Nucleotide Sequence Research Articles

Determination and Characterization of Novel Papillomavirus and Parvovirus Associated with Mass Mortality of Chinese Tongue Sole (Cynoglossus semilaevis) in China.

A massive mortality event concerning farmed Chinese tongue soles occurred in Tianjin, China, and the causative agent remains unknown. Here, a novel Cynoglossus semilaevis papillomavirus (CsPaV) and parvovirus (CsPV) were simultaneously isolated and identified from diseased fish via electron microscopy, virus isolation, genome sequencing, experimental challenges, and fluorescence in situ hybridization (FISH). Electron microscopy showed large numbers of virus particles present in the tissues of diseased fish. Viruses that were isolated and propagated in flounder gill cells (FG) induced typical cytopathic effects (CPE). The cumulative mortality of fish given intraperitoneal injections reached 100% at 7 dpi. The complete genomes of CsPaV and CsPV comprised 5939 bp and 3663 bp, respectively, and the genomes shared no nucleotide sequence similarities with other viruses. Phylogenetic analysis based on the L1 and NS1 protein sequences revealed that CsPaV and CsPV were novel members of the Papillomaviridae and Parvoviridae families. The FISH results showed positive signals in the spleen tissues of infected fish, and both viruses could co-infect single cells. This study represents the first report where novel papillomavirus and parvovirus are identified in farmed marine cultured fish, and it provides a basis for further studies on the prevention and treatment of emerging viral diseases.

First report of cucumber green mottle mosaic virus infecting Cynanchum rostellatum in China.

Cucumber green mottle mosaic virus (CGMMV) was first discovered on cucumber in the United Kingdom in 1935 (Ainsworth, 1935), and has spread worldwide except to Antarctica (Jones, 2021). Given its extensive damage, it is considered an important pathogen on global cucurbit plants and fruit crops. In China, CGMMV was first reported on pumpkin in Guangxi Province in 2003 (Qin et al., 2005), and occurred on 34 plants species across 23 provinces (Liu et al., 2016). Cynanchum rostellatum is a member of the family Apocynaceae. In July 2021, leaves of C. rostellatum exhibiting virus-like symptoms (yellowing, severe crinkling, deformation) were observed and collected in Liaoning Province, China. Aphids were also observed on the leaves and stems (Fig. S1) of the plants and were collected. Total RNA was extracted from diseased leaves following the CTAB method, followed by the depletion of ribosomal RNAs (rRNA) with TIANSeq rRNA Depletion Kit (Tiangen, China). The RNAs were, then processed into a DNBSEQ LncRNA-Seq library, and sequenced on the MGISEQ-2000 platform at BGI Genomics (Wuhan, China). A total of 106.98 M clean reads were obtained after data filtering using SOAPnuke software (BGI, China). The clean reads were assembled into contigs using CLC Genomics Workbench 11 (Qiagen, USA) and Trinity v2.0.6 (Haas et al., 2013). A contig (4,760 reads, average coverage:73.76) of 6,391 nucleotides was found to share the highest sequence identity (99.83%) with CGMMV isolate GDLZ (MK933286), irrespective of other virus-like contigs related to Polerovirus and Totivirus. Based on the genome of GDLZ isolate, seven specific primers (Table S1) were designed to amplify the full viral genomic sequences using a PrimeScriptTM One-Step RT-PCR Kit. Seven expected amplicons were obtained, cloned, and sequenced. The complete genome was determined to be 6,423 nucleotides (GenBank accession number OR854819) in length and designated as LNMJ isolate. LNMJ shared 96.8%-99.7% nucleotide sequence identities with CGMMV isolates from China. Phylogenetic analysis based on the complete genome sequences showed that LNMJ clustered together with CGMMV isolates hn (GenBank accession number KC851866), GDLZ (GenBank accession number MK933286), and JD8 (GenBank accession number KM873784) from China. The specific primers LM-TJ-3F/3R were designed to determine the virus-symptom association for LNMJ, and all twelve symptomatic C. rostellatum plants collected from fields tested positive for LNMJ. Two out of six randomly selected aphids from the diseased plants also tested positive. To further prove its infectivity, LNMJ was inoculated mechanically onto ten healthy Nicotiana benthamiana plants, and the results indicated a high infection rate of 80% (8/10), at 30 days post-inoculation despite no distinct symptoms observed. To our knowledge, this is the first report of the natural infection of C. rostellatum plants with CGMMV. C. rostellatum is a widespread herb in China (Wei et al., 2019) and more surveys are needed to determine the distribution of CGMMV. The habitats of C. rostellatum span diverse agroecological zones, and thus our study underscores the potential spillover of CGMMV to neighboring crops as a significant risk.

HCV drug resistance mutations in HIV-infected patients

The aim of our work was to assess prevalence in the HCV drug resistance mutations in the NS3, NS5A, NS5B genes in HIV-infected patients. The material of the study was 157 blood plasma samples collected from HIV patients living in the Leningrad Region, with virological inefficiency of antiretroviral therapy. Samples were examined for the presence of anti-HCV antibodies and HCV RNA using commercial test systems in accordance with the manufacturer’s recommendations. In the case of detecting HCV RNA, amplification reaction was carried out using a set of primers co-flanking the NS3, NS5A, and NS5B genes. After sequencing the nucleotide sequences of the above genes, the virus subtype was determined. To assess HCV drug resistance mutations to direct-acting antiviral agents (DAAs), the Geno2pheno HCV resistance software (https:// hcv.geno2pheno.org) was used. The age of the patients varied from 18 to 65 and averaged 34.3±7.27 years. The number of males vs females prevailed comprising 71% and 28%, respectively. Antibodies against HCV were detected in 94.2% cases, whereas HCV RNA — in 98 (61.7%) HIV-infected persons. The distribution of HCV genotypes in this group was as follows: 1a — 7% (n = 7), 1b — 53% (n = 52), 2 — 2% (n = 2), 3a — 38% (n = 37). The results of determining the viral load varied from 5.3 × 103 to 2.3 × 108 IU/ml. The nucleotide sequence of all three regions NS3, NS5A, NS5B was determined in 73 samples. Analysis of drug resistance mutations in the NS3 region was performed for 82 HCV isolates of genotypes 1b (n = 46), 3a (n = 31), 1a (n = 4), 2 (n = 1). In total, the proportion of strains containing mutations in the NS3 region was 9.8%. The presence of significant amino acid substitutions in the NS5A region was tested for 83 HCV isolates of genotypes 1b (n = 47), 3a (n = 30), 1a (n = 6). The percentage of strains containing mutations in the NS5A region was 19.3%. Resistance mutations in the NS5B region were analysed for 87 HCV isolates of genotypes 1b (n = 48), 3a (n = 32), 2 (n = 2), 1a (n = 5). The proportion of strains containing mutations in the NS5B region was 11.5%. In the study group, mutations associated with hepatitis C virus resistance to DAAs in all regions were found in 16.6% (95% CI: 11.11–23.32%) cases (n = 26). In the NS3, NS5A and NS5B, there have been identified 6, 15 and 10 significant amino acid substitutions, respectively.

Non-Pigmented Antarctic Yeasts and Their Resistance to Toxic Metals

Despite the key role in biogeochemical processes and in the functioning of terrestrial ecosystems, yeasts of Antarctic regions still remain insufficiently studied. The study and analysis of the composition of Antarctic microbial communities remains relevant and is carried out using molecular biological approaches. The investigation of their resistance to toxic metal ions is essential to select industrially promising strains that can contribute to the development of new methods of metals detoxification via microorganisms. Aim. To determine the taxonomic position of non-pigmented Antarctic yeasts and investigate their resistance to toxic metal ions. Methods. The objects of the research are yeasts isolated from Antarctic phytocenoses. They were grown on malt wort (pH 5.0–5.5, temperature 18–20 °C). Isolation of genomic DNA was performed via the commercial DNA-sorb kit. Amplification of DNA was carried out using primers NL1 and NL4. Phylogenetic analysis was conducted by construction of trees (dendrograms) showing the position of the studied strains among closely related and typical species. The resistance of yeasts to toxic metal ions was established by cultivation in the concentration gradient of Ni2+, Co2+, CrO42-, and Сu2+. The ecophysiological traits of the isolated yeast strains including psychro- and halotolerance were determined. Results. Phylogenetic analysis showed a high percentage of similarity (99.5–99.6 %) of sequences of 18S rRNA genes of Antarctic yeast strains with the yeast sequences from the GenBank database. Psychrotolerant and halotolerant Antarctic yeast strains S11 and S12 were identified as Leucosporidium scottii and Debaryomyces hansenii, respectively. The studied yeast strains were found to be the most resistant to metal ions Ni2+ and Co2+. Strain of L. scottii S11 grew at 800 mg/L of Co2+, and D. hansenii S12 – at 750 mg/L of Ni2+. The yeasts were the least resistant to CrO42-: the L. scottii S11 and D. hansenii S12 strains grew at concentrations of 25 mg/L and 150 mg/L, respectively. In the presence of Cu2+, they grew at the same concentration – 600 mg/L. The combined action of toxic metal ions resulted in the increased toxic effects on the studied yeasts. Conclusions. The nucleotide sequences of 18S rRNA gene fragment of yeast strains S11 and S12 were included in the GenBank database under the numbers LT220858 and LT220859. Metal-resistant psychrotolerant yeast strains can be used to evaluate the metals content in polar regions as well as to bioremediate metal-contaminated ecosystems. However, further research is needed to develop and optimize bioremediation processes.

Development and application of a TaqMan-probe-based multiplex real-time PCR assay for simultaneous detection of porcine circovirus 2, 3, and 4 in Guangdong province of China.

Porcine circoviruses disease (PCVD), caused by porcine circovirus (PCVs), is an important swine disease characterized by porcine dermatitis, nephrotic syndrome and reproductive disorders in sows. However, diseases caused by PCV2, PCV3, or PCV4 are difficult to distinguish, so a simple, rapid, accurate and high-throughput diagnostic and identification method is urgently needed to differentiate these three types. In this study, specific primers and probes were designed based on the conserved region sequences of the Rep gene of PCV2, and the Cap gene of PCV3 and PCV4. A multiplex qPCR assay was developed and optimized that the limit of detection concentration could reach as low as 3.8 copies/μL, with all correlation coefficients (R2) exceeding 0.999. Furthermore, the method showed no cross-reaction with other crucial porcine viral pathogens, and both intra-repeatability and inter-reproducibility coefficients of variation were below 2%. The assay was applied to the detection of 738 pig samples collected from 2020 to 2021 in Guangdong Province, China. This revealed positive infection rates of 65.18% for PCV2, 29.27% for PCV3, and 0% for PCV4, with a PCV2/PCV3 co-infection rate of 23.17%. Subsequently, complete genome sequences of 17 PCV2 and 4 PCV3 strains were obtained from the above positive samples and pre-preserved positive circovirus samples. Nucleotide sequence analysis revealed that the 17 PCV2 strains shared 96.7-100% complete nucleotide identity, with 6 strains being PCV2b and 11 strains being PCV2d; the 4 PCV3 strains shared 98.9-99.4% complete nucleotide identity, with 2 strains being PCV3a-1 and 2 strains being PCV3b. This research provides a reliable tool for rapid PCVs identification and detection. Molecular epidemiological investigation of PCVs in pigs in Guangdong Province will help us to understand PCV2 and PCV3 epidemiological characteristics and evolutionary trends.

First Report of Panax notoginseng Leaf spot Disease Caused by Boeremia exigua in China.

Panax notoginseng a perennial herb native to China, is widely grown in the Yunnan Province. (Yang et al. 2022). From July to August 2022, a new leaf spot disease was observed on fully expanded leaves of P. notoginseng from a planting base in the Xundian, Yunnan Province, China. Approximately 250 ha. of P. notoginseng is the cultivated area, and the incidence of leaf spot disease was around 10-15%. Round spots appeared on the infected leaves and as the disease progressed these leaves fell off the plant. A total 21 symptomatic leaves were randomly collected from the planting base to isolate the pathogens and further study in the laboratory. The surface of infected leaves were sanitized with 0.5% sodium hypochlorite for 2 min. and 75% alcohol for 1 min., and then rinsed thrice with sterile water. Once drying, the samples were placed on potato dextrose agar (PDA), plates and incubated at 25 °C for 5 days. The fungus was isolated from the symptomatic tissue, but only three isolates were preserved for further identification. Pure cultures of the representative strain Zhaochanglin 118 were obtained using the singlespore method, and the colonies obtained were dark-green to dark-black in appearance. The pycnidia were dark brown, solitary, or congregated with an inconspicuous neck. The conidia were colorless, ellipsoidal, and measured between 4.5 to 7 × 2 to 3 μm (n = 30). These morphological characteristics were similar to those described for Boeremia exigua (Valenzuela-Lopezi et al. 2018). The genomic DNA of the isolate was extracted using the DN14 cetyltrimethylammonium bromide rapid plant genome extraction kit. The internal transcribed spacer (ITS), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) genes were amplified via polymerase chain reaction using the primers ITS1/ITS4 (White et al. 1990), Af/Cf (Matheny et al. 2002), and EF1-983F/EF1-2218R (Chen et al. 2015), respectively. All sequences were deposited in GenBank (OQ996531 for ITS; OR291158 for RPB2 and OR291159 for TEF1). A BLASTN homology search using the ITS nucleotide sequence indicated that this has 99.6% identity with the sequence MH859059, named B. exigua from CBS culture collection (517/519 bp); the RPB2 sequence has 97.5% identity with sequence GU371780, named B. exigua from CBS culture collection (704/722 bp); and the TEF1 sequence has 98.4% identity with sequence GU349080, named B. exigua from CBS culture collection (871/885 bp). To test Koch's postulates, a pathogenicity test was carried out on the leaves of six fully expanded P. notoginseng plants in the Xundian planting base. Conidial suspensions were prepared for one isolates at a concentration of 106 spores per milliliter. Three leaflets on different plants were applied with 20µl spore suspension and the other three leaflets were drop of 20 µl sterile distilled water. The whole experiment was repeated three times. The P. notoginseng plants were incubated under sterile conditions at 25°C for 7 days. Inoculated leaves showed the characteristic brown round spots, while control leaves were asymptomatic so, Koch's postulates were fulfilled by re-isolating the pathogen from symptomatic tissue, which was subsequently confirmed as B. exigua through morphological and molecular analyses. Koch's postulates were fulfilled. To our knowledge, this is the first report of B. exigua causing leaf spot disease in P. notoginseng in China, which lays a foundation for further study and developing disease control methods.

Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus.

Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.

Towards parsimonious generative modeling of RNA families.

Generative probabilistic models emerge as a new paradigm in data-driven, evolution-informed design of biomolecular sequences. This paper introduces a novel approach, called Edge Activation Direct Coupling Analysis (eaDCA), tailored to the characteristics of RNA sequences, with a strong emphasis on simplicity, efficiency, and interpretability. eaDCA explicitly constructs sparse coevolutionary models for RNA families, achieving performance levels comparable to more complex methods while utilizing a significantly lower number of parameters. Our approach demonstrates efficiency in generating artificial RNA sequences that closely resemble their natural counterparts in both statistical analyses and SHAPE-MaP experiments, and in predicting the effect of mutations. Notably, eaDCA provides a unique feature: estimating the number of potential functional sequences within a given RNA family. For example, in the case of cyclic di-AMP riboswitches (RF00379), our analysis suggests the existence of approximately 1039 functional nucleotide sequences. While huge compared to the known <4000 natural sequences, this number represents only a tiny fraction of the vast pool of nearly 1082 possible nucleotide sequences of the same length (136 nucleotides). These results underscore the promise of sparse and interpretable generative models, such as eaDCA, in enhancing our understanding of the expansive RNA sequence space.

DNASCANNER v2: A Web-Based Tool to Analyze the Characteristic Properties of Nucleotide Sequences.

Throughout the process of evolution, DNA undergoes the accumulation of distinct mutations, which can often result in highly organized patterns that serve various essential biological functions. These patterns encompass various genomic elements and provide valuable insights into the regulatory and functional aspects of DNA. The physicochemical, mechanical, thermodynamic, and structural properties of DNA sequences play a crucial role in the formation of specific patterns. These properties contribute to the three-dimensional structure of DNA and influence their interactions with proteins, regulatory elements, and other molecules. In this study, we introduce DNASCANNER v2, an advanced version of our previously published algorithm DNASCANNER for analyzing DNA properties. The current tool is built using the FLASK framework in Python language. Featuring a user-friendly interface tailored for nonspecialized researchers, it offers an extensive analysis of 158 DNA properties, including mono/di/trinucleotide frequencies, structural, physicochemical, thermodynamics, and mechanical properties of DNA sequences. The tool provides downloadable results and offers interactive plots for easy interpretation and comparison between different features. We also demonstrate the utility of DNASCANNER v2 in analyzing splice-site junctions, casposon insertion sequences, and transposon insertion sites (TIS) within the bacterial and human genomes, respectively. We also developed a deep learning module for the prediction of potential TIS in a given nucleotide sequence. In the future, we aim to optimize the performance of this prediction model through extensive training on larger data sets.

A Critical Review on Some Recent Developments in Comparison of Biological Sequences

The present review highlights some of the very important contributions to non-alignment ways of comparing biological sequences, which may be genome sequences of nucleotides, protein sequences of amino acids, or sequences of protein secondary structures. The discussion centers around specific methods applicable to the comparison of three types of sequences. The methods of comparison of genome sequences are based on three pairs of biological groups of nucleotides; the same for protein sequences are based on either physio-chemical property values of amino acids or on classified groups of amino acids of different cardinalities obtained from the physio-chemical properties; the same for sequences of secondary structures of proteins are based on their sequential expressions of structure elements of cardinality three and four. Comparison is made in the time domain and also in the frequency domain. Different taxa of known phylogeny are considered for comparison. It tries to find out the specific method of comparison, which can show the exact phylogeny of the taxa. If a new sequence appears in the database, it becomes essential to know its phylogeny. For this purpose, a phylogenetic tree is drawn on the sequences of the known taxa together with this new sequence using the best possible method. If the species having this new sequence belongs to the old taxa, there is nothing to worry about. Otherwise, the species with the new sequence has to be studied separately. This is the general reason for the construction of a phylogenetic tree in any form of biological sequence comparison.

First report of the Horse nettle virus infecting tomato (Solanum lycopersicum L.) in the United States.

Tomato (Solanum lycopersicum L.), a member of the Solanaceae family, represents one of the most extensively cultivated vegetable species worldwide and traces its origin to western South America (Caruso et al. 2022). In a field survey conducted in 2023 in Bixby, Tulsa County, Oklahoma, distinct symptoms were noted in two plants: one exhibited mottling and cupping of leaves and brown discoloration on leaves, petioles, and stems, while the other displayed a downward curling of leaves. Leaf samples from both symptomatic tomato plants (labelled as K4 and K5) were collected, and total RNA was extracted individually via the TRI Reagent® method (Molecular Research Center Inc., Cincinnati, OH, USA). Subsequently, the RNA samples were pooled and subjected to high-throughput sequencing (HTS) on the NextSeq 500/550 high-output kit v2.5 (Illumina, U.S.A.) at the genomic facility, Oklahoma State University (Stillwater, OK). Total read count of 8,227,020 (average length =150.5 bp) was obtained, trimmed, and de novo assembled using CLC Genomics Workbench v22.0.1 (QIAGEN) and used for BLASTn and BLASTx analysis. Two contigs: 6,375 bp (average coverage 2,915.92, read count 142,538) and 3,564 bp (average coverage 3,035.91, read count 82,370) from the pooled sample showed 88.6% and 96.7% nucleotide identities with RNA 1 (OP292294) and RNA 2 (OP292295) of Horse nettle virus A (HNA-A) isolate MD-1, respectively. Sequences of both partial contigs (RNA 1, accession no. PP063196) and RNA 2, accession no. PP063197) were submitted to GenBank. The HTS data did not reveal any other viral or viroid sequences in these two tomato samples. To further confirm the presence of HNV-A, total RNA from K4 and K5 samples was tested individually by RT-PCR using HNV specific primers (Supplementary Table 1) based on the two partial contig sequences. The expected PCR products (491 bp and 451 bp) were obtained only from the K4 sample and none from the K5 sample. PCR products were extracted from an agarose gel, cloned into the pGEM®-T Easy vector (Promega), and transformed into Escherichia coli DH5α cells (New England Bio Labs). Two clones for each PCR product were sequenced by Sanger sequencing. Nucleotide sequence comparisons and BLASTn analysis of 491 bp and 451 bp showed 86% and 97% nucleotide identity with RNA 1 and RNA 2 of HNV-A isolate MD-1 (OP292294 and OP292295), respectively. Additionally, eight more leaf samples from eight different symptomatic tomato plants were collected in the same field and tested by RT-PCR as described above. All eight samples were positive by RT-PCR, but no PCR band was obtained in the total RNA from a healthy tomato leaf used as a control. Sequences from the PCR products were identical to the obtained HTS sequences. Our results confirmed for the first time that HNV-A can infect tomatoes. Currently, HNV-A has been reported to only infect a single weed (Horse nettle, Solanum carolinense) (Zhou et al. 2023). The identification of HNV-A in tomatoes in Oklahoma suggests a potential host shift is of concern for local growers as well as tomato growers worldwide. This shift underscores the urgency for an in-depth investigation into the transmission and host specificity of HNV-A. This is the first report in the United States and the world that HNV-A could infect tomatoes naturally in a grower field.

Molecular And Serological Detection Of Newcastle Disease Virus In Live-Bird Markets, Jos, Plateau State In Nigeria

Newcastle disease (ND) is a highly infectious viral disease of birds caused by the Newcastle disease virus (NDV) and it has been reported in domestic birds in Nigeria. Waterfowls and village poultry in live bird markets (LBM) acts as reservoirs, potentially reintroducing the virus to commercial poultry. This study aims at molecular and serological detection of NDV at live bird markets in Plateau State, Nigeria. A cross sectional analysis involved 309 pooled cloacal and tracheal swabs over three months were analyzed by reverse transcriptase polymerase chain reaction (RT-PCR), RT-qPCR, virus isolation and haemagglutination and haemagglutinationinhibition test (HA &amp;HI). Virus isolation was attempted in 9 to 11 days old specific antibody negative (SAN) embryonated chicken eggs and fifteen samples showed haemagglutination. Subsequent tests confimed nine of these as NDV positive through haemagglutination and haemagglutination inhibition (HI) tests. Conventional RT-PCR and RT-qPCR further validated five of the nine NDV positive isolates. The phylogenetic analysis of partial F gene nucleotide sequences revealed that all three isolates belonged to class II genotype XIV.2_XIVb. This finding underscores the persistent threat of NDV to local poultry, necessitating comprehensive virological surveillance to understand, isolate and characterize the virus in Nigeria. Therefore, monitoring for emerging lineages and sub-lineages in Nigeria birds is crucial for safeguarding commercial poultry production.

Investigation of Presumptive HIV Transmission Associated with Receipt of Platelet-Rich Plasma Microneedling Facials at a Spa Among Former Spa Clients - New Mexico, 2018-2023.

HIV transmitted through cosmetic injection services via contaminated blood has not been previously documented. During summer 2018, the New Mexico Department of Health (NMDOH) was notified of a diagnosis of HIV infection in a woman with no known HIV risk factors who reported exposure to needles from cosmetic platelet-rich plasma microneedling facials (vampire facials) received at a spa in spring 2018. An investigation of the spa's services began in summer 2018, and NMDOH and CDC identified four former spa clients, and one sexual partner of a spa client, all of whom received HIV infection diagnoses during 2018-2023, despite low reported behavioral risks associated with HIV acquisition. Nucleotide sequence analysis revealed highly similar HIV strains among all cases. Although transmission of HIV via unsterile injection practices is a known risk, determining novel routes of HIV transmission among persons with no known HIV risk factors is important. This investigation identified an HIV cluster associated with receipt of cosmetic injection services at an unlicensed facility that did not follow recommended infection control procedures or maintain client records. Requiring adequate infection control practices and maintenance of client records at spa facilities offering cosmetic injection services can help prevent the transmission of HIV and other bloodborne pathogens and ensure adequate traceback and notification in the event of adverse clinical outcomes, respectively.

Mutation of the Thap4 gene causes dwarfism and testicular anomalies in rats and mice.

The petit (pet) locus is associated with dwarfism, testicular anomalies, severe thymic hypoplasia, and high postnatal lethality, which are inherited in autosomal recessive mode of inheritance in rats with a Wistar strain genetic background. Linkage analysis localized the pet locus between 98.7Mb and 101.2Mb on rat chromosome 9. Nucleotide sequence analysis identified 2bp deletion in exon 2 of the Thap4 gene as the causative mutation for pet. This deletion causes a frameshift and premature termination codon, resulting in a truncated THAP4 protein lacking approximately two-thirds of the C-terminal side. Thap4 is expressed in various organs, including the testis and thymus in rats. To elucidate the biological function of THAP4 in other species, we generated Thap4 knockout mice lacking exon 2 of the Thap4 gene through genome editing. Thap4 knockout mice also exhibited dwarfism and small testis but did not show high postnatal lethality. Thymus weights of adult Thap4 knockout male mice were significantly higher compared to wild-type male mice. Although Thap4 knockout male mice were fertile, their testis contained seminiferous tubules with spermatogenesis and degenerative seminiferous tubules lacking germ cells. Additionally, we observed vacuoles in seminiferous tubules, and clusters of cells in the lumen in seminiferous tubules in Thap4 knockout male mice. These results demonstrate that spontaneous mutation of Thap4 gene in rats and knockout of Thap4 gene in mice both cause dwarfism and testicular anomalies. Thap4 gene in rats and mice is essential for normal testicular development, maintaining spermatogenesis throughout the entire region of seminiferous tubules.

Evaluation of Antifungal Effect of Allium jesdianum Bacterial Endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes

: Antimicrobial resistance (AMR) is the ability of microbes to survive and grow in the presence of antimicrobial drugs. Bacterial endophytes, which reside within plants, can promote plant growth and other essential activities. Endophytes have the potential to produce novel and unique products for use in modern medicine, agriculture, and industry. They may hold the key to combating drug-resistant strains by providing new antimicrobial compounds, potentially leading to the development of new medications. In this study, bacterial endophytes of Allium jesdianum were extracted and characterized. The antifungal effect of these endophytes on Rhizopus stolonifer, Penicillium, Cladosporium, and Trichophyton mentagrophytes was evaluated. Various parts of the plant were used to isolate ten bacterial endophytes to assess their antifungal properties. Universal eubacterial primers were used to amplify a 1500 bp region of the 16S rRNA gene. The resulting partial nucleotide sequences were compared with sequences available from the National Center for Biotechnology Information (NCBI) and EzBioCloud Database. Subsequent comparisons determined their similarity. Each isolated endophyte was cultured with equal amounts of R. stolonifer, Penicillium, Cladosporium, and T. mentagrophytes. This study measured the level of antagonism by assessing the extent of potential interactions. Ten bacterial endophytes, primarily cocci and bacilli, were extracted from different parts of A. jesdianum. The isolates were identified as Staphylococcus warneri AJB1, Staphylococcus succinus AJB2, Pseudomonas thivervalensis AJB3, Bacillus subtilis AJB4, Acinetobacter lwoffii AJB5, and Pantoea brenneri AJB6. AJB1 and AJB3 showed no antagonistic activity. AJB2, AJB5, and AJB6 displayed antagonistic action against R. stolonifer. Only AJB4 showed strong antagonistic activity against Penicillium. Further research is necessary to determine whether these endophytes possess antibiotic activity and can be used for food preservation.

Next step in Monachacantiana (Montagu, 1803) phylogeography: northern French and Dutch populations (Eupulmonata, Stylommatophora, Hygromiidae).

Features of shell and genitalia as well as nucleotide sequences of selected mitochondrial and nuclear genes of specimens of Monachacantiana from ten northern French and two Dutch populations were compared with the same features of British and Italian populations. They were found to be very similar to populations previously identified as belonging to the CAN-1 lineage of M.cantiana. This confirms previous suggestions that M.cantiana was introduced to western Europe (England, France and the Netherlands) in historical times.

Current status of Nosema spp. infection cases in apis mellifera in eurasian countries and Ptp3 gene haplotypes in the Republic of Tatarstan, Russia.

The current status of Nosema spp. infections in A. mellifera throughout Eurasia was characterized using electronic databases. Although N. ceranae was predominantly detected in southwestern and south-central regions and N. apis in northwestern and north-central areas, most studies reported the occurrence of both species in Eurasia. In addition, the occurrence of Nosema spp. and Ptp3 gene haplotypes was investigated in the Republic of Tatarstan, Russia. Most of the examined honey bees were infected with both N. apis and N. ceranae. N. apis and N. ceranae isolates were either heterozygous or belonged to different strains and showed infection with more than one strain. New haplotypes were found for N. apis and N. ceranae in the Republic of Tatarstan, Russia. This study expands the data regarding existing haplotypes of Nosema species: there are currently 9 shared and 56 unique Ptp3 nucleotide sequence haplotypes of N. ceranae, and 2 shared and 7 unique haplotypes of N. apis, respectively.

New Genera and Species of Caulobacter and Brevundimonas Bacteriophages Provide Insights into Phage Genome Evolution.

Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs.

The vicuna (Vicugna vicugna) as a natural host of Dictyocaulus filaria in Peru

Lungworm infection, or verminous pneumonia, is a parasitic disease that causes serious problems in small and large ruminants. Despite the fact that nematodes of the genus Dictyocaulus in cattle and sheep are the main cause of this disease, there are few studies on the natural infections of South American camelids. For this reason, this study aims to report the natural infection by Dictyocaulus filaria in vicunas (Vicugna vicugna) for the first time. During a shearing season (chaku) in Cuzco, Peru, two accidentally killed adult vicunas were submitted to the IVITA-Marangani research center in Cuzco for their respective necropsies. The tracheas of both vicunas had numerous nematodes, as seen during the necropsy. The nematodes were collected in 70% ethanol and were morphologically identified as D. filaria. Likewise, the DNA of six nematodes was extracted, and the ITS2 region and the 28S rRNA gene were amplified and sequenced. The nucleotide sequences of both genetic markers were up to 100% identical with previously reported D. filaria DNA sequences found in the goat yearlings from Turkey, sheep from Iran, Turkey, and India, and the argali from Uzbekistan, which confirmed the morphological diagnosis. This finding represents the first molecular confirmation of a natural D. filaria infection in a South American camelid. It will be necessary to carry out future studies to know the current situation of verminous pneumonia in domestic and wild South American camelids and to know the negative effects of the disease on them.

Identification of Bacteria and Viruses Associated with Patients with Acute Febrile Illness in Khon Kaen Province, Thailand.

The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93-97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness.