Asian Isolates Research Articles

Haemoprotozoan and haemorickettsial carrier status in pet and community owned dogs of south India

The increasing population of dogs and changes in the climatic conditions have resulted in the emergence and re-emergence of vector-borne diseases in canines. These vectors borne diseases in canines pose a diagnostic challenge to the field veterinarians because of co-infections with several pathogens. Comprehensive data on the prevalence of haemoparasites and haemorickettsiales in pet and community owned dogs from south India are scant. Hence, the present study aims to find and compare the prevalence of these infections in the pet and the community owned dogs of Kerala, a south Indian state. Two hundred and seventy-two pets and 150 community owned dogs were examined by microscopy and polymerase chain reaction (PCR) for infections with different heamoparasites and haemorickettsials from January 2018–November 2020 in the state of Kerala. A high prevalence of Babesia gibsoni infection (42.2–60.0 %) in pet and community owned dogs, followed by Babesia vogeli (5.8–39.3 %), Hepatozoon canis (0.7–28.0 %), Trypanosoma evansi (0.0–27.3 %), Ehrlichia canis (0.3–0.6 %) and Anaplasma platys (0.0–0.6 %) was observed in the present study. Eighty-eight per cent (132/150) of the community owned dogs and 49.2 % (134/272) of the pet dogs were positive for at least one pathogen. Phylogenetic analysis based on the partial nucleotide sequences of 18S rRNA and TRAP gene of B. gibsoni, 18S rRNA genes of B. vogeli and H. canis and RoTat, 1.2 virB9 and 16S rRNA genes of T. evansi, E. canis and A. platys, respectively was carried out. B. vogeli, H. canis, E. canis and A. platys revealed genetic relatedness between the Indian isolates and the isolates from other countries. However, B. gibsoni isolates from the Indian sub-continent were genetically unique compared to other Asian isolates. The clustering of T. evansi isolates from India in two clades viz., livestock origin (cattle, buffalo) and others indicated their genetic variability. The present study summarizes the prevalence of some of the haemoparasites and haemorickettsials in the dog populations of Kerala (south India) and also determined their genetic relationship with the isolates prevalent in dogs in other countries.

Recent increase in Candida auris frequency in the SENTRY surveillance program: antifungal activity and genotypic characterization.

We observed an increase in the frequency of Candida auris among invasive candidiasis isolates in the 2022 SENTRY Antifungal Surveillance Program compared to prior years: ≤0.1% before 2018, 0.4%-0.6% from 2018 to 2021, and 1.6% in 2022. C. auris isolates were collected in seven countries, but 28 (35.9%) isolates were recovered in the USA (five states; more common in New York, Texas, and New Jersey) and 26 (33.3%) in Panama. Greece and Turkey had 12 and 9 isolates, respectively. Overall, 82.1% of the isolates were resistant to fluconazole; 17.9% were resistant to amphotericin B; and 1.3% were resistant to caspofungin, anidulafungin, or micafungin (Centers for Disease Control and Prevention tentative resistance breakpoints). Rezafungin inhibited 96.2% of the isolates (Clinical and Laboratory Standards Institute susceptibility breakpoint). Pandrug resistance was not observed, but 17.9% of the isolates were resistant to fluconazole and amphotericin B. South Asian (Clade I) isolates were most common (n = 40, 51.3%); of these, 97.5% were resistant to fluconazole and 30.0% were resistant to amphotericin B. Thirty (38.5%) isolates belonged to the South American region (Clade IV), and 56.7% of those were resistant to fluconazole and 6.7% to amphotericin B. Seven isolates belonged to the South African Clade III and one to East Asian Clade II. Erg11 (Y132F, K143R, and F126L) and MRR1 (N647T) alterations were detected. One isolate that was resistant to all echinocandins carried an FKS R1354G alteration. Two isolates displayed elevated rezafungin minimum inhibitory concentration (MIC) values but low MIC values against other echinocandins and no FKS alterations. As C. auris is spreading globally, monitoring this species is prudent.

The Comparative Full-Length Genome Characterization of African Swine Fever Virus Detected in Thailand.

African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study aimed to characterize the full-length genomic pattern of the ASFV strain from Thailand, TH1_22/CR (Accession No. PP915735), which was then compared with genomic diversity across other Asian isolates using Georgia 2007/1 (Accession No. FR682468) as the reference. Viral DNA was isolated from the pig spleen sample following library preparation and paired-end sequencing using the MiSeq Illumina platform. The sequenced TH1_22/CR isolate spanned 189,395 nucleotides encoding 193 open reading frames (ORFs), exhibiting maximum nucleotide similarity (99.99%) with Georgian (Georgia 2007/1) and Chinese (Wuhan 2019-1 and China HLJ) isolates. Based on phylogenetic analysis, the TH1_22/CR isolate (Accession No. PP915735) was characterized as genotype II, serogroup 8, and IGR-II due to the presence of three tandem repeat sequences (TRSs). Genetic variations including SNPs and single and polynucleotide indels were identified in TH1_22/CR in agreement with other Asian isolates. For comprehensive analysis, the genome was divided into four regions (I-IV) based on gene location. Overall, the TH1_22/CR isolate demonstrated eight SNPs and indels in its genome. Two unique SNPs were reported in the coding regions of the TH1_22/CR isolate, out of which, a C-591-T substitution was seen in MGF 360-4L and a C-297-T was found in A238L, and four unique SNPs were reported in non-coding regions (NCRs). Furthermore, a 29 bp deletion was observed in the IGR between MGF 110-13La and MGF 110-13Lb, as well as 52 bp deletion in the ASFV G ACD 00350 gene. This comparative analysis establishes the foundational information for future studies on the diversity and phylogeography of this regionally significant genetic sub-group of ASFV.

Genetic diversity of Cotton leafroll dwarf virus from the Southwestern United States, and its implications for the multi-introduction event hypothesis and future evolution.

Cotton leafroll dwarf virus (CLRDV) is a viral agent recently identified in the United States (US) in 2017 in Alabama. Since its identification, CLRDV has spread to every cotton-growing state east of New Mexico. Oklahoma, Kansas, and Texas comprise the westernmost border of reported CLRDV incidence, making monitoring of these states vital for proper control. Additionally, as the virus evolves, mutations that alter symptomology, such as mutations in the F-box-like motif in ORF0/P0, may occur and need to be monitored thoroughly during the growing seasons. Using High-throughput sequencing (HTS) and PCR-derived Sanger sequencing, four CLRDV genomes and 21 P0 gene isolates were sequenced from Oklahoma, Kansas, and Texas from 2019 to 2021 to determine the genetic diversity among CLRDV isolates. Phylogenetic analyses of the complete genomes revealed seven clades while ORF0 gene analyses resulted in large polytomic clusters. BEAST analyses of the 114 total P0 sequences from GenBank, downloaded before 2024, revealed a lower mean substitution rate than previously reported as well as an earlier root year (1914). In addition, using all available CLRDV genome sequences, 11 likely recombination events were determined. Examination of the P0 amino acid sequences revealed 13 mutations unique to the isolates collected in this study. Based on the phylogenetic and amino acid analyses, the CLRDV isolates from Texas (TX clade) may represent evidence for the multi-introduction event hypothesis into the US. Additionally, based on our analyses in this study, we propose the Asian CLRDV isolates should be constituted as a potentially separate strain of CLRDV.

Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates

Plasmodium vivax, traditionally overlooked has experienced a notable increase in cases in East Africa. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan using 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two different ecogeographical zones, New Halfa and Khartoum, in Sudan. Additionally, 841 geographical samples from the database were incorporated for a global genetic analysis to discern genetic relationships among P. vivax isolates on regional and worldwide scales. On the regional scale, our findings revealed 91 unique and 8 shared haplotypes among the Sudan samples, showcasing a remarkable genetic diversity compared to other geographical isolates and supporting the hypothesis that P. vivax originated from Africa. On a global scale, distinct genetic clustering of P. vivax isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) was observed, with limited admixture among the three clusters. Principal component analysis emphasized the substantial contribution of African isolates to the observed global genetic variation. The Sudanese populations displayed extensive genetic diversity, marked by significant multi-locus linkage disequilibrium, suggesting an ancestral source of P. vivax variation globally and frequent recombination among the isolates. Notably, the East African P. vivax exhibited similarity with some Asian isolates, indicating potential recent introductions. Overall, our results underscore the effectiveness of utilizing microsatellite markers for implementing robust control measures, given their ability to capture extensive genetic diversity and linkage disequilibrium patterns.

Molecular epidemiology of the Old World screwworm fly (OWSF) in Iraq, and the genetic structure of various OWSF populations worldwide

Despite being endemic in Iraq, no reports have been published in the past 10 years to update the molecular epidemiology of the Old World screwworm fly (OWSF), Chrysomya bezziana, in this country. In the present study, 130 sheep from 10 Iraqi governorates were found infected with C. bezziana larvae, whose identities were PCR-confirmed based on the cytochrome b (Cytb) gene, and 23 isolates from various tested governorates were successfully sequenced. Although most isolates (n = 20) belonged to the common haplotype circulating in Iraq, two new haplotypes were detected. Significant changes in OWSF epidemiology in Iraq were also suggested, since infestations were detected, for the first time, in Nineveh governorate. Isolates of the present study were combined to those previously published from Iraq and worldwide, collected after searching the GenBank, and various genetic and population structure analyses were conducted. These isolates displayed a great statistically significant value when tested for the purifying (negative) selection, suggesting the limited occurrence of genetic variations, which was evidenced by the high sequence conservation (C = 0.937) value detected. A few isolates from Africa were revealed during our search, and clustered in a separate lineage other than that of the Asian isolates. The latter displayed different genetic variation patterns when compared. For example, isolates from geographically separate regions, e.g., the Gulf Arab countries and South-Eastern Asia had marked genetic differences. On the other hand, isolates from regions with close geographic proximity (the Gulf Arab countries and Iran) had limited genetic subdivision. This is not the case when comparing isolates from 10 islands in the Indonesian Archipelago. Populations from Sumatra and Sumba were isolated and displayed high genetic variations toward the other populations. On the contrary, populations from Sulawesi, Lombok and Sumbawa displayed limited genetic variations. This is particularly important, since it can help detecting the dynamics of establishing the sterile insect technique over various regions as an effective control strategy against the OWSFs.

Far-East Asian Toxoplasma isolates share ancestry with North and South/Central American recombinant lineages.

Toxoplasma gondii is a global protozoan pathogen. Clonal lineages predominate in Europe, North America, Africa, and China, whereas highly recombinant parasites are endemic in South/Central America. Far East Asian T. gondii isolates are not included in current global population genetic structure analyses at WGS resolution. Here we report a genome-wide population study that compared eight Japanese and two Chinese isolates against representative worldwide T. gondii genomes using POPSICLE, a novel population structure analyzing software. Also included were 7 genomes resurrected from non-viable isolates by target enrichment sequencing. Visualization of the genome structure by POPSICLE shows a mixture of Chinese haplogroup (HG) 13 haploblocks introgressed within the genomes of Japanese HG2 and North American HG12. Furthermore, two ancestral lineages were identified in the Japanese strains; one lineage shares a common ancestor with HG11 found in both Japanese strains and North American HG12. The other ancestral lineage, found in T. gondii isolates from a small island in Japan, is admixed with genetically diversified South/Central American strains. Taken together, this study suggests multiple ancestral links between Far East Asian and American T. gondii strains and provides insight into the transmission history of this cosmopolitan organism.

Genetic Analysis of the Emerging Citrus Yellow Vein Clearing Virus Reveals a Divergent Virus Population in American Isolates.

Citrus yellow vein clearing virus is a previously reported citrus virus from Asia with widespread distribution in China. In 2022, the California Department of Food and Agriculture conducted a multipest citrus survey targeting multiple citrus pathogens including citrus yellow vein clearing virus (CYVCV). In March 2022, a lemon tree with symptoms of vein clearing, chlorosis, and mottling in a private garden in the city of Tulare, California, tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and noncitrus species, were collected and tested for CYVCV using conventional reverse transcription polymerase chain reaction, reverse transcription quantitative polymerase chain reaction, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using 17 complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study made up the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, the CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area.

Resistome Diversity in Escherichia coli Isolates of Global Wastewaters.

Antimicrobial resistance (AMR) is a global health threat requiring urgent attention and effective strategies for containment. AMR is fueled by wastewater mismanagement and global mobility, disseminating multidrug-resistant (MDR) strains worldwide. While global estimates of AMR burden have been informative, community-level understanding has received little attention despite reports of high AMR prevalence in healthy communities. We assessed the "invasion" of antibiotic resistance genes (ARGs) into the normal human flora by characterizing AMR Escherichia coli in local wastewaters contributed by a healthy youth population. This study estimated 26% (out of 300 isolates) resistant and 59% plasmid-bearing E. coli in local wastewater. Of the 78 AMR isolates, the frequency of mono-resistance was higher against tetracycline (32%), followed by kanamycin (17%) and chloramphenicol (9%). Five isolates were potentially MDR. We further sequenced four MDRs and four sensitive strains to comprehend the genome and resistome diversity in comparison to the global wastewater E. coli (genomes from the PATRIC database). The whole-genome analysis revealed extensive genome similarity among global isolates, suggesting global dissemination and colonization of E. coli. Global wastewater resistome majorly comprised ARGs against aminoglycosides (26%), beta-lactam (17%), sulfonamide (11%), and trimethoprim (8%). Resistance to colistin, a last-resort antibiotic, was prevalent in MDRs of European and South Asian isolates. A systems approach is required to address the AMR crisis on a global scale, reduce antibiotic usage, and increase the efficiency of wastewater management and disinfection.

Global phylodynamics of two relevant aphid-transmitted viruses in cucurbit crops: cucurbit aphid-borne yellows virus and watermelon mosaic virus

AbstractCucurbit aphid-borne yellows virus (CABYV) and watermelon mosaic virus (WMV) are major plant pathogens that cause severe epidemics in cucurbit crops. While there has been an increasing interest in molecular epidemiological studies on both viruses at regional scales, their phylodynamic analysis by using the temporal data at global scale remains unexplored. In this study, we implemented the Nextstrain phylodynamic approach to comprehensively examine the coat protein gene and full-length genome sequences of the CABYV and WMV worldwide populations. Our analyses reconstructed a robust phylogeny of CABYV and confirmed the occurrence of isolates grouped into three clusters (Asian, Mediterranean, and Recombinant). Nextstrain analysis suggested that CABYV epidemics likely originated in Southeast Asia in fourteenth century, while the Mediterranean population emerged in Spain in seventeenth century. We also found a high divergence between Asian and Mediterranean isolates, with low genetic diversity and scarce evidence of selection, as reflected by the lack of gene flow. Moreover, the hierarchical analysis of molecular variance revealed a significant differentiation between CABYV populations grouped by geographical location and plant host. Additionally, the global phylogenetic reconstruction of the WMV population confirmed a clear differentiation among isolates, which grouped into two clusters (classical and emergent), and Nextstrain analysis suggested that WMV epidemics were most probably originated in USA during the sixteenth century. The initial WMV population diverged in the eighteenth century, with the origin of the emergent population in the nineteenth century. Our analysis confirmed that WMV population has a polyphyletic origin, defining an extensive genetic diversity. Overall, this work provides insights into the CABYV and WMV origin and evolutionary dynamics, gaining an understanding of the global spread of both viral diseases. Additionally, the integration of all spatio-temporal CABYV and WMV data, along with their genome sequence data by open access (https://github.com/PiR92) and the Nextstrain approach, provides a valuable tool for compiling and sharing current knowledge of these viral diseases in cucurbit crops.

Morishitium polonicum (Machalska, 1980) is a junior synonym of Morishitium dollfusi (Timon-David, 1950) (Trematoda: Cyclocoeliidae).

Species of the genus Morishitium Witenberg, 1928 are parasites of the body cavity, air sacs, and lungs of birds. At least 14 species are considered valid, but molecular confirmation of their status is lacking. Here, we provide the first molecular data on Morishitium dollfusi isolated from their type host Pica pica, compared them with previously reported molecular data from Morishitium polonicum isolated from their type and paratype hosts, Turdus merula and Turdus philomelos, and performed extensive measurements of 511 individuals of Morishitium spp. across a broad host spectrum, at multiple infection intensities, and year-round. We analyzed the molecular phylogenetics of Morishitium spp. adults isolated from bird hosts of Czech origin and provide comparative measurements of the analyzed specimens. Based on the molecular examination of morphologically identified specimens of M. dollfusi and M. polonicum (CO1, ND1, and ITS2 markers), we propose synonymization of Morishitium dollfusi (Timon-David, 1950) with Morishitium polonicum (Machalska, 1980) (isolates of European origin). The three markers were either identical (CO1, ITS2) or formed haplotypes shared by the two species (ND1). Morphological analyses revealed a continuum of key identification features for the two above-named species, although we used specimens matching the original descriptions and isolated them from the type hosts. Therefore, Morishitium polonicum is a junior synonym of Morishitium dollfusi. Attention is needed regarding the status of East Asian isolates identified previously as M. polonicum (or M. polonicum malayense). The molecular analysis revealed that these isolates form a distinct clade, and further research is needed to produce data allowing the likely separation of the malayense clade as a separate species.

A new Plasmodium vivax reference genome for South American isolates

BackgroundPlasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering.ResultsThis study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions.ConclusionsOur findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.

Tal6b/AvrXa27A, a hidden TALE targeting the susceptibility gene OsSWEET11a and the resistance gene Xa27 in rice

Xanthomonas oryzae pv. oryzae (Xoo) secretes transcription activator-like effectors (TALEs) to activate rice susceptibility (S) genes, causing bacterial blight (BB), as well as resistance (R) genes, leading to defense against BB. This activation follows a gene-for-gene paradigm that results in an arms race between the TALE of the pathogen and effector-binding elements (EBEs) in the promoters of host genes. In this study, we characterized a novel TALE, designated Tal6b/AvrXa27A, that activates the rice S gene OsSWEET11a and the rice R gene Xa27. Tal6b/AvrXa27A is a member of the AvrXa27/TalAO class and contains 16 repeat variable diresidues (RVDs); one RVD is altered and one is deleted in Tal6b/AvrXa27A compared with AvrXa27, a known avirulence (avr) effector of Xa27. Tal6b/AvrXa27A can transcriptionally activate the expression of Xa27 and OsSWEET11a via EBEs in their corresponding promoters, leading to effector-triggered immunity and susceptibility, respectively. The 16 RVDs in Tal6b/AvrXa27A have no obvious similarity to the 24 RVDs in the effector PthXo1, but EBETal6b and EBEPthXo1 are overlapped in the OsSWEET11a promoter. Tal6b/AvrXa27A is prevalent among Asian Xoo isolates, but PthXo1 has only been reported in the Philippine strain PXO99A. Genome editing of EBETal6b in the OsSWEET11a promoter further confirmed the requirement for OsSWEET11a expression in Tal6b/AvrXa27A-dependent susceptibility to Xoo. Moreover, Tal6b/AvrXa27A resulted in higher transcription of Xa27 than of OsSWEET11a, which led to a strong, rapid resistance response that blocked disease development. These findings suggest that Tal6b/AvrXa27A has a dual function: triggering resistance by activating Xa27 gene expression as an avirulence factor and inducing transcription of the S gene OsSWEET11a, resulting in virulence. Intriguingly, Tal6b/AvrXa27A, but not AvrXa27, can bind to the promoter of OsSWEET11a. The underlying recognition mechanism for this binding remains unclear but appears to deviate from the currently accepted TALE code.

Coat protein is responsible for tomato leaf curl New Delhi virus pathogenicity in tomato.

Tomato leaf curl New Delhi virus (ToLCNDV), a bipartite Begomovirus belonging to the family Geminiviridae, causes severe damage to many economically important crops worldwide. In the present study, pathogenicity of Asian (ToLCNDV-In from Pakistan) and Mediterranean isolates (ToLCNDV-ES from Italy) were examined using infectious clones in tomato plants. Only ToLCNDV-In could infect the three tomato cultivars, whereas ToLCNDV-ES could not. Genome-exchange of the two ToLCNDVs revealed the ToLCNDV DNA-A segment as the main factor for ToLCNDV infectivity in tomato. In addition, serial clones with chimeric ToLCNDV-In A and ToLCNDV-ES A genome segments were generated to identify the region determining viral infectivity in tomatoes. A chimeric clone carrying the ToLCNDV-In coat protein (CP) exhibited pathogenic adaptation in tomatoes, indicating that the CP of ToLCNDV is essential for its infectivity. Analyses of infectious clones carrying a single amino acid substitution revealed that amino acid at position 143 of the CP is critical for ToLCNDV infectivity in tomatoes. To better understand the molecular basis whereby CP function in pathogenicity, a yeast two-hybrid screen of a tomato cDNA library was performed using CPs as bait. The hybrid results showed different interactions between the two CPs and Ring finger protein 44-like in the tomato genome. The relative expression levels of upstream and downstream genes and Ring finger 44-like genes were measured using quantitative reverse transcription PCR (RT-qPCR) and compared to those of control plants. This is the first study to compare the biological features of the two ToLCNDV strains related to viral pathogenicity in the same host plant. Our results provide a foundation for elucidating the molecular mechanisms underlying ToLCNDV infection in tomatoes.

Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

AbstractVenturia inaequalis, the causal fungal pathogen of apple scab, has evolved with its Malus hosts during apple domestication. This co‐evolution has resulted in a genetic structure in V. inaequalis populations from Europe and central Asia based on host species and geographic isolation. However, it is not yet clear if geographic isolation has led to population differentiation in North American isolates. We resequenced the genomes of 54 V. inaequalis isolates from North America and analysed them with publicly available genome sequences of 90 European and central Asian isolates for variant discovery and population structure. A total of 204,566 high‐quality single‐nucleotide polymorphisms (SNPs) were identified and used to assess population genetic structure and genomic diversity across 123 Venturia spp. isolates from around the world. Population genetic analysis identified four clusters based on Malus and non‐Malus hosts and Venturia species; this differentiation was supported by genetic diversity parameters including FST, Nei's π and Tajima's D. Genetic structure analysis did not reveal a distinct subpopulation of North American V. inaequalis isolates within the global isolates. Additionally, structure was not observed in V. inaequalis isolates collected on M. × domestica between North America and Europe. These observations indicate that geographical isolation has not contributed to the population differentiation between North America and Europe/central Asia. These results will enhance our understanding of the evolution of V. inaequalis, the emergence of virulent isolates and their implications for managing apple scab effectively.

Genomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence

PurposeBrucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform. MethodsThe two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out. ResultsPhylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes. ConclusionHere we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.

Emergence and genomic analysis of a novel sublineage of bovine ephemeral fever virus in Southwest China.

Bovine ephemeral fever virus (BEFV), belonging to the genus Ephemerovirus under the family Rhabdoviridae, is the etiological cause for the bovine ephemeral fever (BEF) in cattle and water buffalo. In this study, we report recent BEF outbreaks in Southwest China and sequence the complete genome sequence of one BEFV isolate BEFV/CQ1/2022. Comparative genomic analyses between BEFV/CQ1/2022 and isolates available in GenBank revealed remarkable inter-isolate divergence. Meanwhile, the sequence divergence was related to the evolutionary relationships and geographical distribution of the isolates. Phylogenetic analysis indicated that the global BEFV isolates can be divided into 4 distinct lineages. The East Asia lineage was the most diverse and could be subdivided into 4 sublineages. Notably, BEFV/CQ1/2022 and other 10 recent isolates from Mainland China were found to be clustered in sublineage 2. Additionally, recombination analysis provided evidence of BEFV recombination among East Asian isolates for the first time. Taken together, a novel sublineage of the East Asian BEFV emerged in Southwest China, and large divergence and potential recombination among BEFV strains were investigated in this study, which may improve understanding of BEFV epidemiology and evolution.

Characterization of a recombinant tomato leaf curl New Delhi Virus (ToLCNDV) in a perennial medicinal climber host (Ipomoea cairica (L.) Sweet).

During the year 2020-2021, a disease syndrome very commonly observed in railway creepers (Ipomoea cairica(L.) Sweet) was taken into consideration from Gorakhpur Province (UP East region). Whitefly, a common vector for plant-related viral diseases was observed for wide transmission of disease. DNA from 17 infected leaf samples was isolated and analyzed through PCR using specific primers designed for the detection of Begomoviruses. Further amplification of isolated DNA fragments supporting a begomovirus infection with an estimated size of (2.7kb). RCA of the isolated DNA sample was carried out using ϕ29 DNA polymerase by digesting it through a set of restriction endonucleases (such as BamHI, Kpn1, HindIII, EcoRI) obtaining the best result through KpnI. The amplified segment was cloned into pUC 18vectors. The obtained sequences were matched using the NCBI BLAST database showing the highest sequence similarity of 98.7% with ToLCNDV of snake gourd (Accession no.KY780199), isolates of CP genes sequence in Varanasi. ToLCNDV, a begomovirus of bipartite nature was first reported to be from Tomato (Solanaceae), later affecting certain members of the Cucurbitaceae family in India and adjacent countries. The obtained DNA sequence was submitted at NCBI with the name ToLCNDV-IP (GenBank Accession no. OM777194). The phylogenetic analysis clubbed the current isolate ToLCNDV-IP with Asian isolates. All European isolates were clubbed in separate clades indicating two distinct groups of ToLCNDV isolates. ToLCNDV-IP isolate was found to be an intralineage recombinant between two Asian isolates viz ToLCNDV isolate from Papaya (India) and ToLCNDV isolate from Tomato (Pakistan). This study shows the association of recombinant ToLCNDV infection in a new hostIpomoea cairicafor the first time in India.

ОТЕЧЕСТВЕННЫЕ ИЗОЛЯТЫ ВИРУСА АФРИКАНСКОЙ ЧУМЫ СВИНЕЙ В ФИЛОГЕНЕТИЧЕСКОМАНАЛИЗЕ ПО ГЕНУ B602L

African swine fever virus has its own genetic mechanisms of variability. Of great interest to the scientific community is the problem of the evolutionary variability of the ASF virus genome. Namely, the problem of the evolutionary variability of the ASF virus genome, the study of the functions of individual genes, their role in interaction with the host cell and the impact on the evolutionary variability of both the virus itself and the susceptible organism. The diversity of genetic variants of the virus is the main property of this pathogen, as well as the lack of a vaccine against this disease. Having data on the genetic features of the ASF virus, as well as the study of the variability of known genes, allow us to expand information about the nature of genetic changes, as well as to obtain a molecular epizootological picture of the circulation of the ASF virus both in the Russian Federation and in the world as a whole. Analysis of a number of marker genes will make it possible to comprehensively assess the genetic changes in the ASF virus and their possible phenotypic manifestations. The study of the B602L gene allows more accurate differentiation of European and Asian isolates within the same genotype. Phylogenetic analysis for the B602L gene of sixty domestic isolates of the ASF virus isolated in the Russian Federation from 2016 to 2017 was carried out. As a result of the study, the isolates used in the work were divided into two clusters. Analysis of the obtained data showed the high conservation of isolates and strains and made it possible to establish their genotypic affiliation. The nature of genetic and phenotypic changes in the genome of the ASF virus still remains unclear.

Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N.

Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4-99.0 and 79.1-99.0), P1 (59.1-98.3 and 36.8-98.3), and CP (76.6-100 and 75.7-100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types.