Evaluation of white spot syndrome virus genome stability across serial passages.

The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

Feline bocaparvovirus in domestic cats with gastrointestinal disease.

Host-pathogen interplay of Orientia tsutsugamushi: pathomolecular epidemiology and phylo-immuno profiling in naturally infected rodents and shrews.

The cocirculation of CRF01_AE and CRF07_BC among men who have sex with men (MSM) in China may facilitate the emergence of genetically complex HIV-1 recombinants. Here, we identified and characterized a novel second-generation HIV-1 CRF01_AE/CRF07_BC recombinant, designated GY0192, from a 25-year-old MSM individual in Guiyang, Guizhou Province, southwest China, using near full-length genome (NFLG) analysis. Recombination analyses identified four breakpoints at HXB2 positions 3,125, 5,687, 6,375, and 9,176, generating a distinct five-segment mosaic genome. Subregion phylogenetic analyses showed that the two CRF01_AE-derived fragments clustered with the CRF01_AE cluster 5 lineage, while all three CRF07_BC-derived fragments grouped with CRF07_BC lineages frequently circulating among MSM in China, indicating that both parental components of GY0192 were phylogenetically related to lineages frequently reported among MSM populations in China. The virus was also predicted to be CCR5-tropic, adding epidemiological relevance because CCR5-tropic viruses are commonly involved in transmission and early infection. Together, these findings identify GY0192 as a distinct CRF01_AE/CRF07_BC mosaic and suggest that cocirculating MSM-associated HIV-1 lineages may provide opportunities for interlineage recombination. This case expands the known spectrum of CRF01_AE/CRF07_BC recombinants in Guizhou and underscores the value of NFLG-based surveillance for detecting underrecognized HIV-1 genetic complexity in southwest China.

The evolutionary relationship between amphibian IgM, IgY, and IgX/A-like antibodies has remained difficult to resolve, largely because repetitive heavy-chain loci are often incompletely or inconsistently annotated. In this study, I re-analyzed reconstructed four-domain heavy-chain constant regions from amphibian loci to test whether the evolution of IgXA is better explained by uniform divergence or by a mosaic history involving partial exon replacement. The reconstructed dataset comprised 86 complete antibodies from 29 species (29 IgM, 33 IgY, and 24 IgXA). Exact nucleotide matching against the reconstructed exon set yielded 79 antibodies, allowing the identification of 21 strictly microsyntenic species-level IgM/IgY/IgXA trios for recombination analyses. Domain alignments, Poisson-corrected amino-acid distances, and UMAP embeddings revealed a clear structural transition: IgXA clustered closer to IgY in CH1 and CH2, remained nearly intermediate in CH3, and shifted decisively toward IgM in CH4. Mean inter-class distances (IgY-IgXA vs. IgM-IgXA) reflected this pattern: 0.964 vs. 1.275 in CH1, 1.254 vs. 1.477 in CH2, 1.242 vs. 1.248 in CH3, and 1.220 vs. 0.962 in CH4. Within-species trio comparisons reinforced this polarity: 16 of 21 trios displayed an IgY-like CH1-CH2, 16 exhibited an IgM-like CH4, and 12 combined both features. Furthermore, GARD detected recombination breakpoints close to the CH3/CH4 boundary in 6 of the 21 trios, including three cases within 30 nucleotides of the exon junction. Maximum-likelihood domain trees confirmed that the strongest IgXA-IgM sister relationship occurred in CH4, where the largest relevant clade showed 91.7/89.0 SH-aLRT/UFBoot support. Together, these reconstructed sequence data support a mosaic origin for amphibian IgXA, most parsimoniously explained by partial exon shuffling or replacement within a conserved constant-region genomic block.

ABSTRACT Infectious bursal disease (IBD), caused by infectious bursal disease virus (IBDV), poses a major threat to the global poultry industry. In this study, we identified and characterized a novel field IBDV strain NN040124, which exhibits both reassortment and recombination features. Genotyping identified this field strain as A3B1a, with segment A derived from a very virulent IBDV (vvIBDV) strain (A3) and segment B from a classical-like attenuated vaccine (attIBDV) strains (vv-A/att-B IBDV)). Crucially, recombination analysis revealed that segment B is a backbone originated from vaccine strain B87, with the N-terminal part replaced by the homologous region from a vvIBDV strain (Harbin-1). This replacement is implicated in the restored virulence of the strain, as demonstrated by a challenge experiment in 4-week-old commercial Three-Yellow chickens, which resulted in 40% mortality, typical clinical signs, and severe bursal lesions. These findings confirm the emergence of a novel dually reassortant and recombinant IBDV in Southern China, identify the N-terminal region of segment B as a potential virulence determinant in a naturally occurring field strain, and highlight the potential risks of live vaccine use. Our findings underscore the importance of continuous genetic and pathogenic surveillance of IBDV to inform effective prevention and control strategies.

Chromosomal instability (CIN) is a hallmark of cancer, and a primary cause of genetic heterogeneity in tumors. Depending on the degree of CIN and the affected tissue, CIN can promote or suppress tumor formation, and high CIN induction has been proposed as a therapeutic strategy. How CIN achieves these effects is unclear. Here we use a conditional mouse model of graded CIN in combination with longitudinal monitoring of DMBA/TPA-initiated skin tumors to show that low CIN increases the frequency of skin tumor initiation, while higher CIN accelerates tumor onset and growth rates. Strikingly, gene recombination analysis of the tumors reveals that upon high CIN induction the fast-growing tumors originate from rare low CIN cells, suggesting a strong non-cell-autonomous effect of high CIN. Gene expression analysis and immunohistochemistry show that high CIN causes epidermal hyperplasia, immune evasion, and a regenerative response that stimulates low CIN tumor growth beyond what is achieved by induction of low CIN alone. Such cell-extrinsic effects may be a common mechanism of tumor formation by CIN, as we observe it also in CIN-induced tumors of the intestine, breast, and mesentery. When high CIN is induced in established skin tumors, mimicking CIN-based therapy, tumors regress but relapse quickly. Relapsed tumors, too, arose from rare low CIN cells. Our findings have implications for our understanding of the contributions of CIN to cancer initiation and progression and give caution to the rationale for CIN therapies.

Molecular characterization and pathogenicity of a HP-like PRRSV strain and a NADC30 recombinant strain.

Human adenovirus B7 (HAdV-B7) has emerged as an increasingly important respiratory pathogen in recent years. Ten first grade students experienced symptoms of acute respiratory infection at a primary school in Beijing from November 13 to 21, 2024. We investigated the cause of this outbreak. In partnership with the local center for disease prevention and control, we collected demographic information (age and gender) of the affected students and obtained pharyngeal swab specimens from six students. We used multiplex real-time PCR to screen for 22 common respiratory viruses in these samples. To isolate HAdV, Hep-2 cells were inoculated with HAdV-positive pharyngeal swab samples. Isolates were sequenced by Sanger and whole-genome sequencing. In addition, four HAdV-B7 strains isolated from 2024 to 2025 influenza-like illness surveillance cases were also sequenced as a control to determine whether the same mutations existed. The strains were characterized molecularly using gene homology analysis, recombination analysis and phylogenetic reconstruction. We collected six pharyngeal swab samples from ten students based on consent. All samples were HAdV-positive as determined by multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated the HAdV strain from each student sample. Blast analysis and phylogenetic analysis of the hexon, penton, and fiber genes suggested that this outbreak was caused by HAdV-B7 (P7H7F7). A unique T335S mutation was identified within the RGD loop of the penton base in this outbreak. Whole-genome sequencing confirmed high sequence identity between our isolates and HAdV-B7 strains from multiple regions in China and abroad. In addition, all strains obtained in this outbreak had 57 nucleotides deletion in the E3 region. Interestingly, the same deletion mutants were also found in HAdV-B7 strains isolated from 2024 to 2025 influenza-like illness surveillance cases, indicating that this deletion mutation has been prevalent and may represent an established molecular signature of a circulating HAdV-B7 sublineage. We report the first detection of a human adenovirus type 7 deletion mutant associated with an outbreak of acute respiratory infections in Beijing in 2024. This deletion mutation was prevalent and may represent an established molecular signature of a circulating HAdV-B7 sublineage. How this mutation affects viral pathogenicity remains unclear and needs further investigation. Our findings underscore the critical importance of implementing timely molecular surveillance for guiding outbreak control and informing prevention strategies against respiratory pathogens.

This study presents a comprehensive SCAPS-1D simulation of an ultra-thin CIGSe/CdS/i-ZnO/ITO solar cell with a 420 nm absorber layer, focusing on the influence of key physical parameters and back surface field engineering. The effects of acceptor doping density in CIGSe (Na = 1013 to 1018 cm−3), interface defect density (Ni–t = 109 to 1018 cm−3), bulk defect density (Nt = 1012 to 1020 cm−3), and electron affinity (χ = 4.35–4.65 eV) were systematically investigated. Increasing Na significantly enhanced device performance by strengthening the internal electric field and increasing the carrier concentration, thereby improving Voc, fill factor, and efficiency. In contrast, elevated interface and bulk defect densities led to severe recombination losses and significant degradation of all photovoltaic parameters. Optimal band alignment was obtained at χ ≈ 4.35 eV, corresponding to a slight negative conduction-band offset that facilitates carrier transport and suppresses recombination. Recombination analysis showed stable performance of the radiative recombination coefficient over the range 10−16 to 10−8 cm3 s−1, while Auger recombination became dominant at coefficients above 10−23 cm6 s−1. Among the investigated back surface field layers, Cu2O provided the best performance due to its wide band gap (2.2 eV) and strong back-surface electric field, yielding a maximum simulated efficiency of ∼40.3% with Voc = 0.817 V, Jsc = 30.03 mA cm−2, and FF = 82.88%. Capacitance–voltage and Mott–Schottky analyses revealed that capacitance increases from 57.6 to 109.9 nF cm−2 with increasing Na, and the built-in potential ranges from 0.80 to 1.32 V, confirming enhanced junction properties. These results provide practical guidelines for optimizing ultra-thin CIGSe solar cells through defect control, band alignment tuning, and back surface field design.

Wild rosaceous species may act as reservoirs for viruses infecting cultivated stone fruits. In this study, we surveyed wild cherry (Prunus avium) populations in forested areas of Tunisia in spring 2024. High-throughput sequencing (HTS) of pooled leaf samples revealed viral genomic fragments related to members of the genus Robigovirus. Here, we report the identification, complete genome sequencing, and preliminary prevalence assessment of a novel RNA virus from wild cherry, tentatively named wild cherry-associated virus (WCaV). The 8,254-nt genome comprises five canonical open reading frames (ORFs) exhibiting the typical organization of Robigovirus. These ORFs encode an RNA-dependent RNA polymerase (228.2kDa), three triple gene block proteins (24.6, 12.4, and 7.2kDa, respectively), a coat protein (28.8kDa), and an overlapping hypothetical protein (ORF5a; 14.5kDa). Phylogenetic inference, single nucleotide polymorphism (SNP) mapping, and recombination analyses indicate that WCaV constitutes a genetically distinct lineage within the genus. Field surveys showed limited local prevalence, consistent with a single-strain infection. Overall, this work broadens the known diversity of Robigovirus and provides the first molecular evidence of a novel Robigovirus infecting wild P. avium in Tunisia.

Senegal has a high burden of hepatitis B virus (HBV); however, HBV molecular epidemiology is sparse, and coinfection with hepatitis delta virus (HDV) is poorly investigated. A blood donor panel was evaluated to characterize circulating HBV genotypes, HDV prevalence, and assess the performance of ultrasensitive HBsAg Next, HBV DNA, anti-HDV Total Ig, and HDV RNA diagnostic assays. Pre-screened, non-transfused specimens (n = 320) were tested for HBV and HDV biomarkers on the Alinity i platform. Comparator HBsAg testing was assessed with Elecsys HBsAg II. Specimens reactive for HBsAg and/or anti-HDV were tested for HBV DNA and HDV RNA. Specimens with sufficient viral load underwent next-generation sequencing. Phylogenetic inference was assessed with maximum likelihood trees and recombination analysis conducted on basal sequences. Testing revealed reactive results for HBsAg (87.2%), anti-HBc (92.8%), anti-HBs (6.9%), HBeAg (3.8%), and anti-HDV (1.3%). HBsAg Next Qualitative and Elecsys HBsAg II concordance was 311/319 (97.5%), with n = 8 (2.5%) samples not detected by Elecsys HBsAg II. Confirmatory testing verified HBsAg positivity for the 8 discordant specimens. Sequencing (n = 104) resulted in >70% genome coverage for n = 74 specimens and phylogenetic analysis identified HBV Quasi-subgenotype A3 (QSA3) (40.5%), A basal (1.4%), D (5.4%), E (52.7%), and 2 HDV GT5 genomes. Recombination analysis revealed two HBV QSA/E 3 recombinants. This study provides, to our knowledge, the first HBV sequences from Senegal in 20 years and highlights a predominance of genotypes E, QSA3, and notably two unique QSA3/E recombinants. The improved detection of HBsAg Next Qualitative on samples with low levels of HBsAg highlights the importance of ultrasensitive assays.

Detection, isolation and molecular characterization of Senecavirus A in porcine semen: Implications for control programs.

Characterization of the pathogenicity of newly emerged NADC30-Like PRRSV strains causing severe brain infections via twice inter-lineage recombination.

Molecular epidemiological and genetic characteristics of coxsackievirus A6 circulating in mainland China from 1992 to 2023.

Human adenovirus (HAdV)-114 (P7H3F3) is a newly identified recombinant genotype, while recent studies suggest that it likely represents a previously circulating HAdV-3 strain. A total of 413 strains previously identified as HAdV-3 from 20 Chinese provinces during 2000-2024, along with 125 GenBank-derived HAdV-3 strains (1988-2023), underwent genotype reconfirmation and genetic evolutionary analysis using the penton base, hexon, and fiber genes. Furthermore, 97 representative strains were selected for whole-genome analysis to determine their genetic recombination patterns. Of the 538 analyzed strains, 537 were identified as HAdV-114 using three genes, with only one 2010 U.S strain classified as HAdV-3. Phylogenetic analysis revealed three HAdV-114 clades (Clades 1-3): Clade 1 (1988-2019) displayed sporadic circulation, Clade 2 (2023-2024) appeared geographically restricted to three Chinese provinces, and Clade 3 (2000-2024) likely represented the globally dominant strain. Genetic evolutionary analyses indicated that, although HAdV-114 originated from recombination between HAdV-7 and HAdV-3, its three Clades diverged from the parental trajectories, with Clades 1 and 3 sharing a common evolutionary origin and Clade 2 forming an independent terminal cluster. Genomic recombination analysis identified two recombination patterns across the three clades. All clades shared a 3' terminal genomic region (nt 18,794-end) derived from HAdV-3, whereas their 5' ends comprised gene fragments recombined from unknown sources and epidemic HAdV-7 strains, with varied breakpoints. HAdV-114, historically identified as HAdV-3, is the predominant genotype associated with HAdV-related respiratory infections. Therefore, enhanced surveillance of recombinant HAdV strains is imperative for effective disease control.

Genomic variation and recombination dynamics of duck hepatitis A virus type 3 (DHAV-3) in clinical isolates from Shandong and Anhui, China.

Characterization of a novel mosaic-like mtr operon and inter-regional transmission of dual-resistant Neisseria gonorrhoeae ST7363 sub-lineage in China.

Neisseria meningitidis stands as one of the predominant etiological agents of bacterial meningitis worldwide. Sequence type (ST) 4821 clonal complex (cc4821), notably linked to the hyperinvasive and quinolone-resistant clone ChinaCC4821-R1-C/B, has emerged and caused the epidemiological shift from serogroup A (MenA, mostly cc5 and cc1) to MenC in China since 2003 and the subsequent introduction of MenA + C vaccination. However, the evolution path of capsule in MenB ChinaCC4821-R1-C/B under the vaccine-induced selective pressure remains unclear. For phylogenetic analysis, nucleotide sequences of the capsular polysaccharide synthesis (cps) gene cluster were extracted from MenC and MenB ChinaCC4821-R1-C/B genomes in the Neisseria PubMLST Database. Recombination analyses were conducted using software MEGA and RDP. The capsule switching from MenC to MenB in ChinaCC4821-R1-C/B was conducted via natural transformation. Phylogenetic analysis of the cps loci revealed that recombination events probably occurred in region A. Among MenB ChinaCC4821-R1-C/B isolates, isolate Nm119 (B: P1.7-2,14: F3-3: ST-9455 [cc4821]) was selected as the representative strain. Through sequence analysis, a potential donor strain (2061370; B: P1.19-1,15 - 11: F3-7: ST-269 [cc269]) was identified from 80 candidate isolates, with a 5,527-bp recombination sequence spanning the region between ctrG and cssA in region A. To further validate capsule switching from MenC to MenB, we performed biological experiments using a MenC ChinaCC4821-R1-C/B isolate (Nm044; C: P1.7-2,14: F3-3: ST-4821 [cc4821]) as a recipient strain. The recombination sequence identified in the transformant (Nm044Nm119_T20) was only 414bp larger than the sequence predicted by the in silico analysis. Functional analysis of the transformant revealed that its capsular polysaccharide expression and serum survival capacity were comparable to those of the donor strain. The capsule switching pattern, exemplified by Nm119, could serve as a model for MenB ChinaCC4821-R1-C/B. Through MenC→MenB capsule switching, ChinaCC4821-R1-C/B isolates have gained the capacity to evade immunity induced by MenA + C vaccines. The potential capsule switch from MenC→MenB in ChinaCC4821-R1-C/B isolates has been confirmed through both sequence-based analyses and molecular biological experiments. The MenB capsule likely originated from a cc269 strain. Given the potential of capsule switching events to compromise vaccine efficacy, enhanced surveillance of capsule variation in cc4821 isolates is warranted under current immunization strategies in China.