Nucleotide Sequence Analysis Research Articles

Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains.

Two approaches to the synthesis of 2D binary identifiers ("fingerprints") of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).

Identification, characterization and functional analysis of Rap1 in response to bacterial infection in tilapia

Rap1 (Ras-related protein 1), as a member of the Ras-like small GTP binding protein family, involves in the regulation of cell life activities and mediates a variety of biological events including cell junctions, cell polarity, cell proliferation and differentiation by binding to GDP/GTP. In addition, Rap1 also plays an important role in innate immune response by regulating the adhesion, diffusion and migration of white blood cells. However, it is still unclear how Rap1 affects the innate immunity of teleost fish against bacterial infections. In this study, we amplified the Rap1 from tilapia and conducted the sequence analysis of Rap1 nucleotide and amino acid sequences, then characterized its tissue distribution and expression pattern in response to pathogen infection in tilapia for the first time, and explored the bacteriostatic and bacterial binding effects of Rap1. The results showed that the Rap1 possessed a whole open reading frame (ORF) with 558 bp, encoding 185 amino acids. The Rap1 protein was highly homologous with Rap1 from other species. Conserved domain analysis revealed that Rap1 contained five G box domains that mediated its binding to ornithine. Rap1 mRNA was widely expressed in tilapia tissues, and the highest level was found in spleen. Under Streptococcus agalactiae (S. agalactiae) infection, the expression of Rap1 was significantly up-regulated in head kidney and brain. In addition, the recombinant protein Rap1 hold the ability binding to S. agalactiae and inhibit the proliferation of S. agalactiae. In conclusion, this study not only provided a reference for exploring the function of Rap1 in teleost against pathogen infection, but also enriched the basic theoretical research of Rap1 function and antibacterial immune response in teleost.

Molecular analysis of the blood cockle, Tegillarca granosa (Linnaeus 1758) from Indonesia

The blood cockle, Tegillarca granosa, is one of the key member of shellfish communities that are ecologically and economically important specially in Indonesia. We collected samples from four sites in Indonesia: Banyuwangi, Bali Island, Maros and Buru Island. Nucleotide sequence analysis was performed on PCR-amplified mitochondrial DNA COI gene. In total, 556-558 base pair nucleotide sequences were obtained from 12 individuals. Molecular analyses revealed samples belonging to the T. granosa species. Phylogenetic analyses were carried out by comparing the gene sequences of T. granosa haplotypes in Indonesia with gene sequences of the same base pair length and with the of Anadara tuberculosa which was used as an outgroup. The phylogenetic trees were consistent and indicated in the two sub-clades. The presence of T. granosa and the phylogenetic status of the T. granosa Indonesian haplotype were reported. Clarifying the phylogenetic status of ecologically important species provides basic information studies for possible future conservation and control programs.

Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China

BackgroundAtypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce.MethodsEleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined.ResultsIn abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein.ConclusionsWe reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China.

Molecular Characterization and Zoonotic Significance of Cryptosporidium spp. and Giardia duodenalis in Asymptomatic Adult Stray Cats and Dogs in Turkey

Background: Cryptosporidium species and Giardia duodenalis are important protozoan parasites due to their wide host range and potential as zoonotic diseases. These parasites, responsible for Cryptosporidiosis and Giardiasis, are significant health concerns and have garnered attention from both the public and veterinary fields. Pets, such as dogs and cats, are susceptible to these infections and play a crucial role in transmitting these protozoans to humans. This study was conducted to determine the prevalence, species, genotypes and zoonotic significance of Cryptosporidium and Giardia in asymptomatic adult stray cats and dogs. Methods: Fecal samples from 75 adult stray animal, 42 dogs and 33 cats, were collected in Diyarbakýr city, southeastern Anatolia, Turkey. Direct immunofluorescence test was used to confirm the presence of G. duoenalis cysts and cryptosporidium spp. oocysts in collected fecal samples. Microscopic analysis was used to count the number of cysts/oocysts per gram as specified by the manufacturer. Molecular confirmation was done with Polymerase chain reaction (PCR) using Giardia SSU-rDNA and Cryptosporidium spp. SSU rRNA gene. The secondary PCR products of all positive samples were sequenced in one directions on an automated sequencer. Nucleotide sequence analysis was performed by BLAST alignment using the National Center for Biotechnology Information database. Result: The prevalence of Cryptosporidium was 7.14% in 42 cats and 9.09% in 33 dogs. The prevalence of G. duodenalis was 23.80% in cats and 54.54% in dogs. The average number of Cryptosporidium spp. oocysts per gram of cat and dog feces was 1866.3 and 1813.3, respectively. The average number of G. duodenalis cysts per gram of cat and dog feces was 1011.6 and 4786, respectively. All Cryptosporidium isolates were determined as C. canis in dogs and C. felis in cats. C. canis and C. felis isolates identified in the study, MT329018.1 and MN696800.1, AF159113.1 and KM977642.1 showed similarity with Genbank number, respectively. Assemblages A, E, C, D were found in dogs and assemblages A and E in cats in the result of the sequence of 130 bp gene fragments obtained from G. duodenalis isolates. This study sequence analysis of G. duodenalis cat isolates identified assemblages A (50%/10) and E (50%/10). In this study, assemblage E was the most common genotype isolated in dogs (38.8%), followed by Assemblage C (27.7%), Assemblage D (16.6%) and Assemblage A (15.5%). Assemblage A, which has zoonotic importance, was detected in cats and dogs, while assemblage E in cats and dogs was reported for the first time in Turkey.

Molecular phylogenetic analysis of commercially important Asian monsoon scallop, Amusium pleuronectes (Linnaeus 1758) from Indonesia

The Asian monsoon scallop, Amusium pleuronectes, is a key member of shellfish communities that are the most commercially harvested in Asia. Materials were obtained from four sites in Indonesia: Semarang, Bali Island, Maros and Buru Island. Nucleotide sequence analysis was performed on PCR-amplified mitochondrial DNA 16S rRNA. In total, 556-558 base pair nucleotide sequences were obtained from 8 individuals. Molecular analyses revealed that the samples belong to the A. pleuronectes species. Phylogenetic analyses were carried out by comparing the gene sequences of A. pleuronectes haplotypes in Indonesia with gene sequences of the same base pair length and with the of A. japonicum which was used as an outgroup. The phylogenetic trees were consistent and indicated in the two sub-clades. The presence of A. pleuronectes and the phylogenetic status of the A. pleuronectes Indonesian haplotype were reported. Clarifying the phylogenetic status of ecologically important species provides basic information for biosecurity studies for possible future conservation and control programs.

A new Leccinum species from the Altai Mountains

A new Leccinum species has been described based on morphological and molecular data. Its characteristic features are medium-sized basidiomata, pores cream to cinnamon-brown, and a dark cream pileus with a light marble pattern. It grows under Salix bebbiana and occurs in southeast Altay Mts. We present detailed descriptions with color photos of fresh fruiting bodies, SEM photos of spores, molecular phylogeny, and an analysis of the characteristic nucleotide sequences compared to the related species.

Molecular detection and characterization of Rift Valley fever virus in humans and domestic ruminants in Nigeria

Rift Valley fever virus (RVFV) causes a zoonotic mosquito-borne disease of domestic livestock, wildlife and humans majorly in Africa and the Arabian Peninsula. The virus is a Phlebovirus belonging to the Family Phenuiviridae and constitutes a threat to both human and animal health. Although there has been serological evidence of RVFV in humans and animals in Nigeria, reports on its molecular detection and characterization are absent. Blood samples (n = 1101) were collected between January 2019 and March 2021 from humans, cattle and sheep in four States of Nigeria. The harvested plasma samples were tested using a commercial ELISA kit. All the ELISA-positive, ‘-doubtful’ and some ‘-negative’ samples (n = 436) were further analyzed using nested reverse transcriptase-polymerase chain reaction (nRT-PCR). Eight samples (humans, n = 1; cattle, n = 6; sheep, n = 1) that gave the expected band size of approximately 668 base pairs following gel electrophoresis were sequenced by Sanger method. The sequence data were edited using BioEdit software and RVFV was successfully identified in all of them. Nucleotide sequence and phylogenetic analyses revealed that these eight RVFV strains were 98.3–99.9% identical and clustered with the Ugandan Smithburn strain. Genotyping showed that they belonged to Lineage K. This report, which is the first molecular detection and characterization of RVFV in Nigeria, confirms the circulation of the virus in the country. It also highlights the need for large-scale surveillance for RVFV in Nigeria, including among mosquito vectors, to provide better understanding of its spatiotemporal epidemiology, and thus, aid in preventing potential RVF outbreaks in the country.

A novel mRNA rabies vaccine as a promising candidate for rabies post-exposure prophylaxis protects animals from different rabies viruses

Rabies, caused by the rabies virus (RABV), is the most fatal zoonotic disease. It is a neglected tropical disease which remains a major public health problem, causing approximately 59,000 deaths worldwide annually. Despite the existence of effective vaccines, the high incidence of human rabies is mainly linked to tedious vaccine immunisation procedures and the overall high cost of post-exposure prophylaxis. Therefore, it is necessary to develop an effective vaccine that has a simple procedure and is affordable to prevent rabies infection in humans. RABV belongs to the genus Lyssavirus and family Rhabdoviridae. Previous phylogenetic analyses have identified seven major clades of RABV in China (China I–VII), confirmed by analysing nucleotide sequences from both the G and N proteins.This study evaluated the immunogenicity and protective capacity of SYS6008, an mRNA rabies vaccine expressing rabies virus glycoprotein, in mice and cynomolgus macaques.We demonstrated that SYS6008 induced sufficient levels of rabies neutralising antibody (RVNA) in mice. In addition, SYS6008 elicited strong and durable RVNA responses in vaccinated cynomolgus macaques. In the pre-exposure prophylaxis murine model, one or two injections of SYS6008 at 1/10 or 1/30 of dosage provided protection against a challenge with a 30-fold LD50 of rabies virus (China I and II clades). We also demonstrated that in the post-exposure prophylaxis murine model, which was exposed to lethal rabies virus (China I–VII clades) before vaccination, one or two injections of SYS6008 at both 1/10 and 1/30 dosages provided better protection against rabies virus challenge than the immunization by five injections of commercial vaccines at the same dosage. In addition, we proved that SYS6008-induced RVNAs could neutralise RABV from the China I–VII clades. Finally, 1/10 of the dosage of SYS6008 was able to stimulate significant RABV-G specificity in the T cell response. Furthermore, we found that SYS6008 induced high cellular immunity, including RABV-G-specific T cell responses and memory B cells.Our results imply that the SYS6008 rabies vaccine, with a much simpler vaccination procedure, better immunogenicity, and enhanced protective capacity, could be a candidate vaccine for post-exposure prophylaxis of rabies infections.

Isolation and identification of Tete virus group (Peribunyaviridae: Orthobunyavirus) from Culicoides biting midges collected in Lichuan County, China.

In July 2018, a virus (JXLC1806-2) was isolated from Culicoides biting midges collected in Lichuan County, Jiangxi Province, China. The virus isolate showed significant cytopathic effects within 48 hours after inoculation with mammalian cells (BHK-21). JXLC1806-2 virus could form plaques in BHK-21 cells, and the virus titer was 1×105.6 pfu/mL. After inoculation with the virus, suckling mice developed disease and died. The nucleotide and amino sequence analysis showed that the JXLC1806-2 virus genome was composed of S, M and L segments. Phylogenetic analysis showed that the S, M and L genes of JXLC1806-2 virus belonged to the Tete serogroup, Orthobunyavirus, but formed an independent evolutionary branch from the other members of the Tete serogroup. The results showed that the JXLC1806-2 virus, which was named as Lichuan virus, is a new member of Tete serogroup, and this is the first time that a Tete serogroup virus has been isolated in China.

Phylogenetic analysis of the Klebsiella pneumoniae uge gene in local microbiological monitoring

The aim of the study was to evaluate the data of phylogenetically analyzed nucleotide sequences from the K. pneumoniae strain uge genes carried out in the perinatal center. Materials and methods. Fifty-six sequences of the K. pneumoniae uge gene were analyzed. The uge gene was detected by real-time PCR using DT light amplifier (Russia). Results. The rate of K. pneumoniae strains among patients of obstetric and gynecological departments in 2020–2023 averaged 1.4%. In pediatric hospitals, the isolation of K. pneumoniae strains comprised 12–14% in 2020, 2021 and 2023. In 2022, a fourfold decrease in detected K. pneumoniae strains was recorded. Phylogenetic analysis showed that the nucleotide sequences were significantly grouped into 14 clusters. The K. pneumoniae virulence factor uge gene is found in 64.3% cases. The nucleotide sequences allowed to detect heterogeneous K. pneumoniae strain population isolated from patients at the perinatal center from 2019 to 2023 analyzed by the phylogenetic method. There are clusters that combine K. pneumoniae genovariants isolated in 2019 and not replenished with new isolates, which confirms the effectiveness of ongoing anti-epidemic measures, enhanced during COVID-19 spread, excluding the transmission of an infectious agent from a source to a susceptible organism in nosocomial environment. P249Q, N279L amino acid substitutions within the uge gene were determined, which distinguish hypervirulent strains from those with a lower degree of pathogenicity. Out of five mother-child pairs, in four — nucleotide sequences of K. pneumoniae strain uge gene were genetically closer to each other than to other strains isolated from patients of the Medical Departments suggesting about a high degree of their relationship, highly likely indicating that the source of the strain for the child was the paired mother, and not the patients of the departments or the staff of the institution. In one mother-child pair, K. pneumoniae strains belonged to different clusters. The isolate obtained on 09/06/2021 from neonatal faeces (age: 7 days old) was grouped with strains isolated on 12/12/2020 from a patient in the maternity ward and in Laos in 2013 (CP035196). K. pneumoniae isolated on 06/04/2021 from the urine of a woman, was significantly grouped with strains included in cluster 13. Conclusion. An opportunity for improving local microbiological monitoring by sequencing and phylogenetic analysis of K. pneumoniae uge gene has been demonstrated. Assessment of changes in the intraspecies population pattern of HCAI pathogens is necessary for a timely and reasonable response to the deterioration of the epidemiological situation.

First molecular report of Feline panleukopenia virus infection in diarrheic cats at Can Tho City, Vietnam

Feline panleukopenia virus (FPV) belongs to the family Parvoviridae and causes an acute viral infection in cats worldwide. Information on the circulation of FPV among cats is currently limited in Vietnam. Herein, the full–length VP2 gene and molecular characteristics of FPV isolated in diarrhea cats in Can Tho City were first exhibited. Phylogenetic analysis based on seven obtained nucleotide sequences revealed that the isolated sequences were clustered into a narrow group with FPV sequences in the neighboring countries such as China, Thailand, and Japan, and distantly grouped with the vaccine strains. Regarding nucleotide and amino acid sequence analysis, the nucleotide and amino acid homology of 99.98–100% and 99.99–100% among obtained sequences, and showed high homology with reference sequences, accounting for 97.38–98.51% and 98.96–99.27%, respectively. Besides, the nucleotide and amino acid sequences were a homology of 98.51% and 99.26% with two vaccine strains in GenBank. Regarding amino acid translation, seven obtained sequences were closely related to FPV strains, meanwhile, they were different from CPV–2 strains in GenBank at amino acid substitutions of K80, K93 and V103. Overall, this is the first detection of FPV in diarrhea cats and illustrated the molecular characteristics of FPV in the cat population in Can Tho City of Vietnam.

Phylogenetic Analysis to Detect COVID Superspreaders

Aims: Detection of superspreading events by phylogenetic analysis of nucleotide sequences from a population of individuals collected from a narrow time interval.
 Study Design: Retrieve nucleic acid sequences, construct multiple sequence alignments, and build phylogenetic networks to determine sources of infection.
 Place and Duration of Study: This study was performed at the Delaware Biotechnology Institute of the University of Delaware over the period: June-August, 2022. The data used were from the GIS AID database.
 Methodology: Sequences for analysis were sampled from the GISAID initiative’s open-access SARS-CoV-2 genome database. We selected high-quality nucleotide sequences submitted by Delaware labs between March 18 and April 14, 2021, an important period of 4 weeks which saw the Alpha variant spread rapidly in the Delaware population.
 Results: Four sources accounted for 215 of the 401 sequences. In other words, 54% of all cases were rooted in just five sources.
 Conclusion: Thus, superspreading seems to have a major impact on the proportion of individuals in a population affected with COVID.

L1 Gene based Molecular Characterization of Bovine Papillomavirus Type 1 (BPV1) Isolated from Cutaneous Warts of Cattle, Maharashtra

Background: Bovine papillomatosis (BP) is distributed worldwide among cattle but is relatively less common in buffaloes. Prevalence of this disease is established in buffaloes from India and Italy caused by bovine papilloma virus (BPV). The current study aimed to study the detection of bovine papilloma virus from cutaneous warts by polymerase chain reaction and confirmed by nucleotide sequencing and phylogenetic analysis. Methods: In this study a total of 10 wart samples from affected cattle were aseptically collected. Grossly, most of cutaneous warts were of variable sizes, rough or coarse in texture, grayish/blackish/flesh colored, irregular in shape (dome or button) or resembling cauliflower-like masses and elevated from skin surface by broad base. Molecular characterization of viral DNA from wart samples and partial gene sequencing, its analysis were carried out by using bioinformatics tools to establish the phylogenetic relationship. Result: In our investigation it revealed that out of total 10 cutaneous wart tissue samples, only six cattle were positive for BPV-1 while all the samples were found negative for BPV-2. The phylogenetic analysis of BPV-1gene of papilloma virus of cattle showed 100% homology with already reported sequence from china. The BPV-1 partial sequences generated in present study revealed close homology as well as with the earlier published BPV-1 sequences on NCBI.

Alkyl Sulfatase of Cholera Vibrios

The aim of the work was to study the structure of the alkyl sulfatase (asu) gene in Vibrio cholerae strains of various serogroups, as well as to compare nucleotide and amino acid sequences of alkyl sulfatases using various methods of bioinformatic analysis.Materials and methods. 483 strains of V. cholerae O1, O139 and nonO1/nonO139 serogroups were employed in the work. The search for the gene, its recurrence, and localization was carried out applying the Blast software. The nucleotide and corresponding amino acid sequences of the gene, as well as its structure, were studied using bioinformatic analysis. Sequencing was performed on the MiSeq (Illumina) platform. The enzymatic activity was detected using a medium, confirming the presence/absence of the gene by PCR in vitro and in silico.Results and discussion. Bioinformatic analysis of the nucleotide and corresponding amino acid sequences of the asu gene has been carried out and its structure investigated. Four functional domains have been identified. In the beta-lactamase domain, a conservative amino acid sequence -HAHADH- has been found in all strains of cholera vibrios, which is part of the Zn2+ binding motif. It has been established that the alkyl sulfatase of cholera vibrios belongs to the family of Zn2+-dependent β-lactamases. Blast analysis has revealed the similarity of nucleotide and amino acid sequences of alkyl sulfatases in representatives of V. cholerae O1 and O139 serogroups (ctxAB+tcpA+) and representatives of the genera Aeromonas and Pseudomonas, which is in the line with the data of 3D modeling of the amino acid sequence structures of the alkyl sulfatase enzyme in these microorganisms. The bioinformatic analysis of nucleotide and amino acid sequences of alkyl sulfatases in cholera vibrios has showed the conservativeness of these sequences in toxigenic strains and the presence of a number of single mutations in the asu gene in atoxigenic ones. The presence or absence of the asu gene has been established by PCR in vitro and in silico and confirmed by the results obtained using the Blast program. It is demonstrated that the presence/absence of the asu gene correlates with the ability/inability of O139 strains to hydrolyze SDS on the medium. These results can be used in studying mechanisms of cholera vibrios adaptation, persistence and pathogenicity.

Molecular Characterization of Lyssaviruses Originating from Domestic and Wild Cats Provides an Insight on the Diversity of Lyssaviruses and a Risk of Rabies Transmission to Other Susceptible Mammals and Humans in South Africa.

Rabies is one of the most significant public and veterinary health problems, causing approximately 59,000 human deaths annually in the developing countries of Asia and Africa. The aetiologic agent, a viral species of the Lyssavirus genus, is highly neurotropic and has a wide host range, including terrestrial mammals and several Chiropteran species. The Lyssavirus mokola (MOKV) was first isolated in the late 1960s from organ pools of shrews (Crocidura flavescens manni) in the Mokola forest (Nigeria). To date, at least 30 MOKV isolations have been confirmed, all exclusively from Africa, with 73% from southern Africa. There is limited knowledge about the epidemiology of MOKV, and the reservoir host species is unknown. Here, we report on the molecular characterization of rabies viruses originating from both domestic and African wild cats. A partial region of the lyssavirus genome, encoding the nucleoprotein, was amplified and sequenced. Nucleotide sequence analysis demonstrated that 98% of cats were infected with both the canid and mongoose rabies virus variants, as well as a rare lyssavirus, Lyssavirus mokola, from a domestic cat from Eswatini. Furthermore, the nucleotide sequence divergence between the recently identified MOKV isolate and the historical Lyssavirus mokola isolates ranged from 6.8% to 8.3%. This study further highlights the association between the potential host species of Lyssavirus mokola and the domestic cat as an incidental host, and the important role cats may play in rabies transmission dynamics in the country. Therefore, continuous vaccination of domestic cats against rabies is crucial, even after the elimination of dog-mediated rabies, as spillover related to sylvatic rabies cycles is likely to occur.

Distribution and molecular characterization of saffold virus and human cosavirus in children admitted to hospitals with acute gastroenteritis in Thailand, 2017-2022.

Saffold virus (SAFV) and human cosavirus (HCoSV) are emerging viruses of the Picornaviridae family. They have been shown to associate with gastrointestinal infection and more recently these viruses have also been demonstrated to associate with other clinical infections such as the respiratory tract, cardiovascular system, and the cerebral ventricular system. In this study, 2459 stool specimens collected from pediatric patients admitted to hospitals with acute gastroenteritis from January 2017 to December 2022, were screened for SAFV and HCoSV utilizing reverse transcription-polymerase chain reaction. Positive samples were then characterized into genotypes via nucleotide sequencing and bioinformatic analysis. Of the 2459 samples, 21 and 39 were positive for SAFV (0.9%) and HCoSV (1.6%), respectively. Three genotypes of SAFV were identified-SAFV-1 (38%), SAFV-2 (24%), and SAFV-3 (38%). Two genetic groups of HCoSV were identified-HCoSV-C (97%) and HCoSV-A (3%), demonstrating a large increase of HCoSV-C as compared to those reported previously from the same geographical region in Thailand. This study provides the prevalence of SAFV and HCoSV genotypes in Chiang Mai, Thailand during a period of 6 years from 2017 to 2022.

Metatranscriptome-Based Analysis of Viral Incidence in Jujube (Ziziphus jujuba) in Korea

This work investigated the viral infection in jujube plants in Korea. A total of 61 samples with the symptoms of putative viral infection were collected from experimental fields and orchards. Thereafter, the samples were subjected to metatranscriptome analysis, Reverse transcription polymerase chain reaction analysis, and nucleotide sequence analysis. These analyses identified the presence of two DNA viruses, jujube-associated badnavirus (JuBV), jujube mosaic-associated virus (JuMaV), and one RNA virus, jujube yellow mottle-associated virus (JYMaV). All samples collected were confirmed to be infected by at least one of the three viruses, with most showed multiple infections. The detection rates of JuBV, JYMaV, and JuMaV were 100%, 90.2%, and 8.2%, respectively. Only three combinations of viral infections were found: 9.8% of samples showed single infection of JuBV, 82.0% showed double infection of JuBV+JYMaV, and 8.2% showed triple infection of JuBV+JYMaV+JuMaV. Sequence analysis of the three viruses showed very high homology with respective virus isolates reported in China. This study is predicted to provide fundamental data to produce virus-free jujube seedlings and represents the first report of JuBV and JuMaV infection in Korea.

Association of a novel begomovirus species with fenugreek yellow vein disease in India.

Fenugreek (Trigonella foenum-graecumL.) is an annual medicinal and spice crop belonging to the family Fabaceae. The occurrence of a yellow vein disease was recorded in fenugreek in Jodhpur (India) in 2022. The infection of begomoviruses in legume crops results in significant yield loss and major economic loss. The current study reports an association of a novel begomovirus species associated with yellow vein disease in Fenugreek. In symptomatic fenugreek plants, geminivirus-like particles were visible under a transmission electron microscope. Further, nucleotide sequence analysis of the rolling circle amplified product revealed 2743 nucleotide DNA-A genome with close relatedness to French bean leaf curl virus (88.21%) and Senna leaf curl virus (87.63%). It was proposed as a new begomovirus species, Fenugreek yellow vein Rajasthan virus. The genome organization suggested the presence of a typical nonanucleotide sequence along with 7 ORFs in DNA-A. A possible recombination event took place in the coat protein (V1) region with Pedilanthus leaf curl virus and Chilli leaf curl virus as major and minor parents. The recombinant virus poses possible threats to several other legume crops. To the best of our knowledge, this is the first report of the association of FeYVRaV with fenugreek yellow vein disease from northwestern India. In conclusion, the presence of a novel begomovirus species associated with yellow vein disease in fenugreek is alarming and needs further studies on its infectivity to prevent its spread to legume crops.

Zoonotic simian malaria parasites in free-ranging Macaca fascicularis macaques and human malaria patients in Thailand, with a note on genetic characterization of recent isolates

Despite the natural occurrences of human infections by Plasmodium knowlesi, P. cynomolgi, P. inui, and P. fieldi in Thailand, investigating the prevalence and genetic diversity of the zoonotic simian malaria parasites in macaque populations has been limited to certain areas. To address this gap, a total of 560 long-tailed macaques (Macaca fascicularis) and 20 southern pig-tailed macaques (M. nemestrina) were captured from 15 locations across 10 provinces throughout Thailand between 2018 and 2021 for investigation of malaria, as were 15 human samples residing in two simian-malaria endemic provinces, namely Songkhla and Satun, who exhibited malaria-like symptoms. Using PCR techniques targeting the mitochondrial cytb and cox1 genes coupled with DNA sequencing, 40 long-tailed macaques inhabiting five locations had mono-infections with one of the three simian malaria species. Most of the positive cases of macaque were infected with P. inui (32/40), while infections with P. cynomolgi (6/40) and P. knowlesi (2/40) were less common and confined to specific macaque populations. Interestingly, all 15 human cases were mono-infected with P. knowlesi, with one of them residing in an area with two P. knowlesi-infected macaques. Nucleotide sequence analysis showed a high level of genetic diversity in P. inui, while P. cynomolgi and P. knowlesi displayed limited genetic diversity. Phylogenetic and haplotype network analyses revealed that P. inui in this study was closely related to simian and Anopheles isolates from Peninsular Malaysia, while P. cynomolgi clustered with simian and human isolates from Asian countries. P. knowlesi, which was found in both macaques and humans in this study, was closely related to isolates from macaques, humans, and An. hackeri in Peninsular Malaysia, suggesting a sylvatic transmission cycle extending across these endemic regions. This study highlights the current hotspots for zoonotic simian malaria and sheds light on the genetic characteristics of recent isolates in both macaques and human residents in Thailand.