 in the USA which arrived in continental Europe in 1948, and from there, the virus spread rapidly to other continents. The Canidae family was identified as the original host as well as a source of the subsequent spread. We identified 11 lineages of geographic co-circulating strains globally. The effective population size experienced a two-phase-exponential growth between 2000-2005 and 2010-2012. Our findings provide a novel insight into the epidemic history of canine distemper virus which may facilitate more effective disease management. This study uses a large set of sequencing data on the H gene of CDV to identify distinct lineages of the virus, track its geographic spread over time, analyze its likelihood of transmission within and between animal families, and provide suggestions for improved strategies to combat the virus. Supplementary Information: The online version contains supplementary material available at 10.1007/s10344-023-01685-z.

Prevalence and multilocus genotyping of Giardia duodenalis in zoo animals in three cities in China.

Giardia duodenalis is a flagellated parasitic microorganism that parasitizes in the intestines of humans and animals. Although asymptomatic infections commonly exist in both humans and animals, some enteric symptoms have been reported in immunocompromised individuals, posing a threat to public health. Children could be infected with G. duodenalis through an environment contaminated by infective animals. Thus, the investigation of the prevalence and genotypes of G. duodenalis in zoo animals is important. In this study, 672 fecal samples of 113 species of animals, including non-human primates, artiodactyla, perissodactyla, proboscidian, marsupial, birds, carnivora, and rodents, were collected from three zoos in Hangzhou city, Dalian city, and Suzhou city in China. The samples were screened for the positivity of G. duodenalis by nested PCR based on the ß-giardin (bg), triosephosphate isomerase (tpi), and glutamate dehydrogenase (gdh) gene loci. The overall G. duodenalis prevalence was 10.6% (71/672). The prevalence in non-human primates, artiodactyla, perissodactyla, proboscidian, marsupial, birds, carnivora, and rodent was 6.9% (10/144), 9.0% (12/133), 17.1% (6/35), 0% (0/6), 8.7% (2/23), 13.3% (28/211), 6.7% (7/105), and 40.0% (6/15), respectively. The region and category were considered risk factors for G. duodenalis infection in zoo animals (p < 0.001). Additionally, four genotypes of G. duodenalis were identified in zoo animals, including assemblage E (n = 46), assemblage A (n = 18), assemblage B (n = 6), and assemblage D (n = 1). The assemblages A, B, D, and E are also genotypes observed in humans and other animals. Among the sequences obtained in our study, one multilocus genotype (MLG) of the sub-assemblage AI was observed within assemblage A. Furthermore, three MLGs were detected within assemblage B. These findings reveal G. duodenalis genetic variability in zoo animals in three cities in China and suggest that zoo animals could be a potential source of human infection with G. duodenalis.

Environmental suitability of Yersinia pestis and the spatial dynamics of plague in the Qinghai Lake region, China.

Plague, a highly infectious disease caused by Yersinia pestis, has killed millions of people in history and is still active in the natural foci of the world nowadays. Understanding the spatiotemporal patterns of plague outbreaks in history is critically important, as it may help facilitate the prevention and control for potential future outbreaks. This study's objective was to estimate the effect of the topography, vegetation, climate, and other environmental factors on the Y. pestis ecological niche. A maximum entropy algorithm spatially modelled plague occurrence data from 2004-2018 and the environmental variables to evaluate the contribution of the variables to the distribution of Y. pestis. Our results found that the average minimum temperature in September (-8 °C to +5 °C) and the sheep population density (250 sheep per km2) were influential in characterising the niche. The rim of Qinghai Lake showed more favourable conditions for Y. pestis presence than other areas within the study area. Identifying various factors will assist any future modelling efforts. Our suitability map identifies hotspots and will help public health officials in resource allocation in their quest to abate future plague outbreaks.

Prevalence and subtypes of Blastocystis sp. infection in zoo animals in three cities in China.

Blastocystis is a highly prevalent eukaryotic parasite of many animals and humans worldwide. It can compromise the gastrointestinal tract and cause gastrointestinal symptoms, constituting a serious threat to human health and animal growth. Many animals are potential sources of Blastocystis infection in humans. However, limited data are available regarding the prevalence and subtype distribution of Blastocystis infection among zoo animals in China. Therefore, the present study examined the prevalence and subtypes of Blastocystis in zoo animals in Hangzhou, Dalian, and Suzhou cities, China. Of 450 fecal samples from zoo animals, 27 (6.0%) were PCR-positive for Blastocystis, with 7.7% (8/104), 11.3% (7/62), 16.7% (3/18), 1.8% (2/114), 6.3% (1/16), 9.5% (2/21), and 3.6% (4/109) in artiodactyla, aves, rodentia, nonhuman primates, perissodactyla, marsupialia, and carnivora, respectively. Significant differences in the prevalence of Blastocystis were found among different animal groups (P < 0.05). Sequence analysis showed 7 known subtypes (ST2, ST4, ST5, ST7, ST8, ST10, and ST14) of Blastocystis in the present study, with ST10 (10/27) as the predominant subtype in all three of the examined zoos. To our knowledge, this is the first report of Blastocystis infection in Damaliscus dorcas, Cervus elaphus, Macropus rufogriseus, Grus japonensis, Trichoglossus haematodus, Panthera tigris ssp. tigris (white), Panthera tigris ssp. altaica, Lycaon pictus, Suricata suricatta, and Dolichotis patagonum in China. These results demonstrate the presence of Blastocystis infection in zoo animals and provided baseline data for preventing and controlling Blastocystis infection in zoo animals and humans in China.

A novel picornavirus in feces of a rainbow lorikeet (Trichoglossus moluccanus) shows a close relationship to members of the genus Avihepatovirus.

A novel picornavirus, named "lorikeet picornavirus 1" (LoPV-1), was detected in a fecal sample from rainbow lorikeets using viral metagenomic analysis, and its complete genome sequence was determined and analyzed. The genome of LoPV-1 is 7862 nt long, including a 617-nt 5' UTR, a type IV IRES 5'UTR with an '8-like' motif, a 7032-nt polyprotein ORF, and a 213-nt 3' UTR. Phylogenetic analysis and pairwise asequence comparisons based on the amino acid sequences of P1, P2, and P3 indicated that LoPV-1 showed the closest relationship to two picornaviruses that were isolated recently from red-crowned cranes and clustered together with members of the genus Avihepatovirus.

Asian black bear (Ursus thibetanus) picornavirus related to seal aquamavirus A.

The complete genome of a bear picornavirus 1 (BePV-1) in the viscera of an Asian black bear (Ursus thibetanus) from China was characterized using viral metagenomics and RT-PCR/Sanger sequencing. The genome of BePV1 is 6703 nt long, contains a type-IV IRES 5'UTR with the '8-like' motif, encodes a 2053-aa-long polyprotein showing a 3-4-4 organization pattern and two 2A genes. BePV-1 showed the highest overall genome nucleotide sequence identity of 71.7% to a picornavirus genome from an Arctic ringed seal (Phoca hispida) from Canada, classified as a member of the species Aquamavirus A, currently the only one in the genus Aquamavirus. Phylogenetic and genetic distance analyses of P1 and 3D indicated that Asian bear picornavirus (aquamavirus B) represents the second sequenced member of the genus Aquamavirus.

Analysis of codon usage bias in the VP1 gene of the human norovirus GII.2 genotype.

To investigate the codon usage patterns of all available VP1 gene sequences of the GII.2 genotype, to determine the factors that affect these patterns, and to provide comprehensive details of the characteristics and evolution of the gene. Complete 519 sequences of VP1 gene of the HuNoV GII.2 genotype with known sampling dates and geographic locations from 1971 - 2017 were retrieved from the GenBank nucleotide database of the National Center for Biotechnology Information (NCBI) and analyzed. The percentage composition of T, C, A, and G nucleotides were 24.80 ± 0.30, 26.61 ± 0.31, 25.84 ± 0.13, and 22.75 ± 0.17 %, respectively, with C and A relatively more abundant than T and G, and C the most abundant (p < 0.0001). The values of T3s (34.10 ± 0.90 %) and C3s (33.54 ± 0.90 %) were significantly higher than those of A3s (29.98 ± 0.43 %) and G3s (24.13 ± 0.51 %) (p < 0.0001). While T3s was highest among the four nucleotides, G3s was the lowest. Among the 18 most frequently employed synonymous codons, six optional codons ended with T, five ended with C, five ended with A and two ended with G. Codons ending with T were the most frequently used. The ENC ranged from 51.90 to 54.25 (mean = 52.38 ± 0.43) among the 519 VP1 gene sequences. There were significant correlations between ENC and C % and G % (p < 0.01). Codons containing CpG (1 and 2 or 2 and 3 codon positions) showed the lowest frequencies, while 30, 29, and 2 codons were above, below and on the mean line, respectively. The first four principal components accounted for 69.11 % of the total variation, with the first, second, third, and fourth principal axes contributing 37.90, 14.83, 9.61, and 6.77 %, respectively. The strains were not clustered by country of isolation or year of sampling. Gravy were significantly correlated with T3s, C3s, G3s, GC3s, and ENC (p < 0.01). Mutation pressure and natural selection contributed to the codon usage bias of the VP1 gene of the HuNoV GII.2 genotype. There was a correlation between GC12s and GC3s (R2 = 0.032; p < 0.0001). The relative neutrality was 3.20 %, while natural selection was 96.80 %. The VP1 gene exhibits low codon usage bias which is affected primarily by natural selection, followed by mutation pressure and translational selection.

Enhanced field emission from in situ synthesized 2D copper sulfide nanoflakes at low temperature by using a novel controllable solvothermal preferred edge growth route.

A facile one-pot solvothermal route using the reaction of sputtered copper film and sulfur powder in ethanol solution at a low temperature of 90 °C for 12 hours has been implemented to in situ synthesize 2D hexagonal copper sulfide (CuS) nanoflakes. Their field electron emission (FE) characteristics were investigated and were found to have a close relationship with the copper film's thickness. The lowest turn on electric field (Eon) was 2.05 V µm(-1) and the largest field enhancement factor (ß) was 7261 when the copper film's thickness was 160 nm. Furthermore, through a preferred edge growth route, patterned CuS nanoflakes were synthesized with the combined effect from a copper film seed layer and a passivation layer to further improve FE properties with an Eon of 1.65 V µm(-1) and a ß of 8351. The mechanism of the patterned CuS nanoflake preferred edge growth is reported and discussed for the first time.

Enhanced electroluminescence using Ta2O5/ZnO/HfO2 asymmetric double heterostructure in ZnO/GaN-based light emitting diodes.

ZnO/GaN-based light-emitting diodes (LEDs) with improved asymmetric double heterostructure of Ta2O5/ZnO/HfO2 have been fabricated. Electroluminescence (EL) performance has been enhanced by the HfO2 electron blocking layer and further improved by continuing inserting the Ta2O5 hole blocking layer. The origins of the emission have been identified, which indicated that the Ta2O5/ZnO/HfO2 asymmetric structure could more effectively confine carriers in the active i-ZnO layer and meanwhile suppresses of radiation from GaN. This device exhibits superior stability in long-time running. It's hoped that the asymmetric double heterostructure may be helpful for the development of the future ZnO-based LEDs.

Unusual electroluminescence from n-ZnO@i-MgO core-shell nanowire color-tunable light-emitting diode at reverse bias.

Light-emitting diodes (LEDs) based on n-ZnO@i-MgO core-shell (CS) nanowires (NWs) are herein demonstrated and characterized. MgO insulating layers were rationally introduced as shells to modify/passivate the surface defects of ZnO NWs. A high-quality ZnO/MgO interface was attained and the optically pumped near-band-edge emission of the bare ZnO NWs was greatly enhanced after cladding i-MgO shells. Electroluminescence (EL) spectra measured in the whole UV-visible range revealed that light emission can only be detected when LEDs were applied with reverse bias. Moreover, the emission color can be tuned from orange to bright white with increasing reverse bias. We explored these interesting results tentatively in terms of the energy-band diagram of the heterojunction and it was found that the interfacial i-MgO shells not only acted as an insulator to prevent a short circuit between the two electrodes, but also offered a potential energy difference so that electron tunneling was energetically possible, both of which were essential to generate the reverse-bias EL. The dipole-forbidden d-d transitions by the Laporte selection rule in the p-NiO might be the reason to why there is no light being detected from the CS NW LED under forward bias. It is hoped that this simple and facile route may provide an effective approach in designing low-cost CS NW LEDs.

Unveiling the spatial distribution and transboundary pathways of FMD serotype O in Western China and its bordering countries.

Foot-and-mouth disease (FMD) is a severe, highly contagious viral disease of livestock that has a significant economic impact on domestic animals and threatens wildlife survival in China and border countries. However, effective surveillance and prevention of this disease is often incomplete and unattainable due to the cost, the great diversity of wildlife hosts, the changing range and dynamics, and the diversity of FMDV. In this study, we used predictive models to reveal the spread and risk of FMD in anticipation of identifying key nodes to control its spread. For the first time, the spatial distribution of FMD serotype O was predicted in western China and border countries using a niche model, which is a combination of eco-geographic, human, topographic, and vegetation variables. The transboundary least-cost pathways (LCPs) model for ungulates in the study area were also calculated. Our study indicates that FMD serotype O survival is seasonal at low altitudes (March and June) and more sensitive to temperature differences at high altitudes. FMD serotype O risk was higher in Central Asian countries and both were highly correlated with the population variables. Ten LCPs were obtained representing Pakistan, Kazakhstan, Kyrgyzstan, and China.

Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard (Panthera uncia).

The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.

Highly diverse RNA viruses and phage sequences concealed within birds.

The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.

Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2.

SARS-CoV-2 infections in animals have been reported globally. However, the understanding of the complete spectrum of animals susceptible to SARS-CoV-2 remains limited. The virus's dynamic nature and its potential to infect a wide range of animals are crucial considerations for a One Health approach that integrates both human and animal health. This study introduces a bioinformatic approach to predict potential susceptibility to SARS-CoV-2 in both domestic and wild animals. By examining genomic sequencing, we establish phylogenetic relationships between the virus and its potential hosts. We focus on the interaction between the SARS-CoV-2 genome sequence and specific regions of the host species' ACE2 receptor. We analyzed and compared ACE2 receptor sequences from 29 species known to be infected, selecting 10 least common amino acid sites (LCAS) from key binding domains based on similarity patterns. Our analysis included 49 species across primates, carnivores, rodents, and artiodactyls, revealing complete consistency in the LCAS and identifying them as potentially susceptible. We employed the LCAS similarity pattern to predict the likelihood of SARS-CoV-2 infection in unexamined species. This method serves as a valuable screening tool for assessing infection risks in domestic and wild animals, aiding in the prevention of disease outbreaks.

Seedless synthesis of layered ZnO nanowall networks on Al substrate for white light electroluminescence.

In this paper, layered ZnO nanowall networks were directly grown on Al substrates using a hydrothermal method without predepositing seed layers. The individual ZnO nanowalls with a thickness of several nanometers and a size of several hundred nanometers were (002) surface dominated, in which the preferential growth direction of ZnO was suppressed. White electroluminescence devices were fabricated based on Au/polymethylmethacrylate/ZnO-nanowall (metal-insulator-semiconductor) structures. The chromaticity coordinate of the electroluminescence spectrum for the optimal device was calculated as (0.27, 0.34), which is close to (0.33, 0.33) of standard white light.

Gut phageome of the giant panda (Ailuropoda melanoleuca) reveals greater diversity than relative species.

The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals. IMPORTANCE Gut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.

Modeling the environmental suitability for Bacillus anthracis in the Qinghai Lake Basin, China.

Bacillus anthracis is a gram-positive, rod-shaped and endospore-forming bacterium that causes anthrax, a deadly disease to livestock and, occasionally, to humans. The spores are extremely hardy and may remain viable for many years in soil. Previous studies have identified East Qinghai and neighbouring Gansu in northwest China as a potential source of anthrax infection. This study was carried out to identify conditions and areas in the Qinghai Lake basin that are environmentally suitable for B. anthracis distribution. Anthrax occurrence data from 2005-2016 and environmental variables were spatially modeled by a maximum entropy algorithm to evaluate the contribution of the variables to the distribution of B. anthracis. Principal Component Analysis and Variance Inflation Analysis were adopted to limit the number of environmental variables and minimize multicollinearity. Model performance was evaluated using AUC (area under the curve) ROC (receiver operating characteristics) curves. The three variables that contributed most to the suitability model for B. anthracis are a relatively high annual mean temperature of -2 to 0°C, (53%), soil type classified as; cambisols and kastanozems (35%), and a high human population density of 40 individuals per km2 (12%). The resulting distribution map identifies the permanently inhabited rim of the Qinghai Lake as highly suitable for B. anthracis. Our environmental suitability map and the identified variables provide the nature reserve managers and animal health authorities readily available information to devise both surveillance strategy and control strategy (administration of vaccine to livestock) in B. anthracis suitable regions to abate future epidemics.

Spatial modeling and ecological suitability of monkeypox disease in Southern Nigeria.

The reemergence of monkeypoxvirus (MPXV) in 2017 after about 39 years of no reported cases in Nigeria, and the recent incidence in countries such as the United States of America, United Kingdom, Singapore, and Israel which have been reportedly linked with travelers from Africa, have heightened concern that MPXV may have emerged to occupy the vacant ecological and immunological niche created by the extinct smallpox virus. This study was carried out to identify environmental conditions and areas that are environmentally suitable (risky areas) for MPXV in southern Nigeria. One hundred and sixteen (116) spatially unique MPXV occurrence data from 2017-2021 and corresponding environmental variables were spatially modeled by a maximum entropy algorithm to evaluate the contribution of the variables to the distribution of the viral disease. A variance inflation analysis was adopted to limit the number of environmental variables and minimize multicollinearity. The five variables that contributed to the suitability model for MPXV disease are precipitation of driest quarter (47%), elevation (26%), human population density (17%), minimum temperature in December (7%), and maximum temperature in March (3%). For validation, our model had a high AUC value of 0.92 and standard deviation of 0.009 indicating that it had excellent ability to predict the suitable areas for monkeypox disease. Categorized risk classes across southern states was also identified. A total of eight states were predicted to be at high risk of monkeypox outbreak occurrence. These findings can guide policymakers in resources allocation and distribution to effectively implement targeted control measures for MPXV outbreaks in southern Nigeria.

Predicting the possibility of African horse sickness (AHS) introduction into China using spatial risk analysis and habitat connectivity of Culicoides.

African horse sickness (AHS) is a devastating equine infectious disease. On 17 March 2020, it first appeared in Thailand and threatened all the South-East Asia equine industry security. Therefore, it is imperative to carry out risk warnings of the AHS in China. The maximum entropy algorithm was used to model AHS and Culicoides separately by using climate and non-climate variables. The least cost path (LCP) method was used to analyze the habitat connectivity of Culicoides with the reclassified land cover and altitude as cost factors. The models showed the mean area under the curve as 0.918 and 0.964 for AHS and Culicoides. The prediction result map shows that there is a high risk area in the southern part of China while the habitats of the Culicoides are connected to each other. Therefore, the risk of introducing AHS into China is high and control of the border area should be strengthened immediately.

Parvovirus dark matter in the cloaca of wild birds.

With the development of viral metagenomics and next-generation sequencing technology, more and more novel parvoviruses have been identified in recent years, including even entirely new lineages. The Parvoviridae family includes a different group of viruses that can infect a wide variety of animals. In this study, systematic analysis was performed to identify the "dark matter" (datasets that cannot be easily attributed to known viruses) of parvoviruses and to explore their genetic diversity from wild birds' cloacal swab samples. We have tentatively defined this parvovirus "dark matter" as a highly divergent lineage in the Parvoviridae family. All parvoviruses showed several characteristics, including 2 major protein-coding genes and similar genome lengths. Moreover, we observed that the novel parvo-like viruses share similar genome organizations to most viruses in Parvoviridae but could not clustered with the established subfamilies in phylogenetic analysis. We also found some new members associated with the Bidnaviridae family, which may be derived from parvovirus. This suggests that systematic analysis of domestic and wild animal samples is necessary to explore the genetic diversity of parvoviruses and to mine for more of this potential dark matter.