Distinct Clades Research Articles

Molecular identification of Baylisascaris melis (Gedoelst, 1920) from the Eurasian badger (Meles meles) and ascarids from other wild carnivores in Kazakhstan.

The presence of gastrointestinal nematodes, including zoonotic ascarids, in wild canids, felids and mustelids as definitive hosts in Central Asian countries has been documented in many studies based on traditional morphological methods. In contrast, relevant data for the badger are scarce. The aim of this study was the molecular identification of ascarid nematodes from five wild carnivore species in different regions of Kazakhstan. A total of 211 adult ascarids were collected from gray wolves (Canis lupus, 8 of 83 infected with 2-6 Toxascaris leonina), red foxes (Vulpes vulpes, 26 of 53, with 2-8 Toxascaris leonina), corsac foxes (Vulpes corsac, 6 of 11, 3-6 Toxascaris leonina), lynx (Lynx lynx, 2 of 3, with 2-5 Toxocara cati) and badgers (Meles meles, 2 of 4, with 2-7 Baylisascaris melis). Genomic DNA was extracted from the worms and ribosomal DNA, including the first and second internal transcribed spacer genes, was amplified by polymerase chain reaction using specific oligonucleotide primers and then sequenced. Toxascaris leonina, but not Toxocara canis, was molecularly identified in the wild canids, Toxocara cati in the lynx and Baylisascaris melis in the badger. The maximum likelihood phylogenetic tree showed three distinct clades: the canid Toxascaris leonina was placed in one clade, Toxocara cati in another and Baylisascaris melis in a third. The study provides the world's first molecular data and phylogenetic analysis of Baylisascaris melis, identified for the second time since its description over 100 years ago. This species was shown to be genetically distinct from other Baylisascaris spp. (B. columnaris, B. procyonis, B. transfuga, B. devosi). The possible zoonotic significance of ascarids from wild carnivores is discussed in the light of conditions in Central Asia.

Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae)

BackgroudScrophularia L., a genus of the Scrophulariaceae, is a group of important medicinal plants used for eliminating heat and detoxifying. East Asia has an abundance of potentially medicinal Scrophularia species, and it serves as a secondary diversity center of the genus. However, the genomic resources available for germplasm identification and pharmaceutical exploration of East Asian Scrophularia are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian Scrophularia species remain unclear.MethodsIn this study, we sequenced the leaves of 25 East Asian species of the genus Scrophularia, assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes.Results and discussionThe conserved plastome length of these 25 species ranged from 151,582 bp to 153,239 bp, containing a total of 132 coding genes, including 18 duplicated genes and 114 unique genes. Through genome alignment of these 25 species, 38-53 repeated sequences and 7 shared SSRs were identified, along with regions with high nucleotide polymorphism (Pi), which could potentially serve as molecular markers for species identification. The genome structure, gene content, and arrangement showed conservation, while variations were observed in the IR boundary regions and IGS. Phylogenetic inferences based on whole plastomes or on coding sequences (CDS) only yielded congruent results. We categorized the 25 East Asian Scrophularia species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. This could lay a genetic basis for future resource development of Scrophularia in East Asia.

Armillaria Species Causing Kiwifruit Vine Decline and Root Rot in Northeastern Türkiye: A Growing Concern for Kiwifruit Health

ABSTRACTKiwifruit (Actinidia deliciosa) production in northeastern Türkiye is facing an emerging threat from Armillaria root rot. Surveys conducted in August 2021 and 2022 revealed that 10.5%–17.5% of the 200–500 vines within each of 35 kiwifruit orchards in the Perşembe, Gülyalı and Altınordu districts of Ordu province exhibited symptoms of Armillaria root rot, including complete defoliation. Diseased plants exhibited diagnostic signs on their root collars and woody roots, including white mycelial fans, extensive wood rot and rhizomorphs. A single Armillaria isolate was obtained from each of the 35 symptomatic orchards. Molecular identification, employing DNA sequencing of the large subunit (LSU) region of rDNA, the translation elongation factor subunit 1‐alpha (TEF1) gene and the second largest RNA polymerase II B‐subunit (RPB2) gene, identified 20 isolates as Armillaria gallica and 15 as A. mellea. Phylogenetic analyses, based on TEF1 alignments, further supported the species identification with a 100% bootstrap value. To examine genetic diversity, start codon targeted (SCoT) marker 13 was used, successfully differentiating the two Armillaria species and revealing three distinct clades. Clades I and II comprised 15 and 5 isolates of A. gallica, respectively, while Clade III contained all 15 A. mellea isolates. Pathogenicity testing on kiwifruit seedlings (cv. Hayward) revealed the ability of both A. gallica and A. mellea isolates to induce disease. Rhizomorph‐producing isolates in kiwifruit seedlings displayed high virulence, inducing severe leaf necrosis and seedling mortality, while isolates lacking these structures were non‐pathogenic. This study identifies the first global instance of A. gallica causing kiwifruit root rot. This finding, along with the identification of A. mellea as a causal agent in the country, highlights the emerging threat of Armillaria root rot to kiwifruit production in the region.

A Novel Natural Graph for Efficient Clustering of Virus Genome Sequences

Background: This study addresses the need for analyzing viral genome sequences and understanding their genetic relationships. The focus is on introducing a novel natural graph approach as a solution. Objective: The objective of this study is to demonstrate the effectiveness and advantages of the proposed natural graph approach in clustering viral genome sequences into distinct clades, subtypes, or districts. Additionally, the aim is to explore its interpretability, potential applications, and implications for pandemic control and public health interventions. Methods: The study utilizes the proposed natural graph algorithm to cluster viral genome sequences. The results are compared with existing methods and multidimensional scaling to evaluate the performance and effectiveness of the approach. Results: The natural graph approach successfully clusters viral genome sequences, providing valuable insights into viral evolution and transmission dynamics. The ability to generate directed connections between nodes enhances the interpretability of the results, facilitating the investigation of transmission pathways and viral fitness. Conclusion: The findings highlight the potential applications of the natural graph algorithm in pandemic control, transmission tracing, and vaccine design. Future research directions may involve scaling up the analysis to larger datasets and incorporating additional genetic features for improved resolution. : The natural graph approach presents a promising tool for viral genomics research with implications for public health interventions.

Phylogenetic analyses and antigenic characterization of foot-and-mouth disease virus PanAsia lineage circulating in China between 1999 and 2023

Foot-and-mouth disease (FMD) is one of the most important transboundary animal diseases caused by foot-and-mouth disease virus (FMDV), leading to significant economic losses worldwide. The first report of PanAsia lineage of FMDV in China was in 1999. Since 2011, 18 outbreaks attributed to PanAsia lineage viruses have been reported across 7 provinces or municipality in China. Phylogenetic analysis indicated that these PanAsia strains were clustered into three distinct clades (clade 1, clade 2, and clade 3), with nucleotide homology ranging from 91.4% to 100%. The outbreaks of FMD caused by clade 1 strains occurred around 1999 when this lineage was prevalent globally. Clade 2 strains dominated from 2011 to 2013, while clade 3 strains were prevalent during 2018–2019, sharing only 93% homology with clade 2 strains and 91% with clade 1 strains. Tracing analysis showed that these outbreaks represented 3 distinct introductions of PanAsia viruses into China. Virus neutralization tests (VNT) have demonstrated that current commercial vaccines are effective to protect susceptible animals against these strains (r1 ​> ​0.3). However, the growing demand for livestock has promoted animal movement and encouraged the exchange of products, services, and materials between countries, thereby heightening the risk of exotic strain incursions. Therefore, it is imperative to reinforce border controls and limit animal movements among various Asian countries continually to reduce the risk of new transboundary diseases, such as FMD incursion. Additionally, PanAsia-2 strains need to be taken seriously to prevent its incursions, and the relevant vaccines against PanAsia-2 strains need to be stockpiled in preparation for any possible incursion.

Stomatal response to VPD in C4 plants with different biochemical sub-pathways.

C4 NAD-malic enzyme (NAD-ME) species occurs in drier regions and exhibit different drought responses compared to C4 NADP-malic enzyme (NADP-ME) species. However, a physiological mechanism explaining the geographical discrepancies remains uncertain. This study examined gas exchange patterns that might explain different distributions observed between two subtypes of C4 photosynthesis. We measured the response of leaf gas exchange to vapour pressure deficit (VPD) and CO2 in plants from six distinct C4 clades having closely related NAD-ME and NADP-ME species using a Li-Cor 6400 gas exchange system. We found that NAD-ME species exhibited greater relative reductions in stomatal conductance with increases in VPD than NADP-ME species but observed no consistent subtype differences in C4 cycle activity as indicated by the initial slope of the A response to intercellular CO2 concentration. Based on these results, we hypothesise the greater response of gs to increasing VPD may enable NAD-ME plants to outperform NADP-ME plants in hot, dry environments where VPD is normally high.

Coahuilasaurus lipani, a New Kritosaurin Hadrosaurid from the Upper Campanian Cerro Del Pueblo Formation, Northern Mexico

The Late Cretaceous of Western North America (Laramidia) supported a diverse dinosaur fauna, with duckbilled dinosaurs (Hadrosauridae) being among the most speciose and abundant members of this assemblage. Historically, collecting and preservational biases have meant that dinosaurs from Mexico and the American Southwest are poorly known compared to those of the northern Great Plains. However, evidence increasingly suggests that distinct species and clades inhabited southern Laramidia. Here, a new kritosaurin hadrosaurid, represented by the anterior part of a skull, is reported from the late Campanian of the Cerro del Pueblo Formation, ~72.5 Ma, in Coahuila, Mexico. The Cerro del Pueblo Formation kritosaur was originally considered to represent the same species as a saurolophine from the Olmos Formation of Sabinas, but the Sabinas hadrosaur is now considered a distinct taxon. More recently, the Cerro del Pueblo Formation kritosaur has been referred to Kritosaurus navajovius. We show it represents a new species related to Gryposaurus. The new species is distinguished by its large size, the shape of the premaxillary nasal process, the strongly downturned dentary, and massive denticles on the premaxilla’s palatal surface, supporting recognition of a new taxon, Coahuilasaurus lipani. The dinosaur assemblage of the Cerro del Pueblo Formation shows higher diversity than the contemporaneous fauna of the Horseshoe Canyon Formation in Alberta. Furthermore, Kritosaurini, Lambeosaurini, and Parasaurolophini all persist into the latest Campanian in southern Laramidia after disappearing from northern Laramidia. These patterns suggest declining herbivore diversity seen at high latitudes may be a local, rather than global phenomenon, perhaps driven by cooling at high latitudes in the Late Campanian and Maastrichtian.

Molecular phylogenetic analysis and seasonal dynamics of Eimeria species infecting broilers of Kashmir, India.

Globally, the poultry industry is seriously threatened by coccidiosis caused by various species of Eimeria. This protozoan parasite inhabits the epithelial lining of the gastrointestinal tract of poultry globally and can cause serious clinical disease. The present study was carried out on poultry farms located in various regions of Kashmir, India, to investigate the prevalence and phylogenetic relationships of Eimeria species affecting broiler chickens. Over a period of one year, fecal samples were collected from 60 poultry farms in Kashmir and morphological and molecular techniques were employed for Eimeria species identification. Results revealed a high prevalence of coccidiosis, with 58.3% (35/60) of farms positive for Eimeria. The most prevalent species were E. tenella (31/35, 88.6%) followed by E. acervulina (25/35, 71.4%), E. maxima (19/35, 54.3%), E. mitis (18/35, 51.4%), and E. necatrix (9/35, 25.7%). Seasonal variation in prevalence was also observed, with the highest rates in autumn (86.7%) and summer (66.7%). Additionally, younger birds (3-4weeks) exhibited higher infection rates (85.7%) compared to older birds (57.9%) (5-6weeks). Mixed infection was found in 94.2% (33/35) of positive farms. Phylogenetic analysis using ITS1 sequences confirmed species clustering and revealed evolutionary relationships among Eimeria species. E. tenella and E. necatrix formed a distinct clade, while E. acervulina formed another. The study underscores the importance of molecular techniques in accurate species identification and provides valuable insights into the epidemiology of coccidiosis in poultry in Kashmir. Effective control strategies, including vaccination and improved management practices, are necessary to mitigate the economic losses associated with this widespread poultry disease.

Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs

Six strains, WILCCON 0050, WILCCON 0051, WILCCON 0052, WILCCON 0053, WILCCON 0054, WILCCON 0055T, were isolated from four different fecal samples of wild boars on Pulau Ubin, Singapore, Singapore. Based on core genome phylogenetic analysis, the six strains formed a distinct clade within the genus Limosilactobacillus, with the most closely related type strain being Lm. mucosae DSM 13345T. The minimum ANI, dDDH, and AAI values within these six strains were 97.8 %, 78.8 %, and 98.6 %, respectively. In contrast, the ANI, dDDH, and AAI values with Lm. mucosae DSM 13345T were lower, ranging between 94.8–95.1 %, 57.1–59.0 %, and 95.9–97.0 %, respectively. While ANI and AAI were close to the thresholds of 95 % and 97 % for bacterial species delineation, respectively, dDDH was significantly lower than the threshold value of 70 %. Based on our phylogenomic, phenotypic and chemotaxonomic analyses, we propose a novel species with the name Limosilactobacillus allomucosae sp. nov., with WILCCON 0055T (DSM 117632T = LMG 33563T) as the designated type strain. In vitro investigations revealed the strains’ ability to break down raffinose-family oligosaccharides, and to utilize prebiotics such as xylo-oligosaccharides and galacturonic acid, thereby enhancing fibre digestion and nutrient absorption. Moreover, strong auto-aggregation properties, as well as resistance to low pH and porcine bile were observed, suggesting their potential survival and persistence during passage through the gut. The high bile tolerance of these strains appears to be attributed to their ability to deconjugate a wide range of conjugated bile compounds. In silico analysis indicated a strong potential for mucin-binding activity, which aids their colonization in the gut. These characteristics indicate the potential suitability of strains of Lm. allomucosae as probiotics for domestic pigs.

Characterization and phylogenetic analysis of the Talaromyces liani (kamyschko) Yilmaz, Frisvad & Samson, 2014 (Eurotiales: trichocomaceae) mitochondrial genome

The filamentous fungus Talaromyces liani (Kamyschko) Yilmaz, Frisvad & Samson, 2014, has attracted considerable interest in biotechnology due to its diverse industrial applications and physiological characteristics. However, the mitochondrial genome of T. liani remains uncharacterized. Here, we present the complete mitochondrial genome of T. liani, comprising 38,000 bp with a GC content of 24.61%. This genome includes 15 core protein-coding genes, 4 independent ORFs, 6 intronic ORFs, 26 tRNAs, and 2 rRNA genes. Phylogenetic analysis using Bayesian inference (BI) revealed the evolutionary relationships among 15 fungi from Eurotiales, strongly supporting distinct clades and indicating that T. liani most closely related to T. pinophilus.

DNA Barcoding of the Endemic Freshwater Catfish Encheloclarias tapeinopterus (Bleeker, 1853) (Siluriformes:Clariidae) from Bangka Island, Indonesia

Abstract Encheloclarias tapeinopterus, an endemic catfish exclusively found in Bangka Island, Indonesia. The population of this species has been observed to be decreasing at an alarming rate, which has resulted in the IUCN Red List classifying it as a species that is vulnerable (VU). During our expedition on the 25th and 26th of January 2023, a total of Two specimens of E. tapeinopterus were collected from Kelumpik River, Pinang Sebatang Village, Central Bangka Regency, Bangka Island, Indonesia. In this groundbreaking study, we proudly present the pioneering documentation of E. tapeinopterus DNA barcoding, focusing on the Cytochrome C oxidase Subunit I (COI) gene. The recorded DNA Barcode of E. tapeinopterus has been officially registered in the Genbank under the accession code OQ281707. By employing DNA barcoding, we offer an advanced and expedient method for precise species identification and discovery, revolutionizing the field of taxonomy. Phylogenetic analysis revealed that E. tapeinopterus forms a distinct clade alongside the Clarias and Heterobranchus genus, shedding light on its evolutionary relationships and genetic affinities.

Exploring Aquaporin Diversity in Elateroidea: Insights From RNA-Seq Data Sets.

Osmoregulation, the physiological regulation of water and ion balance, is vital for the survival of both aquatic and terrestrial insects. In freshwater aquatic insects, such as those within the Lampyridae family, this function is important due to the natural variation of aquatic habitats. Aquaporins play a key role in this process by facilitating the rapid transport of water molecules across cell membranes, maintaining cellular water balance, and adapting to changes in external salinity. In this study, I investigate the genetic diversity and expression levels of aquaporins in Elateroidea, particularly focusing on the Lampyridae family, using transcriptomic data and in silico analyses. The results reveal the diversity of aquaporins and compare gene expression patterns between freshwater aquatic Lampyridae and terrestrial Elateroidea species, such as Lycidae, Phengodidae, and Elateridae. Phylogenetic analyses identify seven distinct clades of aquaporins and uncovered gene duplication events related to the diversification of Elateridae and Lampyridae. A comparative abundance analysis indicated higher aquaporin expression in aquatic fireflies, aligning with the need for efficient osmoregulation in aquatic environments. Additionally, stage-specific expression patterns in Aspisoma lineatum (Neotropical firefly) and Aquatica lateralis (Paleartic firefly) suggest species-specific strategies for coping with osmotic challenges during development. This study provides insights into the evolutionary adaptations of aquaporins in Elateroidea, highlighting their importance in both aquatic and terrestrial insect physiology.

DNA BARCODING OF HIPPOPHAE RHAMNOIDES L. COLLECTED FROM NATURAL AND INTRODUCED POPULATIONS IN KAZAKHSTAN

In this study, we analyzed eight samples of Hippophae rhamnoides L. collected in Kazakhstan, along with twenty-five samples of Hippophae species and three outgroup species from NCBI GenBank, using ITS sequences. The alignment of the ITS sequences, which was 639 bp in length with outgroup samples and 642 bp without them, revealed polymorphism, with 31 positions (4.85%) being polymorphic among the ingroup samples. The highest number of polymorphic sites was found in ITS1 (13 sites), followed by ITS2 (10 sites) and the 5.8S rRNA region (8 sites). The maximum likelihood (ML) phylogenetic tree delineated four distinct clades within the Hippophae species. The H. rhamnoides samples from northeastern Kazakhstan clustered with H. rhamnoides ssp. mongolica from GenBank suggests a close genetic relationship. Introduced samples formed separate subclades and clustered with various subspecies from GenBank. Notably, hybrid peaks were observed in the ITS sequences of introduced plants, which were not present in samples from natural populations. This study underscores the utility of ITS sequences in identifying plants from natural and introduced populations of H. rhamnoides and highlights the marker's importance in plant genetic research and biodiversity conservation.

Population structure of longtail tuna (Thunnus tonggol) within and across Indonesia’s fisheries management areas (FMAs) and neighboring countries based on mitochondrial control region

Longtail tuna (Thunnus tonggol), one of the neritic tuna species commonly found in the coastal areas of the Indo-Pacific region, is known to be in an overfishing state in certain areas, including in Indonesia. Understanding the condition of the T. tonggol population within Indonesia is very important in managing its fisheries policy. This research aims to understand the population genetic structure of T. tonggol across Indonesia's Fisheries Management Areas (FMAs), as well as to investigate the phylogeography of T. tonggol within the Indo-Pacific region. A total of 586 samples were collected from 18 locations within Indonesia’s six FMAs, and two locations from Malaysian waters. A 520 bp portion of mtDNA control region was amplified and sequenced. Data analysis was conducted using 586 total sequences generated from this study, and 336 sequences retrieved from GenBank, as well as provided by the author of previous study. Population structure analysis indicated a panmictic population of T. tonggol within six Indonesian FMAs and within the neighboring countries (Malaysia, Andaman Sea, Vietnam, Philippines, and India), with an indication of population expansion. These data do, however, reveal two potentially distinctive clades, one showing an affinity among samples from certain parts of Indonesia (East Aceh, West Aceh, Medan - FMA571 & FMA572) and India. Based on this finding, the T. tonggol fisheries should be managed as a single management unit both within Indonesia’s FMA and within neighboring countries, while also emphasizing localized genetic diversity to protect the sustainability of the species and its fishery.

Parallel evolution of methyltransferases leads to vobasine biosynthesis in Tabernaemontana elegans and Catharanthus roseus.

Monoterpenoid indole alkaloids (MIA) are one of the largest and most complex alkaloid class in nature, boasting many clinically significant drugs such as anticancer vinblastine and antiarrhythmic ajmaline. Many MIAs undergo nitrogen N-methylation, altering their reactivity and affinity to the biological targets through a straightforward reaction. Remarkably, all known MIA N-methyltransferases (NMT) originate from the neofunctionalization of ancestral γ-tocopherol C-methyltransferases (γTMTs), a phenomenon seemingly unique to the Apocynaceae family. In this study, we unveil and characterize a new γTMT-like enzyme from the plant Tabernaemontana elegans (toad tree): perivine Nβ-methyltransferase (TePeNMT). TePeNMT and other homologs form a distinct clade in our phylogenetic study, setting them apart from other γTMTs and γTMT-like NMTs discovered to date. Enzyme kinetic experiments and enzyme homology modeling studies reveal the significant differences in enzyme active sites between TePeNMT and CrPeNMT, a previously characterized perivine Nβ-methyltransferase from Catharanthus roseus (Madagascar periwinkle). Collectively, our findings suggest that parallel evolution of ancestral γTMTs may be responsible for the occurrence of perivine N-methylation in T. elegans and C. roseus.

Characterization of the 2ODD genes of DOXC subfamily and its members involved in flavonoids biosynthesis in Scutellaria baicalensis

Background2-oxoglutarate-dependent dioxygenase (2ODD) superfamily is the second largest enzyme family in the plant genome and plays diverse roles in secondary metabolic pathways. The medicinal plant Scutellaria baicalensis Georgi contains various flavonoids, which have the potential to treat coronavirus disease 2019 (COVID-19), such as baicalein and myricetin. Flavone synthase I (FNSI) and flavanone 3-hydroxylase (F3H) from the 2ODDs of DOXC subfamily have been reported to participate in flavonoids biosynthesis. It is certainly interesting to study the 2ODD members involved in the biosynthesis of flavonoids in S. baicalensis.ResultsWe provided a genome-wide analysis of the 2ODDs of DOXC subfamily in S. baicalensis, a total of 88 2ODD genes were identified, 82 of which were grouped into 25 distinct clades based on phylogenetic analysis of At2ODDs. We then performed a functional analysis of Sb2ODDs involved in the biosynthesis of flavones and dihydroflavonols. Sb2ODD1 and Sb2ODD2 from DOXC38 clade exhibit the activity of FNSI (Flavone synthase I), which exclusively converts pinocembrin to chrysin. Sb2ODD1 has significantly higher transcription levels in the root. While Sb2ODD7 from DOXC28 clade exhibits high expression in flowers, it encodes a F3H (flavanone 3-hydroxylase). This enzyme is responsible for catalyzing the conversion of both naringenin and pinocembrin into dihydrokaempferol and pinobanksin, kinetic analysis showed that Sb2ODD7 exhibited high catalytic efficiency towards naringenin.ConclusionsOur experiment suggests that Sb2ODD1 may serve as a supplementary factor to SbFNSII-2 and play a role in flavone biosynthesis specifically in the roots of S. baicalensis. Sb2ODD7 is mainly responsible for dihydrokaempferol biosynthesis in flowers, which can be further directed into the metabolic pathways of flavonols and anthocyanins.

Monkeypox: A Global Challenge - An Overview

Monkeypox is a zoonosis caused by an orthopoxvirus named monkeypox virus MPX, structurally related to smallpox virus, enveloped, brick shaped, replicates in cytoplasm. Currently spreading throughout Africa & different parts of world. Has two distinct clades, West African and Central African (Congo Basin) clades. It manifests as rashes, concentrated on face & extremities like palms & soles. Both humoral and cell mediated immunity are seen in host, diagnosed by polymerase chain reaction PCR and various serological tests. Patients receive supportive treatments along with antiviral drugs. Presently FDA approved new Mpox vaccines. Scientific community needs to extend their research work to enhance knowledge in this field. This review briefs about monkeypox in human life in context of ongoing outbreaks around the world.

Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China.

Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.

Phenotypic and genomic analysis of the hypervirulent methicillin-resistant Staphylococcus aureus ST630 clone in China.

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) is a rarely reported lineage worldwide. This study aimed to trace the dissemination of the emerging MRSA ST630 clones in China and investigate their virulence potential. We collected 22 ST630-MRSA isolates from across China and performed whole-genome sequencing analysis and virulence characterization on these isolates. Epidemiological results showed that MRSA ST630 isolates were primarily isolated from pus/wound secretions, mainly originating from Jiangxi province, and carried diverse virulence and drug resistance genes. Staphylococcal cassette chromosome mec type V (SCCmec V) predominated (11/22, 50.0%) among the MRSA ST630 isolates. Interestingly, nearly half (45.5%) of the 22 ST630-MRSA isolates tested lacked intact SCCmec elements. Phylogenetic analysis demonstrated that ST630-MRSA could be divided into two distinct clades, with widespread dissemination mainly in Chinese regions. Five representative isolates were selected for phenotypic assays, including hemolysin activity, real-time fluorescence quantitative PCR, western blot analysis, hydrogen peroxide killing assay, blood killing assay, cell adhesion and invasion assay, and mouse skin abscess model. The results showed that, compared to the USA300-LAC strain, ST630 isolates exhibited particularly strong invasiveness and virulence in the aforementioned phenotypic assays. This study described the emergence of a highly virulent ST630-MRSA lineage and improved our insight into the molecular epidemiology of ST630 clones in China.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) is an emerging clone with an increasing isolation rate in China. This study raises awareness of the hypervirulent MRSA ST630 clones in China and alerts people to their widespread dissemination. ST630-staphylococcal cassette chromosome mec V is a noteworthy clone in China, and we present the first comprehensive genetic and phenotypic analysis of this lineage. Our findings provide valuable insights for the prevention and control of infections caused by this emerging MRSA clone.

Identification of a novel mitovirus in grapevine through high-throughput sequencing.

Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome. Here, we identify putative novelmitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.), and the identified virus was confirmed using virus-specific primers in RT-PCR assay. The genomic RNA of GMV1 encodes complete open reading frame (ORF) of 2,496 nucleotides (nts) in length. RNA-dependent RNA polymerase (RdRp) encoded by the viral genome contained one RdRp conserved domain. BLASTx analysis of GMV1 genome showed sequence identity of 33.18-56.75% with the existingmitovirus sequences. Phylogenetic analysis based on genome sequences showed thatGMV1 clustered in a distinct clade to other mitoviruses. Grapevine mitovirus 1 represents a newly discovered species within the Unuamitovirus genus of the Mitoviridae family, targeting fungal mitochondria. While the majority of recognized mitoviruses typically lack a functional RdRp as per the plant mitochondrial genetic code,GMV1 encodes a complete RdRp in accordance with both fungal and plant mitochondrial genetic codes.