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Porcine hemagglutinating encephalomyelitis virus (PHEV) is the only known porcine neurotropic coronavirus, which is prevalent worldwide at present. It is of great significance to understand the genetic and evolutionary characteristics of PHEV in order to perform effective measures for prevention and control of this disease. In this study, a total of 6,986 tissue samples and nasopharyngeal swabs were collected from different regions of Guangxi province in southern China during 2021-2024, and were tested for PHEV using a quadruplex RT-qPCR. The positivity rate of PHEV was 2.81% (196/6,986), of which tissue samples and nasopharyngeal swabs had 2.05% (87/4,246) and 3.98% (109/2,740) positivity rates, respectively. Fifty PHEV positive samples were selected for PCR amplification and gene sequencing. Sequence analysis revealed that the nucleotide homology and amino acid similarities of S, M, and N genes were 94.3%-99.3% and 92.3%-99.2%, 95.0%-99.7% and 94.7%-100.0%, 94.0%-99.5% and 93.5%-99.3%, respectively, indicating M and N genes were more conservative than S gene. Phylogenetic trees based on these three genes revealed that PHEV strains from different countries could be divided into two groups G1 and G2, and the PHEV strains from Guangxi province obtained in this study distributed in subgroups G1c and G2b. Bayesian analysis revealed that the population size of PHEV has been in a relatively stable state since its discovery until it expanded sharply around 2015, and still on the slow rise thereafter. S gene sequences analysis indicated that PHEV strains existed variation of mutation, and recombination. The results indicated that the prevalent PHEV strains in Guangxi province had complex evolutionary trajectories and high genetic diversity. To the best of our knowledge, this is the first report on the genetic and evolutionary characteristics of PHEV in southern China. [ABSTRACT FROM AUTHOR]

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potential cure for myelodysplastic neoplasms (MDSs) and other hematologic malignancies. This study investigates post-transplantation genetic evolution and telomere dynamics in hematopoietic cells, with a focus on clonal hematopoiesis (CH). We conducted a longitudinal analysis of 21 MDS patients who underwent allo-HSCT between September 2009 and February 2015. Genetic profiles of hematopoietic cells from both recipients and donors were compared at equivalent pre- and post-transplantation time points. Targeted sequencing identified CH-associated mutations, and real-time quantitative PCR measured telomere length. Furthermore, we compared CH incidence between recipients and age-matched controls from the GENIE cohort from routine health checkups. Post-allo-HSCT, 38% of recipients developed somatic mutations not detected before transplantation, indicating de novo CH originating from donor cells. Compared to age-matched healthy controls, recipients showed a significantly higher incidence of CH, suggesting increased susceptibility to genetic changes post-transplant. Telomere length analysis also revealed accelerated shortening in transplanted cells, highlighting the heightened stress and proliferation demands in the new microenvironment. Our findings reveal a notable incidence of donor-derived CH in allo-HSCT recipients, alongside significant telomere attrition. This suggests the potential influence of the marrow microenvironment on genetic and molecular changes in hematopoietic cells. [ABSTRACT FROM AUTHOR]

Simple Summary: Feline coronavirus (FCoV), as one of the important pathogens of feline viral gastroenteritis, has been attracting great attention. In this study, a total of 1869 rectal and nasal swabs, feces, and ascites samples from Guangxi province in southern China were collected during 2021–2024 and a positivity rate of 17.66% (330/1869) for FCoV was found. The nucleotide and amino acid homologies of S, M, and N genes were 81.2–99.6% and 70.2–99.5%, 89.9–100% and 91.6–100%, and 90.1–100% and 91.5–100%, respectively. All 63 FCoV strains obtained in this study belonged to type I FCoV (FCoV-I). Recombinant signals were detected in the S gene of FCoV strains GXLZ03-2022 and GXLZ08-2022, and in the CCoV strain GD/2020/X9. The results indicate that FCoV is still prevalent in Guangxi province, and the prevalent FCoV strains show high genetic diversity and novel epidemic characteristics. Feline coronavirus (FCoV), as one of the important pathogens of feline viral gastroenteritis, has been attracting great attention. A total of 1869 rectal and nasal swabs, feces, and ascites samples were collected from eight regions in Guangxi province during 2021–2024. The multiplex RT-qPCR established in our laboratory was used to test these samples for FCoV, and 17.66% (330/1869) of the samples were positive for FCoV. The S, M, and N genes of 63 FCoV-positive samples were amplified and sequenced, and the genetic and evolutionary characteristics were analyzed. Similarity analysis showed that the nucleotide and amino acid homologies of S, M, and N genes were 81.2–99.6% and 70.2–99.5%, 89.9–100% and 91.6–100%, and 90.1–100% and 91.5–100%, respectively. Phylogenetic analysis revealed that all 63 FCoV strains, based on S gene sequences, belonged to type I FCoV (FCoV-I), and were clustered with Chinese strains and the Netherlands UU strains. Recombinant signals were detected in the S gene of strains GXLZ03-2022, GXLZ08-2022, and CCoV GD/2020/X9. The results suggest that FCoV is still prevalent in the Guangxi province of southern China, and the prevalent FCoV strains show high genetic diversity and novel epidemic characteristics. [ABSTRACT FROM AUTHOR]

Human Prk kinase plays an important role in the maintenance of inflammatory stability and has been established as an attractive target of diverse rheumatic immune diseases. The kinase possesses a highly conserved polo-box domain (PBD) in its C-terminal noncatalytic region, which exhibits a wide specificity across its various substrates to regulate the kinase-mediated substrate phosphorylation. In this study, peptide quantitative structure-activity relationship (pQSAR) was systematically modeled based on a gene ontology-enriched set of Prk PBD-binding peptide data, which was structurally characterized using global descriptors and statistically correlated with peptide affinities via both linear and nonlinear machine learning regressions. The optimal pQSAR predictor was then employed to guide the genetic evolution (GE) of a random peptide group toward improved potency to Prk PBD domain, from which a number of hits were measured to have moderate or high affinity. The resulting Pm7 peptide was determined as a good binder that can effectively interact with the domain at sub-micromolar level, which was then used as a parent template to further derive other promising candidates by combining systematic residue mutagenesis and structure-based rescoring. Two Pm7-derived counterparts Pm72 and Pm74 were rationally designed to exhibit a satisfactory binding profile to Prk PBD domain, with affinity improved by 3.1-fold and 4.6-fold relative to their parent Pm7. Structural and energetic analyses revealed that the potent Prk PBD-binding sequences can be divided into a N-terminal polar section, a middle positively charged anchor and a C-terminal hydrophobic section, thus conferring both stability and specificity to the domain-peptide recognition and association. [ABSTRACT FROM AUTHOR]

Background: The clinical performance of RHDO‐based NIPD for PKU during early gestation remains under‐evaluated. Furthermore, studies focused on SNP loci obtained by next‐generation sequencing to analyze the genetic evolution of pathogenic variations in PKU is limited. Methods: Maternal peripheral blood, along with proband and paternal samples, was collected between 7 and 12 weeks of gestation. The PAH gene and surrounding high heterozygosity SNPs were targeted for enrichment and sequencing. Fetal genotypes were inferred using RHDO‐based NIPD. High‐resolution PAH haplotypes were used for the analysis of two common pathogenic variants in the Chinese population: c.728G>A and c.1238G>C. Results: Sixty one PKU families participated with an average fetal fraction of 6.08%. The median gestational age was 8+6 weeks. RHDO‐based NIPD successfully identified fetal genotypes in 59 cases (96.72%, 59/62). Two cases failed because of insufficient informative SNPs. In addition, a recombination event was assessed in one fetus of 59 cases. Six, and three haplotypes were identified for c.728G>A(p.Arg243Gln) and c.1238G>C(p.Arg413Pro), respectively. Hap_3 and hap_8 were identified as the ancestral haplotypes for these pathogenic variants, with other haplotypes arising from mutations or recombination based on these ancestral haplotypes. Conclusions: This study validates the feasibility of an RHDO‐based assay for NIPD of PKU in early pregnancy and introduces its application in the demonstration of founder effects in recurrent pathogenic variations, offering new insights into the evolutionary analysis of PAH variations. [ABSTRACT FROM AUTHOR]

Gyrovirus (GyV) is small, single-stranded circular DNA viruses that has recently been assigned to the family Anelloviridae. In the last decade, many GyVs that have an apparent pan-tropism at the host level were identified by high-throughput sequencing (HTS) technology. As of now, they have achieved global distribution. Several species of GyVs have been demonstrated to be pathogenic to poultry, particularly chicken anemia virus (CAV), causing significant economic losses to the global poultry industry. Although GyVs are highly prevalent in various birds worldwide, their direct involvement in the etiology of specific diseases and the reasons for their ubiquity and host diversity are not fully understood. This review summarizes current knowledge about GyVs, with a major emphasis on their morphofunctional properties, epidemiological characteristics, genetic evolution, pathogenicity, and immunopathogenesis. Additionally, the association between GyVs and various diseases, as well as its potential impact on the poultry industry, have been discussed. Future prevention and control strategies have also been explored. These insights underscore the importance of conducting research to establish a virus culture system, optimize surveillance, and develop vaccines for GyVs. [ABSTRACT FROM AUTHOR]

Chemical signals are crucial in mediating ecological and evolutionary adaptation of plants to their environments. Indeed, invasive plants may produce greater amounts of chemical metabolites in their new ranges. Some of these chemicals can enhance their mutualistic interactions and improve invasive plant performance, but genetic mechanisms of such adaptations are unexplored.We used Triadica sebifera plants as a model to investigate evolutionary changes in chemical signals that enhance arbuscular mycorrhizal (AM) fungal associations. Previous studies found that T. sebifera plants from invasive populations had higher root exudate concentrations of the flavonoid quercetin and elevated AM fungal colonization compared with those from native populations. Here, we explored genetic variation in strigolactone concentrations in root exudates and their contribution to AM fungal colonization with strigolactone analogue GR24 additions. In addition, we studied how gene expression patterns related to flavonoid and strigolactone biosynthesis varied among invasive and native populations using comparative genomics, transcriptomics and fluorescent real‐time quantitative PCR.We found that plants from invasive populations had higher concentrations of the strigolactone 5‐deoxystrigol in root exudates that were correlated with higher AM fungal colonization rates, relative to those from native populations. Exogenous applications of GR24, a synthetic analogue of 5‐deoxystrigol, increased AM fungal colonization. We found higher expression of a single gene in flavonoid (FLS) and strigolactone (DAD1) biosynthesis pathways increased levels of quercetin and 5‐deoxystrigol in plants from invasive populations, respectively.Synthesis. Understanding the role of genetic evolution in enhancing mutualisms of invasive plants provides new insights into the underlying mechanisms of plant invasion. This study suggests that an invasive plant enhanced its mutualisms by upregulating the expression of key genes related to secondary metabolites in root exudates which stimulate symbiotic relationships with AM fungi. Thus, these findings provide insights into genetic mechanisms that underlie higher AM fungal colonization and enhanced invasive plant performance. [ABSTRACT FROM AUTHOR]

Chloroplasts and mitochondria, descendants of ancient prokaryotes via endosymbiosis, occupy a pivotal position in plant growth and development due to their intricate connections with the nuclear genome. Genes encoded by the nuclear genome but relocated to or being functional within these organelles are commonly referred as organelle-targeting nuclear genes (ONGs). These genes are essential for maintaining cytonuclear coordination, thereby determining the stability of the life cycle. While molecular function and cytonuclear coordination of some endosymbiosis-derived ONGs (E-ONGs) have been extensively studied, the evolutionary history and characteristics from a more widespread range of non-endosymbiosis-derived ONGs (NE-ONGs) remain largely enigmatic. In this study, we focused on 12 representative species within the Poaceae family to systematically identify NE-ONGs and investigated their evolutionary history and functional significance on a phylogenetic timescale. Upon aligning these 12 species' evolutionary histories, we observed the following phenomena: (i) an exploration of NE-ONGs between the BOP and PACMAD clades unveiled dynamic compositions, potentially influencing their photosynthetic divergence; (ii) the majority of the abundant species-specific NE-ONGs exist in a single-copy status, and functional enrichment analysis further underscored their specialized roles, which could be crucial for species adaptation; and (iii) comparative analyses between plasmid- and mitochondria-related NE-ONGs (pNE-ONGs and mNE-ONGs) revealed a prevalence of pNE-ONGs, indicating tighter control for chloroplast function in Poaceae. In summary, this study offers novel insights into the cytonuclear co-evolutionary dynamics in Poaceae speciation and draws attention to crop improvement by using NE-ONGs. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Preventive Veterinary Medicine / Zhongguo Yufang Shouyi Xuebao is the property of Chinese Journal of Preventive Veterinary Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Simple Summary: Bovine coronavirus (BCoV), bovine rotavirus, bovine viral diarrhea virus, and bovine astrovirus are the most common intestinal pathogenic viruses causing diarrhea in cattle. BCoV was the major pathogen detected, with a positive rate of 34.02% (560/1646) from January 2020 to August 2023. The asymptomatic BCoV-infected rate (351/1646) was higher than the diarrhea BCoV-infected rate (209/1646). Studying the relevance of diarrhea associated with BCoV has shown that the onset of diarrheal symptoms post-infection is strongly correlated with the cattle's age and may also be related to the breed. One the other hand, we amplified and sequenced the hemagglutinin esterase (HE), spike protein, and whole genomes of the partially positive samples and obtained six complete HE sequences, seven complete spike sequences, and six whole genomes. The results of molecular characterization revealed that six strains were in the GⅡb subgroup, and HBSJZ2202 and JSYZ2209 had four amino acid insertions on HE. We also analyzed ORF1a and found disparities across various regions within GIIb, which were positioned on separate branches within the phylogenetic tree. This work provides data for further investigating the epidemiology of BCoV and for understanding and analyzing BCoV distribution and dynamics. Bovine coronavirus (BCoV), bovine rotavirus, bovine viral diarrhea virus, and bovine astrovirus are the most common intestinal pathogenic viruses causing diarrhea in cattle. We collected 1646 bovine fecal samples from January 2020 to August 2023. BCoV was the major pathogen detected, with a positive rate of 34.02% (560/1646). Of the 670 diarrheal samples and 976 asymptomatic samples, 209 and 351 were BCoV-positive, respectively. Studying the relevance of diarrhea associated with BCoV has shown that the onset of diarrheal symptoms post-infection is strongly correlated with the cattle's age and may also be related to the breed. We amplified and sequenced the hemagglutinin esterase (HE), spike protein, and whole genomes of the partially positive samples and obtained six complete HE sequences, seven complete spike sequences, and six whole genomes. Molecular characterization revealed that six strains were branched Chinese strains, Japanese strains, and partial American strains from the GⅡb subgroup. Strains HBSJZ2202 and JSYZ2209 had four amino acid insertions on HE. We also analyzed ORF1a and found disparities across various regions within GIIb, which were positioned on separate branches within the phylogenetic tree. This work provides data for further investigating the epidemiology of BCoV and for understanding and analyzing BCoV distribution and dynamics. [ABSTRACT FROM AUTHOR]

Objective To analyze the genetic evolution and molecular characteristics of the H5N6 avian influenza virus A/Changsha/1/2022(H5N6) in a human infection case in Changsha City, providing insights for the prevention and control of H5N6 avian influenza transmission to humans. Methods The sample underwent whole-genome sequencing on a third-generation sequencing platform. Reference sequences were downloaded from the NCBI and GISAID databases for comparison. The phylogenetic tree was constructed and key amino acid mutation sites were analyzed using MEGA7 software. Results The sequence analysis results revealed that the strain studied belongs to the H5 subtype Clade 2.3.4.4b branch. The PB1 gene shared 99.69% homology with the H5N6 virus A/duck/Hunan/S40199/2021(H5N6) from Hunan Province; PB2 had 98.58% homology with A/Whooper swan/Sanmenxia/Y36/2020(H5N8); and other sequences showed high homology with the strain A/Guangdong/1/2021(H5N6) discovered in Guangzhou in 2021. These results indicate that an infection with a recombinant H5N6 subtype avian influenza virus caused the case. The amino acid composition of the cleavage site was RERRRKR ↓GLF, consistent with high-pathogenicity avian influenza characteristics. The HA sequence showed no mutations at the Q226L and G228S sites, indicating the preservation of characteristics binding to avian receptors. However, mutations at the S127P, S137A, T160A, T192R, and A267T sites increased the virus's affinity for humans. A deletion found in positions 59-70 of the NA protein stalk implies enhanced viral virulence in mammals. Mutations were noted in the internal genes; S622G in PB1, K389R and V598T in PB2, N409S in PA, N30D and T215A in M1, and P42S in NS1, which may enhance the virulence of avian influenza virus in infecting mice. Conclusions The H5N6 virus strain detected in a human case in Changsha City in this study is highly pathogenic, prone to bind to avian receptors, but numerous mutations at key amino acid sites facilitate infection in humans. Continuous monitoring and research on H5N6 avian influenza virus should be strengthened [ABSTRACT FROM AUTHOR]

The article discusses the avian influenza A (H7N5) outbreak, emphasizing the importance of monitoring less common subtypes like H7N5 due to their potential to mutate into highly pathogenic strains. While H7N5 is not widely known compared to other subtypes, a recent outbreak in Germany highlights the need for continuous surveillance and research to prevent major outbreaks. The genetic potential of viruses like H7N5 underscores the necessity of robust surveillance, research, and preparedness strategies to mitigate their impact and prevent widespread disease outbreaks. The establishment of an epidemiological monitoring group is crucial to stay ahead of potential new outbreaks and ensure effective management. [Extracted from the article]

【Objective】The study aimed to isolate Escherichia coli without virulence genes and antibiotic resistance from pig intestines and to analyze their growth performance and genetic evolution, with a view to laying a foundation for the development of microecologics or oral vaccines for pigs.【Method】Fecal samples of 11 and 15 healthy adult pigs were collected from two pig farms in Guangdong Province, respectively. First, E. coli strains were isolated by McConkey plate and identified by 16S rRNA gene sequencing. Then, PCR was used to verify whether the selected E. coli contained 13 common virulence genes of pig pathogenic E. coli. Antimicrobial susceptibility tests were performed with 7 classes (14 kinds) of antimicrobial agents. Finally, the growth curves of selected E. coli strains were analyzed, and a phylogenetic tree was constructed based on the extracted genome sequences.【Result】Among 260 suspected E. coli strains, 206 strains were identified as E. coli by 16S rRNA gene sequencing analysis. 107 strains of E. coli did not contain 13 common virulence genes, of which 25 strains were sensitive to 7 classes (14 kinds) of antibiotics. Among the 25 E. coli strains, 23 non-pathogenic and non-antibiotic resistant E. coli strains (numbered as 2-9, 3-2, 3-4, 5-1, 6-1, 6-2, 6-9, 6-10, 8-2, 8-9, 10-5, B-4, B-6, B-7, B-10, D-10, E-2, E-10, J-1, J-4, K-6, L-6 and O-9) showed similar growth performance to E. coli Nissle 1917 and MG1655, and 2 E. coli strains (numbered as 6-4 and 5-2) showed higher growth rates than those of E. coli Nissle 1917 and MG1655. Among them, 10 strains (numbered as E-10, E-2, 6-4, 6-9, 8-2, O-9, 3-2, 6-2, J-1, K-6) had good acid tolerance and may be suitable for long-term colonization in the gastrointestinal tract of pigs. The phylogenetic tree analysis based on SNP core genome showed that 9 strains (numbered as 3-2, 6-10, 10-5, 6-1, 8-9, 5-2, L-6, O-9 and K-6) of the 25 strains were in the same group at the beginning of the phylogenetic tree, which were most likely to belong to the ancestral group of pig native E. coli.【Conclusion】Based on the comprehensive analysis of antibiotic sensitivity, growth performance, genome-wide evolutionary tree and gastric environment tolerance, one strain (numbered as O-9) was dominant in these four aspects. The growth kinetics of this strain is similar to or even better than that of E. coli Nissle 1977 and MG1655, which means that O-9 strain of E. coli isolates was likely to be high-quality pig native E. coli strain, with great research potential.

Abstract During the last decade, porcine epidemic diarrhea virus has detrimental consequences on swine industry, due to severe outbreaks especially in the suckling piglets. In March 2013, an outbreak was reported on a commercial swine farm in Guangdong Province, Southern China. A wild-type PEDV strain named as CHYJ130330 was identified, complete genome was sequenced and deposited in GenBank (accession no. KJ020932). The molecular epidemiological including evolutionary characteristics and pathogenicity assessment were explored during this study with particular interest and focus to develop this candidate strain for new vaccine. The isolates from China pre- and post-2013 shared 96.5–97.2% and 97–99% nt identity respectively with wild-type CHYJ130330 strain which during experimental studies has demonstrated high virulence and 100% mortality in 104 TCID50 group piglets within 5 days. The 22 reference strains selected from other parts of the world shared 98–99% identity with our sequence except Chinese (CV777) and S. Korean (vir.DR13, SM98 and atten.DR13) strains sharing 96.8, 97.6, 96.6 and 97.1% identity respectively. The phylogenetic tree revealed most strains reported after 2013 in GII genogroup while the prototype (CV777), S.korean and earlier Chinese (JS2008, 85-7mutant, Atten.vaccine, SD-M, LZC and CH/S) were GI Group. The amino acid sequence of CHYJ130330 E and M protein is highly conserved while ORF3 and N protein having 9 and 17 amino acid substitutions respectively in comparison to CV777 strain. The comparison of full length genome and the structural proteins revealed variations signifying that PEDV variant strains are still the main source of outbreaks in spite of continuous vaccination and also explain the variable trend of large scale outbreaks during this decade as compared to sporadic tendency of disease found before 2010. It is evident from this study that Chinese strains display significant level of mixing with the strains reported from other countries. The strain CHYJ130330 was also adapted successfully to Vero cell line and has shown high virulence in piglets. The information/findings will be helpful to develop a strategy for control of PEDV and have also shown that CHYJ130330 strain has strong virulence and is a more popular clinical strain in recent years, which has the potential to be developed into PEDV vaccine.

Avihepadnavirus is a genus of the Hepadnaviridae family. It primarily infects birds, including species of duck, geese, cranes, storks, and herons etc. To understand the genetic relatedness and evolutionary diversity among avihepadnavirus strains, a comprehensive analysis of the available 136 full-length viral genomes (n = 136) was conducted. The genomes were classified into two major genotypes, i.e., GI and GII. GI viruses were further classified into 8 sub-genotypes including DHBV-I (duck hepatitis B virus-I), DHBV-II (Snow goose Hepatitis B, SGHBV), DHBV-III, RGHBV (rossgoose hepatitis B virus), CHBV (crane hepatitis B virus), THBV (Tinamou hepatitis B virus), STHBV (stork hepatitis B virus), and HHBV (Heron hepatitis B virus). DHBV-I contains two sub-clades DHBV-Ia and DHBVIb. Parrot hepatitis B virus (PHBV) stains fall into GII which appeared as a separate phylogenetic branch/clade. All the subtypes of viruses in GI and GII seem to be genetically connected with viruses of DHBV-I by multiple mutational steps in phylogeographic analysis. Furthermore, 16 potential recombination events among different sub-genotypes in GI and one in GII were identified, but none of which is inter-genotypic between GI and GII. Overall, the results provide a whole picture of the genetic relatedness of avihepadnavirus strains, which may assist in the surveillance of virus spreading. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease caused by the porcine reproductive and respiratory syndrome virus (PRRSV). PRRSV exhibits genetic diversity and complexity in terms of immune responses, posing challenges for eradication. The nucleocapsid (N) protein of PRRSV, an alkaline phosphoprotein, is important for various biological functions. This review summarizes the structural characteristics, genetic evolution, impact on PRRSV replication and virulence, interactions between viral and host proteins, modulation of host immunity, detection techniques targeting the N protein, and progress in vaccine development. The discussion provides a theoretical foundation for understanding the pathogenic mechanisms underlying PRRSV virulence, developing diagnostic techniques, and designing effective vaccines. [ABSTRACT FROM AUTHOR]

【Objective】The study aimed to isolate Escherichia coli without virulence genes and antibiotic resistance from pig intestines and to analyze their growth performance and genetic evolution, with a view to laying a foundation for the development of microecologics or oral vaccines for pigs. 【Method】Fecal samples of 11 and 15 healthy adult pigs were collected from two pig farms in Guangdong Province, respectively. First, E. coli strains were isolated by McConkey plate and identified by 16S rRNA gene sequencing. Then, PCR was used to verify whether the selected E. coli contained 13 common virulence genes of pig pathogenic E. coli. Antimicrobial susceptibility tests were performed with 7 classes (14 kinds) of antimicrobial agents. Finally, the growth curves of selected E. coli strains were analyzed, and a phylogenetic tree was constructed based on the extracted genome sequences.【Result】Among 260 suspected E. coli strains, 206 strains were identified as E. coli by 16S rRNA gene sequencing analysis. 107 strains of E. coli did not contain 13 common virulence genes, of which 25 strains were sensitive to 7 classes (14 kinds) of antibiotics. Among the 25 E. coli strains, 23 non-pathogenic and non-antibiotic resistant E. coli strains (numbered as 2-9, 3-2, 3-4, 5-1, 6-1, 6-2, 6-9, 6-10, 8-2, 8-9, 10-5, B-4, B-6, B-7, B-10, D-10, E-2, E-10, J-1, J-4, K-6, L-6 and O-9) showed similar growth performance to E. coli Nissle 1917 and MG1655, and 2 E. coli strains (numbered as 6-4 and 5-2) showed higher growth rates than those of E. coli Nissle 1917 and MG1655. Among them, 10 strains (numbered as E-10, E-2, 6-4, 6-9, 8-2, O-9, 3-2, 6-2, J-1, K-6) had good acid tolerance and may be suitable for long-term colonization in the gastrointestinal tract of pigs. The phylogenetic tree analysis based on SNP core genome showed that 9 strains (numbered as 3-2, 6-10, 10-5, 6-1, 8-9, 5-2, L-6, O-9 and K-6) of the 25 strains were in the same group at the beginning of the phylogenetic tree, which were most likely to belong to the ancestral group of pig native E. coli. 【Conclusion】 Based on the comprehensive analysis of antibiotic sensitivity, growth performance, genome-wide evolutionary tree and gastric environment tolerance, one strain (numbered as O-9) was dominant in these four aspects. The growth kinetics of this strain is similar to or even better than that of E. coli Nissle 1977 and MG1655, which means that O-9 strain of E. coli isolates was likely to be high-quality pig native E. coli strain, with great research potential [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Preventive Veterinary Medicine / Zhongguo Yufang Shouyi Xuebao is the property of Chinese Journal of Preventive Veterinary Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

During the last decade, porcine epidemic diarrhea virus has detrimental consequences on swine industry, due to severe outbreaks especially in the suckling piglets. In March 2013, an outbreak was reported on a commercial swine farm in Guangdong Province, Southern China. A wild-type PEDV strain named as CHYJ130330 was identified, complete genome was sequenced and deposited in GenBank (accession no. KJ020932). The molecular epidemiological including evolutionary characteristics and pathogenicity assessment were explored during this study with particular interest and focus to develop this candidate strain for new vaccine. The isolates from China pre- and post-2013 shared 96.5–97.2% and 97–99% nt identity respectively with wild-type CHYJ130330 strain which during experimental studies has demonstrated high virulence and 100% mortality in 104 TCID50 group piglets within 5 days. The 22 reference strains selected from other parts of the world shared 98–99% identity with our sequence except Chinese (CV777) and S. Korean (vir.DR13, SM98 and atten.DR13) strains sharing 96.8, 97.6, 96.6 and 97.1% identity respectively. The phylogenetic tree revealed most strains reported after 2013 in GII genogroup while the prototype (CV777), S.korean and earlier Chinese (JS2008, 85-7mutant, Atten.vaccine, SD-M, LZC and CH/S) were GI Group. The amino acid sequence of CHYJ130330 E and M protein is highly conserved while ORF3 and N protein having 9 and 17 amino acid substitutions respectively in comparison to CV777 strain. The comparison of full length genome and the structural proteins revealed variations signifying that PEDV variant strains are still the main source of outbreaks in spite of continuous vaccination and also explain the variable trend of large scale outbreaks during this decade as compared to sporadic tendency of disease found before 2010. It is evident from this study that Chinese strains display significant level of mixing with the strains reported from other countries. The strain CHYJ130330 was also adapted successfully to Vero cell line and has shown high virulence in piglets. The information/findings will be helpful to develop a strategy for control of PEDV and have also shown that CHYJ130330 strain has strong virulence and is a more popular clinical strain in recent years, which has the potential to be developed into PEDV vaccine. [ABSTRACT FROM AUTHOR]

Introduction: Porcine circovirus type 2 (PCV2) is the pathogen of Porcine Circovirus Associated Diseases. Porcine circovirus type 3 (PCV3) is a novel porcine circovirus associated with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCV2 is clearly pathogenic, while the pathogenicity of PCV3 remains controversial, so it is crucial to monitor the prevalence of PCV2 and PCV3 in healthy and diseased pigs to investigate the effects of PCV3 and PCV2 on the health status of pigs. Methods: Here, we developed a PCV2 and PCV3 dual TaqMan quantitative PCR (qPCR) method to test samples from healthy and diseased pigs, to clarify the differences in the positive rates and viral copy numbers of PCV2 and PCV3, and to analyze the genetic evolution and molecular characterization of the viral genomes obtained with sequence alignment and phylogenetic analysis, homology and structural analysis of Cap proteins, and selection pressure analysis. Results: We successfully established a dual TaqMan qPCR method for PCV2 and PCV3 with good repeatability, specificity and sensitivity. In total, 1,385 samples from 15 Chinese provinces were tested with the established qPCR. The total positive rates were 37.47% for PCV3 and 57.95% for PCV2, and the coinfection rate for was 25.49%. The positive rates of PCV3 and PCV2 in 372 healthy pigs were 15.05 and 69.89%, respectively, and the coinfection rate was 12.90%. The positive rates of PCV3 and PCV2 in 246 diseased pigs were 55.69 and 83.33%, respectively, and the coinfection rate was 47.97%. Eighteen PCV3 genomes and 64 PCV2 genomes were identified, including nine each of the PCV3a-1 and PCV3b genotypes, eight of PCV2a, 16 of PCV2b, and 40 of PCV2d. The amino acid identity within the PCV3 Cap proteins was 94.00-100.0%, whereas the PCV2 Cap proteins showed an identity of 81.30-100.0%. PCV3 Cap was most variable at amino acid sites 24, 27, 77, 104 and 150, whereas PCV2 Cap had 10-13 unique sites of variation between genotypes. Discussion: These results clarify the prevalence and variations of PCV2 and PCV3 in healthy and diseased pigs, which will provide a basis for the prevention and control of the two viral infections. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious and pathogenic infectious disease caused by the porcine reproductive and respiratory syndrome virus (PRRSV). It manifests as reproductive disorders in sows and respiratory disorders in piglets. PRRSV infects swine herds with symptoms such as abortions, stillbirths, and mummified fetuses in gestating sows. Piglets mainly experience abdominal respiration and respiratory symptoms. To date, the prevention of PRRS relies primarily on vaccination and the implementation of various preventive and control measures. Swine deaths caused by PRRS have resulted in significant economic losses to the pig industry worldwide. Non-structural protein 10 (NSP10) has helicase and adenosine triphosphatase (ATPase) activities that unwind DNA and RNA and play important roles in viral replication and transcription. Hence, it can be potentially used to develop novel reagents for the detection of PPRSV. This article reviews genetic variations, interaction with viral and host proteins, effects on PRRSV replication, immunomodulation, apoptosis, and viral virulence of NSP10, with the aim of providing a theoretical basis for the prevention and control of PRRS and drug development in the future. [ABSTRACT FROM AUTHOR]

Feline coronavirus (FCoV), as one of the important pathogens of feline viral gastroenteritis, has been attracting great attention. A total of 1869 rectal and nasal swabs, feces, and ascites samples were collected from eight regions in Guangxi province during 2021–2024. The multiplex RT-qPCR established in our laboratory was used to test these samples for FCoV, and 17.66% (330/1869) of the samples were positive for FCoV. The S, M, and N genes of 63 FCoV-positive samples were amplified and sequenced, and the genetic and evolutionary characteristics were analyzed. Similarity analysis showed that the nucleotide and amino acid homologies of S, M, and N genes were 81.2–99.6% and 70.2–99.5%, 89.9–100% and 91.6–100%, and 90.1–100% and 91.5–100%, respectively. Phylogenetic analysis revealed that all 63 FCoV strains, based on S gene sequences, belonged to type I FCoV (FCoV-I), and were clustered with Chinese strains and the Netherlands UU strains. Recombinant signals were detected in the S gene of strains GXLZ03-2022, GXLZ08-2022, and CCoV GD/2020/X9. The results suggest that FCoV is still prevalent in the Guangxi province of southern China, and the prevalent FCoV strains show high genetic diversity and novel epidemic characteristics.

An increasing number of studies have reported that atypical hand, foot, and mouth disease (HFMD) is becoming a new concern for children's health. At present, there is no official definition for atypical HFMD, but some studies have defined that it occurs at anatomic sites not listed in the definition of HFMD issued by the World Health Organization. Several pathogens have been reported to cause atypical HFMD, such as Coxsackievirus (CV)A6. As one of the most prevalent enteroviruses in the world, CVA6 seems to affect a wider range of children and causes more severe and prolonged illness than other enteroviruses. The early lesions of atypical HFMD are very similar to the clinical presentations of other diseases, such as eczema, which poses a challenge for clinicians aiming to identify and diagnose HFMD in a timely manner. Here, we report on six atypical HFMD patients caused by recombinant CVA6 variants, and the atypical manifestations include eczema coxsackium, large herpes, rice‐like red papules and herpes, purpuric rash, and onychomadesis, as well as and large red herpes on scalp, perianal, testicles, shoulders and neck, and other atypical eruption sites, hoping to draw the attention of other pediatricians. This study will provide scientific guidance for timely diagnosis of HFMD to prevent serious complications. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Preventive Veterinary Medicine / Zhongguo Yufang Shouyi Xuebao is the property of Chinese Journal of Preventive Veterinary Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Avihepadnavirus is a genus of the Hepadnaviridae family. It primarily infects birds, including species of duck, geese, cranes, storks, and herons etc. To understand the genetic relatedness and evolutionary diversity among avihepadnavirus strains, a comprehensive analysis of the available 136 full-length viral genomes (n = 136) was conducted. The genomes were classified into two major genotypes, i.e., GI and GII. GI viruses were further classified into 8 sub-genotypes including DHBV-I (duck hepatitis B virus-I), DHBV-II (Snow goose Hepatitis B, SGHBV), DHBV-III, RGHBV (rossgoose hepatitis B virus), CHBV (crane hepatitis B virus), THBV (Tinamou hepatitis B virus), STHBV (stork hepatitis B virus), and HHBV (Heron hepatitis B virus). DHBV-I contains two sub-clades DHBV-Ia and DHBV-Ib. Parrot hepatitis B virus (PHBV) stains fall into GII which appeared as a separate phylogenetic branch/clade. All the subtypes of viruses in GI and GII seem to be genetically connected with viruses of DHBV-I by multiple mutational steps in phylogeographic analysis. Furthermore, 16 potential recombination events among different sub-genotypes in GI and one in GII were identified, but none of which is inter-genotypic between GI and GII. Overall, the results provide a whole picture of the genetic relatedness of avihepadnavirus strains, which may assist in the surveillance of virus spreading.

Taraxacum kok-saghyz (TKS) is a model plant and a potential rubber-producing crop for the study of natural rubber (NR) biosynthesis. The precise analysis of the NR biosynthesis mechanism is an important theoretical basis for improving rubber yield. The small rubber particle protein (SRPP) and rubber elongation factor (REF) are located in the membrane of rubber particles and play crucial roles in rubber biosynthesis. However, the specific functions of the SRPP/REF gene family in the rubber biosynthesis mechanism have not been fully resolved. In this study, we performed a genome-wide identification of the 10 TkSRPP and 2 TkREF genes’ family members of Russian dandelion and a comprehensive investigation on the evolution of the ethylene/methyl jasmonate-induced expression of the SRPP/REF gene family in TKS. Based on phylogenetic analysis, 12 TkSRPP/REFs proteins were divided into five subclades. Our study revealed one functional domain and 10 motifs in these proteins. The SRPP/REF protein sequences all contain typical REF structural domains and belong to the same superfamily. Members of this family are most closely related to the orthologous species T. mongolicum and share the same distribution pattern of SRPP/REF genes in T. mongolicum and L. sativa, both of which belong to the family Asteraceae. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the TkSRPP/REFs gene family. The expression levels of most TkSRPP/REF members were significantly increased in different tissues of T. kok-saghyz after induction with ethylene and methyl jasmonate. These results will provide a theoretical basis for the selection of candidate genes for the molecular breeding of T. kok-saghyz and the precise resolution of the mechanism of natural rubber production.

H9N2 avian influenza viruses (AIVs) pose an increasing threat to the poultry industry worldwide and have pandemic potential. Vaccination has been principal prevention strategy to control H9N2 in China since 1998, but vaccine effectiveness is persistently challenged by the emergence of the genetic and/or antigenic variants. Here, we analysed the genetic and antigenic characteristics of H9N2 viruses in China, including 70 HA sequences of H9N2 isolates from poultry, 7358 from online databases during 2010–2020, and 15 from the early reference strains. Bayesian analyses based on hemagglutinin (HA) gene revealed that a new designated clade16 emerged in April 2012, and was prevalent and co-circulated with clade 15 since 2013 in China. Clade 16 viruses exhibited decreased cross-reactivity with those from clade 15. Antigenic Cartography analyses showed represent strains were classified into three antigenic groups named as Group1, Group2 and Group3, and most of the strains in Group 3 (15/17, 88.2%) were from Clade 16 while most of the strains in Group2 (26/29, 89.7%) were from Clade 15. The mean distance between Group 3 and Group 2 was 4.079 (95%CI 3.605–4.554), revealing that major switches to antigenic properties were observed over the emergence of clade 16. Genetic analysis indicated that 11 coevolving amino acid substitutions primarily at antigenic sites were associated with the antigenic differences between clade 15 and clade 16. These data highlight complexities of the genetic evolution and provide a framework for the genetic basis and antigenic characterization of emerging clade 16 of H9N2 subtype avian influenza virus.

ABSTRACTDuring an investigation in October 2018, two people with diarrhoea, mild abdominal pain, and mild arthralgia symptoms in Guangxi, China, were identified as infected by H9N2 avian influenza virus (AIV). Four H9N2 AIVs were isolated from one of two patients, a pet cat, and a dead chicken (two respective isolates from its lung and kidney tissues) bred by the patients at a backyard farm. Epidemiological investigation indicated that the newly bought chicken died first, and clinical syndromes appeared subsequently in the two owners and one cat. Furthermore, the two individuals possessed high H9N2-specific hemagglutination inhibition and microneutralization antibodies. Shared nucleotide sequence identity (99.9% – 100%) for all genes was detected in the four H9N2 isolates, and hemagglutinin (HA) T138A located on the receptor binding domain (RBD), resulted from nucleotide polymorphisms that were exclusively found in the isolate from the female patient. Moreover, HA K137N on the RBD was found in isolates from these three host species. Importantly, these four H9N2 isolates presented an exclusive binding preference for the human-type receptor (α2-6-SA), and could replicate and cause pathological changes in mice. Phylogenetic analyses showed that these four isolates clustered together and belonged to clade C1.2, lineage Y280. In addition, H9N2 viruses of human origin are genetically divergent and interspersed with the widespread poultry-origin H9N2 AIVs. All these results indicate a high risk of H9N2 AIVs in public health, and effective prevention and control measures against H9N2 AIVs should be considered and performed for both animal and human health.

H7N9 avian influenza viruses have caused severe harm to the global aquaculture industry and human health. For further understanding of the characteristics of prevalence and hemagglutinin evolution of H7N9 avian influenza viruses, we generated the global epidemic map of H7N9 viruses from 2013 to 2022, constructed a phylogenetic tree, predicted the glycosylation sites and compared the selection pressure of the hemagglutinin. The results showed that although H7N9 avian influenza appeared sporadically in other regions worldwide, China had concentrated outbreaks from 2013 to 2017. The hemagglutinin genes were classified into six distinct lineages: A, B, C, D, E and F. After 2019, H7N9 viruses from the lineages B, E and F persisted, with the lineage B being the dominant. The hemagglutinin of highly pathogenic viruses in the B lineage has an additional predicted glycosylation site, which may account for their persistent pandemic, and is under more positive selection pressure. The most recent ancestor of the H7N9 avian influenza viruses originated in September 1991. The continuous evolution of hemagglutinin has led to an increase in virus pathogenicity in both poultry and humans, and sustained human-to-human transmission. This study provides a theoretical basis for better prediction and control of H7N9 avian influenza. [ABSTRACT FROM AUTHOR]

The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response. [ABSTRACT FROM AUTHOR]

【Objection】This study aimed to monitor the genetic variation and molecular evolutionary trends of H9N2 avian influenza virus (AIV) in Guangdong, and provide reference data for the evolutionary analysis and prevention and control of H9N2 AIV in China.【Method】The HA and NA genes of three H9N2 AIV strains isolated from Guangdong in 2022 were amplified, cloned, and sequenced. The DNAStar and PhyloSuite software were used for sequence assembly and alignment. The MEGA, Megalign, NetNGlyc 1.0 Server, and other software were used for genetic evolution, percent identity, receptor binding, protein activity, drug resistance, and glycosylation site analysis of their nucleotide and amino acid sequences.【Result】The phylogenetic tree showed that the HA gene of the three isolates belonged to the clade h9.4.2.5 and the NA gene belonged to the clade 1. However, the nucleotide homology with the early strain was only 81.6%~91.7% and 88.2%~91.2%, formed new clade named clade h9.4.2.5c and clade 1.2, respectively. The nucleotide and amino acid sequence analysis revealed that the HA cleavage site was PSRSSR ↓ GLF. The receptor binding site underwent I155T, H183N, A190T/V, T212I, Q226L, and Q227M mutations. The glycosylation site underwent 218N non-glycosylation and acquired new glycosylation site at 313N. The NA stalk showed nine nucleotides deletion at positions 187-195 (ACAGAGATA), leading to the loss of three amino acids at positions 63-65 (TEI). The absorbtion site of NA on red blood cells showed K/E/S368N and D369N mutations. No related mutations to neuraminidase activity and drug resistance were found at the E119, D151, R152, R224, E276, R292, and R371.【Conclusion】The HA and NA genes of the three H9N2 AIV isolated from Guangdong in 2022 had evolved into a new subgroup. Some mutaitons suggest that prevalent H9N2 in Guangdong may enhanc adaptability of mammals and its antigenicity has changed. Moreover, it has not yet acquired resistance to durgs oseltamivir and zanamivir.

Feline panleukopenia virus (FPV) is the causative agent of hemorrhagic gastroenteritis in feline animals. FPV has been evolving over time, and there have been several different strains of the virus identified. Some of these strains may be more virulent or more resistant to current vaccines than others, which highlights the importance of ongoing research and monitoring of FPV evolution. For FPV genetic evolution analysis, many studies focus on the main capsid protein (VP2), but limited information is available on the nonstructural gene NS1 and structural gene VP1. In the present study, we firstly isolated two novel FPV strains circulating in Shanghai, China, and performed full-length genome sequencing for the desired strains. Subsequently, we focused on analyzing the NS1, VP1 gene, and the encoding protein, and conducted a comparative analysis among the worldwide circulating FPV and Canine parvovirus Type 2 (CPV-2) strains, which included the strains isolated in this study. We found that the 2 structural viral proteins, VP1 and VP2, are splice variants, and VP1 has a 143 amino-acid-long N-terminal compared to VP2. Furthermore, phylogenetic analysis showed that divergent evolution between FPV and CPV-2 virus strains were clustered mostly by country and year of detection. In addition, much more continuous antigenic type changes happened in the process of CPV-2 circulating and evolution compared to FPV. These results stress the importance of the continuous study of viral evolution and provide a comprehensive perspective of the association between viral epidemiology and genetic evolution.

Chloroplasts and mitochondria, descendants of ancient prokaryotes via endosymbiosis, occupy a pivotal position in plant growth and development due to their intricate connections with the nuclear genome. Genes encoded by the nuclear genome but relocated to or being functional within these organelles are commonly referred as organelle-targeting nuclear genes (ONGs). These genes are essential for maintaining cytonuclear coordination, thereby determining the stability of the life cycle. While molecular function and cytonuclear coordination of some endosymbiosis-derived ONGs (E-ONGs) have been extensively studied, the evolutionary history and characteristics from a more widespread range of non-endosymbiosis-derived ONGs (NE-ONGs) remain largely enigmatic. In this study, we focused on 12 representative species within the Poaceae family to systematically identify NE-ONGs and investigated their evolutionary history and functional significance on a phylogenetic timescale. Upon aligning these 12 species’ evolutionary histories, we observed the following phenomena: (i) an exploration of NE-ONGs between the BOP and PACMAD clades unveiled dynamic compositions, potentially influencing their photosynthetic divergence; (ii) the majority of the abundant species-specific NE-ONGs exist in a single-copy status, and functional enrichment analysis further underscored their specialized roles, which could be crucial for species adaptation; and (iii) comparative analyses between plasmid- and mitochondria-related NE-ONGs (pNE-ONGs and mNE-ONGs) revealed a prevalence of pNE-ONGs, indicating tighter control for chloroplast function in Poaceae. In summary, this study offers novel insights into the cytonuclear co-evolutionary dynamics in Poaceae speciation and draws attention to crop improvement by using NE-ONGs.

Bovine coronavirus (BCoV), bovine rotavirus, bovine viral diarrhea virus, and bovine astrovirus are the most common intestinal pathogenic viruses causing diarrhea in cattle. We collected 1646 bovine fecal samples from January 2020 to August 2023. BCoV was the major pathogen detected, with a positive rate of 34.02% (560/1646). Of the 670 diarrheal samples and 976 asymptomatic samples, 209 and 351 were BCoV-positive, respectively. Studying the relevance of diarrhea associated with BCoV has shown that the onset of diarrheal symptoms post-infection is strongly correlated with the cattle’s age and may also be related to the breed. We amplified and sequenced the hemagglutinin esterase (HE), spike protein, and whole genomes of the partially positive samples and obtained six complete HE sequences, seven complete spike sequences, and six whole genomes. Molecular characterization revealed that six strains were branched Chinese strains, Japanese strains, and partial American strains from the GⅡb subgroup. Strains HBSJZ2202 and JSYZ2209 had four amino acid insertions on HE. We also analyzed ORF1a and found disparities across various regions within GIIb, which were positioned on separate branches within the phylogenetic tree. This work provides data for further investigating the epidemiology of BCoV and for understanding and analyzing BCoV distribution and dynamics.

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious and pathogenic infectious disease caused by the porcine reproductive and respiratory syndrome virus (PRRSV). It manifests as reproductive disorders in sows and respiratory disorders in piglets. PRRSV infects swine herds with symptoms such as abortions, stillbirths, and mummified fetuses in gestating sows. Piglets mainly experience abdominal respiration and respiratory symptoms. To date, the prevention of PRRS relies primarily on vaccination and the implementation of various preventive and control measures. Swine deaths caused by PRRS have resulted in significant economic losses to the pig industry worldwide. Non-structural protein 10 (NSP10) has helicase and adenosine triphosphatase (ATPase) activities that unwind DNA and RNA and play important roles in viral replication and transcription. Hence, it can be potentially used to develop novel reagents for the detection of PPRSV. This article reviews genetic variations, interaction with viral and host proteins, effects on PRRSV replication, immunomodulation, apoptosis, and viral virulence of NSP10, with the aim of providing a theoretical basis for the prevention and control of PRRS and drug development in the future.

Simple Summary: NSP11 is a non-structural protein of the porcine reproductive and respiratory syndrome virus (PRRSV) that influences viral replication and interacts with the host's innate immune response. We reviewed the genetic evolution of NSP11, its effects on PRRSV replication and virulence, its interactions with other PRRSV and host proteins, the regulation of host immunity, the conserved characteristics of nidovirus-specific endonuclease (NendoU), and its diagnosis, providing an important theoretical basis for in-depth studies on PRRSV pathogenesis and vaccine design. Porcine reproductive and respiratory syndrome (PRRS) is a virulent infectious disease caused by the PRRS virus (PRRSV). The non-structural protein 11 (NSP11) of PRRSV is a nidovirus-specific endonuclease (NendoU), which displays uridine specificity and catalytic functions conserved throughout the entire NendoU family and exerts a wide range of biological effects. This review discusses the genetic evolution of NSP11, its effects on PRRSV replication and virulence, its interaction with other PRRSV and host proteins, its regulation of host immunity, the conserved characteristics of its enzyme activity (NendoU), and its diagnosis, providing an essential theoretical basis for in-depth studies of PRRSV pathogenesis and vaccine design. [ABSTRACT FROM AUTHOR]

Waterfowl, such as ducks, are natural hosts for avian influenza viruses (AIVs) and act as a bridge for transmitting the virus to humans or susceptible chickens. Since 2013, chickens and ducks have been threatened by waterfowl-origin H5N6 subtype AIVs in China. Therefore, it is necessary to investigate the genetic evolution, transmission, and pathogenicity of these viruses. In this study, we determined the genetic characteristics, transmission, and pathogenicity of waterfowl-origin H5N6 viruses in southern China. The hemagglutinin (HA) genes of H5N6 viruses were classified into the MIX-like branch of clade 2.3.4.4h. The neuraminidase (NA) genes belonged to the Eurasian lineage. The PB1 genes were classified into MIXlike and VN 2014-like branches. The remaining five genes were clustered into the MIX-like branch. Therefore, these viruses belonged to different genotypes. The cleavage site of the HA proteins of these viruses was RERRRKR/G, a molecular characteristic of the H5 highly pathogenic AIV. The NA stalk of all H5N6 viruses contained 11 amino acid deletions at residues 58–68. All viruses contained 627E and 701D in the PB2 proteins, which were molecular characteristics of typical bird AIVs. Furthermore, this study showed that Q135 and S23 viruses could replicate systematically in chickens and ducks. They did not cause death in ducks but induced mild clinical signs in them. All the infected chickens showed severe clinical signs and died. These viruses were shed from the digestive and respiratory tracts and transmitted horizontally in chickens and ducks. Our results provide valuable information for preventing H5N6 avian influenza outbreaks. [ABSTRACT FROM AUTHOR]

Copyright of Monatsschrift Kinderheilkunde is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This article seeks to provide some genetic perspectives on the question "Just How Special Are Humans—Really?" It begins with an introduction to how genetic variation can provide information about the past. It continues by discussing two ways in which genetic analyses has, on multiple occasions, shown that humans are less unique than we thought we are. We have a cognitive bias to toward thinking we are special. Our species has colonized an ecological niche not exploited by any other species on our earth, but how much of our adaptation to that niche is cultural rather than genetic? [ABSTRACT FROM AUTHOR]

Background: Dengue virus (DENV) can be divided into four serotypes—DENV-1, DENV-2, DENV-3, and DENV-4. In humans, infection leads to dengue fever (DF), dengue hemorrhagic fever, and dengue shock syndrome, both widely prevalent in tropical and subtropical regions. In 2019, a severe outbreak of DF occurred in Xishuangbanna, Yunnan province. Objective: To investigate the etiology and genotype of the causative agents of this severe dengue outbreak in Xishuangbanna. Methods: Between October and November 2019, the sera of patients clinically diagnosed with DF were collected in the first People's Hospital of Xishuangbanna. RNA was extracted from the sera and amplified by RT-PCR with flavivirus primers. Flavivirus-positive sera were then used to inoculate Aedes albopictus cells (C6/36); viral RNA was extracted from these cells, amplified, and sequenced with DENV E gene-specific primers. Sequence splicing and nucleotide homology genetic evolution analysis were carried out by biological software (DNAStar). Unique mutations in the E genes of isolated DENV were analyzed by SWISS-MODEL and PyMOL. Results: Of the 60 samples collected from DF patients, 39 tested positively with flavivirus primers. The DENV was isolated from 25 of the 39 positive seras, of which 20 showed cytopathic effects (CPE) and 5 were no CPE. In these 25 isolated nucleic acids, 21 strains of DENV-1, 3 strains of DENV-2, and 1 strain of DENV-3 were identified according to the sequence of E protein. In the four unique mutations (D52, Y149, L312, T386), D52 and Y149 in the E protein of DENV-1 were predicted to be exposed on the surface of the prefusion conformation. Conclusion: The 2019 outbreak of DF in Xishuangbanna area of Yunnan Province consists of at least three serotypes of DENV-1, DENV-2, and DENV-3, and the sources of these virus strains are of mixed and complicated origin. [ABSTRACT FROM AUTHOR]

Abstract Background The complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms. Results In this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4. Conclusion We successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

Newcastle disease caused by Newcastle disease virus (NDV) is one of the most serious threats to chickens and has two clinical forms, typical and atypical, caused by velogenic and lentogenic strains, respectively. To control the epidemic, many vaccines against velogenic class II NDVs have been introduced worldwide, but this has led to accelerated mutation of class II viruses under immune pressure and, on the other hand, to non-vaccine targeting class I NDVs becoming the dominant population in poultry. In this context, this study provided the first large-scale genomic epidemiological and quasispecies dynamic analysis of class I NDVs in China, and found that class I viruses that first appeared in East and South China have spread to central China and become the dominant class with an average evolutionary rate of 1.797 × 10−3. In addition, single nucleotide polymorphism and intra-host single nucleotide variation analyses show that HN and P genes have high mutation rates and may act as front-runners for NDV to expand their host range and enhance their virulence. This study also found that the class I NDV population has accumulated a number of mutations under positive selection and that six isolates with shortened C-terminal extensions of the HN protein are evolving toward increased virulence. These results not only enrich the research resources but also help us to better understand the dynamic evolution and mutational trends of NDV at the genomic level, which is crucial for monitoring, early warning, and controlling the outbreak of Newcastle disease.

Rabies virus has existed for thousands of years and is circulating in many species. In the present study, a total of 2896 rabies viruses isolated worldwide were phylogenetically classified into ten clusters based on the G gene sequence, and these clusters showed a close relationship with the hosts and regions that they were isolated from. Eighty-three representative G sequences were selected from ten clusters and were used to construct pseudoviruses using the VSV vector. The phylogenetic relationships, infectivity and antigenicity of the representative 83 pseudotyped rabies viruses were comprehensively analyzed. Eighty three pseudoviruses were divided into four antigentic clusters (GAgV), of which GAgV4 showed poor neutralization to all immunized sera. Further analysis showed that almost all strains in the GAgV4 were isolated from wild animals in the America, especially bats and skunks. No significant relationship in terms of phylogeny, infectivity and antigenicity was proved. Amino acid mutations at residues 231and 436 can affect the infectivity, while mutations at residues 113, 164 and 254 may affect the sensitivity to immunized animal sera, especially residue 254. We recommend close monitoring of infectivity and antigenicity, which should be more precise than simple genetic analysis.

【Objective】Ampelopsis grossedentata belongs to Ampelopsis of the Vitaceae family and it has great medicinal value. The chloroplast genome codon usage bias of A. grossedentata and its main influencing factors are analyzed with a view to providing a reference for chloroplast genomics research, species protection and germplasm innovation of A. grossedentata.【Method】The complete genome sequence of A. grossedentata chloroplast was downloaded from the NCBI online database, and the protein coding sequence was screened. The effective number of codons (ENC), the relative synonymous codons usage (RSCU), and the GC content of the three codons of each gene were calculated by using CodonW software. The correlation between the parameters was calculated and mapped by R software.【Result】A total of 59 protein coding sequences are screened from the chloroplast genome of A. grossedentata. The total average GC content and average GC content of the third base of the codon are 37.98% and 29.45%, respectively. The ENC value ranges from 37.39 to 57.12, suggesting that the chloroplast genome codon use of A. grossedentata has a weak bias. ENC-plot analysis, PR2-plot analysis and neutral plot analysis reveal that natural selection is the most important factor affecting the codon usage bias of the A. grossedentata chloroplast genome. In addition, 13 optimal codons are recognized, including UUU, CUA, AUA, UCA, CCA, ACA, GCA, CAU, GAU, UGA, AGA, GGA and GGG.【Conclusion】The study results provide references for phylogeny and evolution of chloroplast genome codon in A. grossedentata.