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Hepatitis A virus (HAV), a member of the genus Hepatovirus (Picornaviridae HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew (Episoriculus macrurus) and long-tailed brown-toothed shrew (Episoriculus leucops), respectively. Our sequence and phylogenetic analyses of EpMa-HAV and EpLe-HAV indicated that they belong to the species Hepatovirus I (HepV-I) clade II, also known as the Chinese shrew HepV clade. Notably, the codon usage bias pattern of novel shrew HepVs is consistent with that of previously identified Chinese shrew HepV. Furthermore, our structural analysis demonstrated that shrew HepVs differ from other mammalian HepVs in RNA secondary structure and exhibit variances in key protein sites. Overall, the discovery of two novel HepVs in shrews expands the host range of HepV and underscores the existence of genetically diverse animal homologs of human HAV within the genus HepV. [ABSTRACT FROM AUTHOR]

Purpose: To analyze factors affecting segregation and ploidy results from Robertsonian carriers, and determine chromosomes involved impact chromosome stability during meiosis and mitosis. Methods: This retrospective study include 928 oocyte retrieval cycles from 763 couples with Robertsonian translocations undergoing preimplantation genetic testing for structural rearrangements (PGT-SR) using next-generation sequencing (NGS) between December 2012 and June 2020.The segregation patterns of the trivalent of 3423 blastocysts were analyzed according to the carrier's sex and age. A total of 1492 couples who received preimplantation genetic testing for aneuploidy (PGT-A) were included as the control group and matched according to maternal age and testing time stage. Results: A total of 1728 (50.5%) normal/balanced embryos were identified from 3423 embryos diagnosed. The rate of alternate segregation in male Robertsonian translocation carriers was significantly higher than that in female carriers (82.3% vs. 60.0%, P < 0.001). However, the segregation ratio exhibited no difference between young and older carriers. Further, increasing maternal age decreased the proportion of transferable embryo cycle in both female and male carriers. And the ratio of chromosome mosaic from the Robertsonian translocation carrier group was significantly higher than that in the PGT-A control group (1.2% vs. 0.5%, P < 0.01). Conclusions: The meiotic segregation modes were affected by the carrier sex and were independent of the carrier's age. Advanced maternal age decreased the probability of obtaining a normal/balanced embryo. In additional, the Robertsonian translocation chromosome could increase the possibility of chromosome mosaicism during mitosis in blastocysts. [ABSTRACT FROM AUTHOR]

Novel duck orthoreovirus can infect various hosts, mainly causing spleen necrosis and hemorrhagic necrotizing hepatitis, leading to immunosuppression and growth impairment. Infectious diseases characterized by swollen hock joints, movement disorders, and impaired growths have recently occurred in significant duck breeding areas in China. Infected ducks from Shandong Province were selected, and N-DRV-LY20 was isolated from the swollen joints. Next-generation sequencing (NGS) of N-DRV-LY20 and homology analysis showed that all ten fragments had the highest homology to N-DRV and the closest affinity to Duck/N-DRV-XT18/China/2018. After artificial inoculation with N-DRV-LY20 virus solution, Cherry Valley ducks showed the same symptoms of leg swelling and hock joint deformation, which were not explored in previous studies. A long history of evolution has led to significant variation in DRV and altered its pathogenicity. In this study, we confirmed the ability of N-DRV to cause viral arthritis in ducks and clarified this isolate's genetic characteristics and level of variation, providing a basis for the control and variation detection of N-DRV. [ABSTRACT FROM AUTHOR]

A field isolate (Reo/SDWF /Pheasant/17608/20) of avian orthoreovirus (ARV), isolated from a flock of game-pheasants in Weifang, Shandong Province, was genetically characterized being a field variant or novel strain in our recent research studies in conducting whole genome sequencing by using Next-Generation Sequencing (NGS) technique on Illumina MiSeq platform. Among a total of 870,197 35-151-mer sequencing reads, 297,711 reads (34.21%) were identified as ARV sequences. The de novo assembly of the ARV reads resulted in generation of 10 ARV-related contigs with the average sequencing coverage from 1390× to 1977× according to 10 ARV genome segments. The complete genomes of this pheasant-origin ARV (Reo/SDWF /Pheasant/17608/20) were 23,495 bp in length and consist of 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1) encoding 12 viral proteins. Sequence comparison between the SDWF17608 and classic ARV reference strains revealed that 58.1–100% nucleotide (nt) identities and 51.4–100% amino acid (aa) identities were in genome segment coding genes. The 10 RNA segments had conversed termini at 5' (5'-GCUUUU) and 3' (UCAUC-3') side, which were identical to the most published ARV strains. Phylogenetic analysis revealed that this pheasant ARV field variant was closely related with chicken ARV strains in 7 genome segment genes, but it possessed significant sequence divergence in M1, M3 and S2 segments. These findings suggested that this pheasant-origin field variant was a divergent ARV strain and was likely originated from reassortments between different chicken ARV strains. [ABSTRACT FROM AUTHOR]

Background: Tuberculosis (TB) seriously threatens individual and public health. Recently, TB outbreaks in schools have been reported more frequently in China and have attracted widespread attention. We reported three TB outbreaks in high schools in Hunan Province, China. Methods: When a tuberculosis patient was reported in a school, we carried out field epidemiological investigations, including tuberculin skin testing (TST), chest X-ray (CXR) and laboratory test for all close contacts, and whole-genome sequencing (WGS) analyses to understand the transmission patterns, the causes and the risk factors for the outbreaks, thereby providing a foundation for the control of TB epidemics in schools. Results: A total of 49 students with TB patients were identified in the three schools where TB outbreaks occurred, including nine patients in School A, 14 patients in School B, and 26 patients in School C. In Schools A, B and C, the putative attack rates in the classes of the index case were 13.8% (8/58), 7.6% (5/66), and 40.4% (21/52), while the putative attack rates of expanding screening in the school were 0.3% (1/361), 0.2% (9/3955), and 0.2% (5/2080), respectively. Thirteen patients had patient delay, with a median delay interval of 69 days (IQR 30.5– 113 days). Twelve patients had a healthcare diagnostic delay with a median delay interval of 32 days (IQR 24– 82 days). Phylogenetic analysis of culture-positive patients revealed that most of them shared a small genetic distance (≤ 12 SNPs), with three separate genetic clusters (including one MDR-TB genomic cluster), indicating the recent transmission of Mycobacterium tuberculosis strains. Conclusion: This combination of field investigation and WGS analysis revealed the transmission of three TB outbreaks in schools. Reinforced implementation is needed to improve timely case finding and reduce diagnosis delay in routine TB control in the school population. [ABSTRACT FROM AUTHOR]

Since the first report from Cherry Valley ducks on a commercial duck farm in China (2008), duck astrovirus type 1(DAstV‐1)‐associated duck viral hepatitis (DVH) have been detected in several commercial duck flocks. A highly acute disease characterized by hepatitis broke out in ducklings in Shandong Province in March 2021, all diseased ducks have been immunized against the duck viral hepatitis vaccine. One DAstV‐1 strain, designated as DAstV‐SDWF, was isolated from a diseased duckling. Here, the isolation, cultivation, and characterization of DAstV‐1 isolate are described. The isolated astrovirus grew well in the LMH cell line. To determine the entire genomic of the DAstV‐SDWF isolate, the next‐generation sequencing (NGS) technique was conducted on the Illumina HiSeq platform. Complete genome sequence analysis revealed that DAstV‐SDWF isolate was 91.6%–98.6% homology with others DAstV‐1 deposited in Genbank. Similar clinical symptoms were successfully reproduced by an experimental infection study using the DAstV‐SDWF isolate. DAstV‐SDWF is the first DAstV‐1 strain whose experimental infection study has been conducted in China. Results of the above data demonstrated that DAstV‐1 could be one of the causative agents of the DVH occurring in China. The present works are likely to provide new insights into the pathogenicity and evolution of DAstV‐1 in ducks. [ABSTRACT FROM AUTHOR]

Since 2013, there have been an increasing number of cases of arthritis in broilers caused by avian orthoreovirus (ARV) in China, and the virus remains highly virulent in chicks with high‐level maternal antibodies. However, little information is available about the complete gene analysis and pathogenicity of the epidemic ARVs. In the study, the ARV strain (V‐ARV‐SD26) was isolated from broilers associated with arthritis in Shandong Province. To genetically characterize the ARV strain, the whole‐genome sequencing was conducted by next‐generation sequencing (NGS) technique. Sequence analysis demonstrated that V‐ARV‐SD26 might have acquired its current genomic composition through several homologous and, in case of the λC, μA and σB, divergent reassortment events. To further investigate the pathogenicity of the strain, 160 one‐day‐old Ross broilers with maternal antibodies were equally divided into four groups (foodpad‐, eye mucosa‐ and intramuscular‐inoculated groups and the negative control group), three experimental groups were inoculated separately with the low‐dose virus fluid, and the negative control was equally inoculated with sterile PBS. The results showed that the symptoms of broilers in foodpad inoculation group were the most serious, while that of the eye mucosa infection group were the mildest. Meanwhile, the cloacal cotton swabs and organs were collected for qRT‐PCR detection to evaluate the infection status. In conclusion, these findings indicate that V‐ARV‐SD26 is a divergent ARV strain, which provide experimental data for the prevention and control of newly emerged reovirus, and have a certain reference value for the preparation and evaluation of new vaccines. [ABSTRACT FROM AUTHOR]

Objectives: Ongoing acquisition of antimicrobial resistance genes has made Morganella morganii a new clinical treatment challenge. Understanding the molecular epidemiology of M. morganii will contribute to clinical treatment and prevention. Methods: We undertook a 6-year clinical molecular epidemiological investigation of M. morganii from three tertiary hospitals in China since 2014. Antimicrobial susceptibility testing was performed using a VITEK-2 system. All isolates were screened for β-lactam and plasmid-mediated quinolone resistance genes by PCR. Isolates carrying carbapenem-resistant genes were subjected to whole-genome sequencing (WGS). The variation and evolution of these mobile genetic elements (MGEs) were then systematically analyzed. Results: Among all M. morganii isolates (n = 335), forty (11.9%) were recognized as multidrug resistant strains. qnrD1 , aac(6′)-Ib-cr , bla TEM–104, and bla CTX–M–162 were the top four most prevalent resistance genes. Notably, phylogenomic and population structure analysis suggested clade 1 (rhierBAPS SC3 and SC5) associated with multiple resistance genes seemed to be widely spread. WGS showed a bla OXA–181-carrying IncX3 plasmid and a Proteus genomic island 2 variant carrying bla CTX–M–3, aac(6′)-Ib-cr coexisted in the same multidrug resistant strain zy_m28. Additionally, a bla IMP–1-carrying IncP-1β type plasmid was found in the strain nx_m63. Conclusion: This study indicates a clade of M. morganii is prone to acquire resistance genes, and multidrug resistant M. morganii are increasing by harboring a variety of MGEs including two newly discovered ones in the species. We should be vigilant that M. morganii may bring more extensive and challenging antimicrobial resistance issue. [ABSTRACT FROM AUTHOR]

Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024–2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection. [ABSTRACT FROM AUTHOR]

Introduction: In metastatic colorectal cancer (mCRC), the B-type Raf kinase (BRAF)V600E mutation is a molecular biomarker of poor prognosis and is of great importance to drug target. Currently, the commonly used methods for detecting BRAFV600E mutation include immunohistochemistry (IHC) and gene sequencing, but both present certain limitations. Near-infrared (NIR) spectroscopy is a spectroscopy technology that takes advantage of the electromagnetic wavelength between visible light and mid-infrared light. Methods: IHC was used to detect the expression of BRAFV600E protein with the BRAFV600E (VE1) antibody in 42 cases of paraffin-embedded (FFPE) mCRC tissue sections. The NIR-discriminant analysis model (NIRS-DA) was established using 6 cases of wild-type and 6 cases of mutant-type BRAF specimens. Results: IHC detection results revealed 13 cases of weakly positive (+), 1 case of moderately positive (++), and 28 cases of negative (−) CRC. Compared with the next-generation sequencing (NGS) results, the positive rate was 66.7%. The classification accuracy of calibration (CAC) was 100% compared with the results of NGS, demonstrating that the BRAFV600E mutant NIRS-DA model, verified by 2 cases of wild-type and 2 cases of mutant-type CRC samples was established. The NIRS-DA model was used to predict gene mutation in the CRC samples, 7 cases were positive (+), and 35 cases were negative (−), and the classification accuracy of prediction (CAP) was 83.3% (35/42). Discussion: The NIRS-DA model-predicted results were in high agreement with the detection results of NGS, and the difference in IHC is not statistically significant (P> 0.05). However, this study is a preliminary discussion on a methodology due to its small sample size. [ABSTRACT FROM AUTHOR]

Salmonella spp. are a major cause of foodborne illness throughout the world. Traditional serotyping by antisera agglutination has been used as a standard identification method for many years but newer nucleic acid-based tests have become available that may provide advantages in workflow and test turnaround time. In this study, we evaluated the Luminex® xMAP® Salmonella Serotyping Assay (SSA), a multiplex nucleic acid test capable of identifying 85% of the most common Salmonella serotypes, in comparison to the traditional serum agglutination test (SAT) on 4 standard strains and 255 isolates from human (224), environmental, and food (31) samples. Of the total of 259 isolates, 256 could be typed by the SSA. Of these, 197 (77.0%) were fully typed and 59 (23.0%) were partially typed. By SAT, 246 of the 259 isolates (95%) were successfully typed. Sixty isolates had discrepant results between SAT and SSA and were resolved using whole genome sequencing (WGS). By SAT, 80.0% (48/60) of the isolates were consistent with WGS while by SSA 91.7% (55/60) were partially consistent with WGS. By serovar, all 30 serovars except one tested were fully or partially typable. The workflow comparison showed that SSA provided advantages over SAT with a hands-on time (HOT) of 3.5 min and total turnaround time (TAT) of 6 h, as compared to 1 h HOT and 2–6 days TAT for SAT. Overall, this study showed that molecular serotyping is promising as a rapid method for Salmonella serotyping with good accuracy for typing most common Salmonella serovars circulating in China. [ABSTRACT FROM AUTHOR]

Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis , kills over 1 million people worldwide annually. Development of drug resistance (DR) in the pathogen is a major challenge for TB control. We conducted whole-genome analysis of seven Taiwan M. tuberculosis isolates: One drug susceptible (DS) and five DR Beijing lineage isolates and one DR Euro-American lineage isolate. Developing a new method for DR mutation identification and applying it to the next-generation sequencing (NGS) data from the 6 Beijing lineage isolates, we identified 13 known and 6 candidate DR mutations and provided experimental support for 4 of them. We assembled the genomes of one DS and two DR Beijing lineage isolates and the Euro-American lineage isolate using NGS data. Moreover, using both PacBio and NGS sequencing data, we obtained a high-quality assembly of an extensive DR Beijing lineage isolate. Comparative analysis of these five newly assembled genomes and two published complete genomes revealed a large number of genetic changes, including gene gains and losses, indels and translocations, suggesting rapid evolution of M. tuberculosis. We found the MazEF toxin–antitoxin system in all the seven isolates studied and several interesting mutations in MazEF proteins. Finally, we used the four assembled Beijing lineage genomes to construct a high-quality Beijing lineage reference genome that is DS and contains all the genes in the four genomes. It contains 212 genes not found in the standard reference H37Rv, which is Euro-American. It is therefore a better reference than H37Rv for the Beijing lineage, the predominant lineage in Asia. [ABSTRACT FROM AUTHOR]

A severe infectious disease characterized with gout, haemorrhage and swellings of kidneys has affected goslings around the major goose‐producing regions in China since November 2016. A Novel goose‐origin astrovirus (AStV), designated as AStV/SDPY/Goose/1116/17 (AStV‐SDPY) strain, was isolated from diseased goslings, and experimental reproduction of gout was successful using the AStV‐SDPY strain. Additionally, the AStV‐SDPY was conducted for its full genome sequencing characterization using next‐generation sequencing (NGS) technique on Illumina HiSeq platform. A complete genome of the AStV‐SDPY was 7,252 nt in length and encoded three viral proteins. Phylogenetic analysis revealed that AStV‐SDPY strain belongs to an independent branch of avian astroviruses, and the nucleotide homology among AStV‐SDPY and other classic avian astrovirus strains was only 48.8%–68.2%. Results of above data indicated the causative agent of the gosling gout occurring in China is a novel divergent goose astrovirus. [ABSTRACT FROM AUTHOR]

Macrolide-resistant Mycoplasma pneumoniae (MRMP) is highly prevalent in Asia and is now being reported from Europe. Few data on MRMP are available in the United States. Using genotypic and phenotypic methods, we detected high-level MRMP in 13.2% of 91 M. pneumoniae-positive specimens from 6 US locations. [ABSTRACT FROM AUTHOR]

A fowl adenovirus variant designated as DAdV-JSXZ strain was isolated from the tissue specimen of fallopian tubes of a duck case, which was submitted from a 276-day-old Cherry valley breeding duck flock experienced egg-dropping syndromes in March 2022. Full-genome sequence of the DAdV-I JSXZ strain by next-generation sequencing revealed that the complete genome length of DAdV-JSXZ strain was 33,213 nucleotides and shared a high degree of nucleotide identity (97.0–99.4 %) with other DAdV-I reference strains. In pathogenicity studies, this isolated duck JSXZ strain reproduced similar egg-dropping symptoms in healthy breeding ducks, pathologic lesions of follicular hemorrhage, and the laid eggs in low fertilization and hatchability rates. Our research findings demonstrated that DAdV-I JSXZ strain was one of the causative agents of duck egg dropping syndrome in egg-laying ducks and could cause acute respiratory symptoms in ducklings. • This is the first time to report the complete viral genome of DAdV-1 in breeding ducks. • This study provides scientific evidence that DAdV-1 could be one of the pathogens of duck egg drop. • This study provides evidence of possible vertical transmission of DAdV-1. [ABSTRACT FROM AUTHOR]

Highlights • A novel chicken-origin goose reovirus can cause goslings hepatitis, named SDPY-ARV. • The SDPY-ARV showed higher identity with chicken strains instead of waterfowl. • The SDPY-ARV is divergent from reference waterfowl strains in some genome segments. • 10 segments genetic reassortment of SDPY is confirmed among some American strains. • There is no segment reassortment between waterfowl-origin ARV and the SDPY-ARV. Abstract A severe infectious disease characterized by nephritis, hepatitis and splenitis has attacked goslings around Shandong province in China since 2016. A novel chicken-origin avian orthoreovirus (ARV) was isolated with LMH cells from affected goslings named Reo/Goose/SDPY/1116/17 (SDPY-ARV) strain, and the infection was successfully reproduced experimentally. The ARV-SDPY full genome sequencing was conducted using Next-Generation Sequencing (NGS) technique on Illumina HiSeq platform. The complete genome of SDPY-ARV was 23,427 bp in length and consist of 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1) which encoding 12 viral proteins. Genomic sequence analysis showed that the SDPY-ARV strain is in the same branch with broiler, pheasant-origin ARV isolates, and shares 51.8–96.2% of nucleotide identity of σC gene with them; while only 49.3–50.3% with waterfowl isolates. In addition, the occurrence of 10 segments genetic reassortment of SDPY strain is confirmed among the PA15511, the 1733 and the PA13649 strains from America. In conclusion, the causative agent of gosling hemorrhagic necrotic hepatitis and nephritis occurring in China is a novel chicken-origin goose orthoreovirus. [ABSTRACT FROM AUTHOR]

Since March 2021, an infectious characterized by white necrotic foci throughout the goose body has appeared in the major goose-producing regions in China. This disease has caused economic hardship for goose farms in many regions of China with approximately 50 % mortality. A novel goose-origin orthoreovirus was isolated from the spleen of diseased geese and designated as N-GRV/HN/Goose/2021/China (N-GRV-HN21) strain. Next-generation sequencing and phylogenetic analysis revealed that the isolate was a reassortant virus containing viral gene segments from three ARV serotypes that infect duck, muscovy duck, and goose. Geese infection test showed that both N-GRV-HN21-infected and contacted geese displayed whole-body white necrotic foci. N-GRV RNA was detected in different organs of both infected and contacted geese, indicating that the N-GRV isolate is pathogenic and transmissible in geese. Seroconversion was also observed in experimentally infected and contacted geese. A prevalence study of 323 goose serum samples collected from different goose breeding areas showed that 86 % of the geese were positive for N-GRV. In conclusion, all results warrant the necessity to monitor orthoreovirus epidemiology and reassortment as the orthoreovirus could be an important pathogen for the waterfowl industry and a novel orthoreovirus might emerge to threaten animal and public health. • Using the NGS technology, we identified A novel goose-origin orthoreovirus named N-GRV/HN/Goose/2021/China, isolated from the spleen of 30-day-old diseased geese with white necrotic foci in China. • The isolate is a reassortant virus containing fragments of viral genes from three ARV serotypes infecting ducks, ducks, and geese and differs significantly from the known antiretroviral reference strains. • The isolates were pathogenic and transmissible in the goslings and underwent seroconversion. • Serological research revealed that the virus is common in China's main goose breeding regions and poses a substantial risk to both animal and human health. [ABSTRACT FROM AUTHOR]

In recent years, the emerging avian orthoreovirus (ARV) strains that led to viral arthritis have attracted much attention from the chicken industry worldwide, due to the significant economic losses suffered. In mid-2020, with the assistance of next-generation sequencing technology, we achieved success in characterizing two divergent avian orthoreovirus (ARV) variants (0543/SDYT) and isolating them from the broiler tendons characterized by arthritis. As suggested by the genome characterization of the 0543/SDYT strains, they belong separately to clusters Ⅰ and Ⅳ. As revealed by sequence comparison, phylogenetic, and recombination analysis, for μA, μB, and σNS genes, considerable genetic divergences were also observed in the two new isolates. However, in the case of λA, λB, μNS, σA, and σB genes, very clear clustering patterns were observed for SDYT and 0543 field strains, respectively. In terms of the μA, μNS, p10, p17 genes of SDYT isolate and μNS, p17, σC, σA genes of 0543 isolate, the lower similarity was observed with NCBI stored sequences, with nt highest identity values below 90 %. In addition, there is an intra-fragmental recombination event in the M1 gene of the SDYT strain. In regard, the multiple segmental recombination and accumulation of point mutations play a role in the newly-emerging ARV strains. Not only did the isolates strain exhibit strong replication ability in vivo , but they also displayed strong arthritogenicity in broilers with low neutralizing maternal antibodies, indicating that maternal antibody treatment may not effectively reduce the oral infection of avian orthoreovirus. These findings suggest that it is necessary to develop a new strategy for enhanced effectiveness in preventing and controlling ARV infection. • We successfully isolated and identified two broiler-derived Avian orthoreovirus strains, namely SDYT and 0543. • Genetic characterization revealed that SDYT was an intra-segmental recombinant strain, classified as genotype IV, and 0543 was a genotype 1 variant, distinct from the S1133 vaccine strain. • We assessed pathogenicity in vivo by challenging S1133, SDYT, 0543 strains in chicks containing maternally derived antibodies (mainly from S11333 vaccinated breeders). [ABSTRACT FROM AUTHOR]

• Using the NGS technology, we identified a recombinant cluster 2 ARV variant named PHC-2020-0545, isolated from tendons of broilers in China. • The isolate was genetically significantly distinct from known ARV strains in M1 and M3 genes. • Multiple segmental recombination, intra-segmental recombination and point mutations might contribute to the emergence of this isolate. • The isolate had a strong replication ability in 1-day-old broilers, and mainly affected the movement, digestion and metabolism of broilers. In mid-2020, using next-generation sequencing (NGS) technology, we identified a recombinant cluster 2 avian orthoreovirus (ARV) variant named PHC-2020−0545, isolated from tendons of 33-day-old broilers with leg swelling in China. Complete genomic sequencing and analyses demonstrated that the isolate was genetically significantly distinct from known ARV strains in M1 and M3 genes and its σC coding gene had an extremely high variability, compared with the identified ARV strains grouped into other genotyping cluster. Further analysis showed that many base substitutions were silent and non-silent substitutions are most likely to occur in the first positions of codons. Multiple segmental recombination, intra-segmental recombination and accumulation of point mutations might contribute to the emergence of this isolate. The PHC-2020−0545 strain had a strong replication ability in 1-day-old broilers, and mainly affected the movement, digestion and metabolism of broilers. In addition, the infection route of the isolate is related to its pathogenicity to broilers. Therefore, combined with its unique genetic characteristics and potential origin, we determined that the PHC-2020−0545 field strain is a novel recombinant ARV strain, which has certain reference value for the preparation and evaluation of new vaccines. [ABSTRACT FROM AUTHOR]