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Case Reports in Women's Health Mar 2024Whole-exome sequencing is an evolving technology in perinatal diagnosis which allows identification of genetic etiologies that would otherwise go undetermined. In this...
Whole-exome sequencing is an evolving technology in perinatal diagnosis which allows identification of genetic etiologies that would otherwise go undetermined. In this case report, a 38-year-old Hispanic woman, G5P3013, with a monochorionic diamniotic twin gestation with one fetus displaying significant cranial abnormalities on prenatal ultrasound and magnetic resonance imaging (MRI) of the brain is presented. Fetal anomalies included bilateral ventriculomegaly, absent cavum septum pellucidum, and absent corpus callosum. Diagnostic amniocentesis with chromosome analysis, chromosomal microarray, alpha-fetoprotein, cytomegalovirus, toxoplasmosis, and parvovirus had normal results. Whole-exome sequencing for the anomalous fetus detected a de novo mosaic variant of uncertain significance (VUS) in the calcium/calmodulin dependent serine protein kinase () gene: . This variant was absent in the normal twin fetus, the mother, and the father. Pathogenic CASK gene mutations are associated with three syndromes: FG syndrome 4, intellectual developmental disorder and microcephaly with pontine and cerebellar hypoplasia (MICPCH), and intellectual developmental disorder with or without nystagmus. Whole-exome sequencing identified a potential etiology for the anomalies detected. The variant likely arose de novo and was the potential cause of the identified cranial abnormalities in one fetus of this monochorionic diamniotic twin gestation. Whole-exome sequencing may provide additional diagnostic utility when standard diagnostic testing is noncontributory.
PubMed: 38440102
DOI: 10.1016/j.crwh.2024.e00583 -
Polish Journal of Microbiology Mar 2024Feline parvovirus (FPV) is highly infectious for cats and other Felidae and often causes severe damage to young kittens. In this study, we incorporated recombinase...
Feline parvovirus (FPV) is highly infectious for cats and other Felidae and often causes severe damage to young kittens. In this study, we incorporated recombinase polymerase amplification (RPA) and Cas12a-mediated detection and developed an RPA-Cas12a-based real-time or end-point fluorescence detection method to identify the NS1 gene of FPV. The total time of RPA-Cas12a-based fluorescence assay is approximately 25 min. The assay presented a limit of detection (LOD) of 1 copies/μl (25 copies/per reaction), with no cross-reactivity with several feline pathogens. The clinical performance of the assay was examined using total genomic DNA purified from 60 clinical specimens and then compared to results obtained with qPCR detection of FPV with 93.3% positive predictive agreement and 100% negative predictive agreement. Together, the rapid reaction, cost-effectiveness, and high sensitivity make the RPA-Cas12a-based fluorescence assay a fascinating diagnostic tool that will help minimize infection spread through instant detection of FPV.
Topics: Cats; Animals; Female; Recombinases; Feline Panleukopenia Virus; CRISPR-Cas Systems; Limit of Detection
PubMed: 38437470
DOI: 10.33073/pjm-2024-005 -
Scientific Reports Mar 2024In this study, we devised a nanogold lateral flow immunoassay (LFA-CPV antigen test) for detecting canine parvovirus (CPV) in living attenuated CPV vaccines. We...
In this study, we devised a nanogold lateral flow immunoassay (LFA-CPV antigen test) for detecting canine parvovirus (CPV) in living attenuated CPV vaccines. We conducted instrumental characterization of the prepared nanogold particles and the developed LFA-CPV antigen test was rigorously evaluated for its performance verification including limit of detection, sensitivity, specificity, selectivity and accuracy. The LFA-CPV antigen test demonstrated strong performance when assessed against qPCR using different batches of live attenuated CPV vaccines, indicated a sensitivity of 96.4%, specificity of 88.2%, and an overall accuracy of 95%. These results suggest that the developed LFA-CPV antigen test could serve as a viable alternative for evaluation live attenuated CPV vaccines, and provide it as a point of care test for CPV diagnosis, offering a potential substitute for traditional laboratory methods, particularly qPCR.
Topics: Animals; Dogs; Parvovirus, Canine; Dog Diseases; Immunoassay; Vaccines, Attenuated; Parvoviridae Infections
PubMed: 38424259
DOI: 10.1038/s41598-024-55548-x -
Heliyon Feb 2024Since it emerged as a major dog pathogen, canine parvovirus type 2 (CPV-2) has featured a remarkable genetic and phenotypic heterogeneity, whose biological,...
Since it emerged as a major dog pathogen, canine parvovirus type 2 (CPV-2) has featured a remarkable genetic and phenotypic heterogeneity, whose biological, epidemiological, and clinical impact is still debated. The continuous monitoring of this pathogen is thus of pivotal importance. In the present study, the molecular epidemiology of CPV-2 in Sicily, southern Italy, has been updated by analysing 215 nearly complete sequences of the capsid protein VP2, obtained from rectal swabs/faeces or tissue samples collected between 2019 and 2022 from 346 dogs with suspected infectious gastrointestinal disease. The presence of the original CPV-2 type (4%) and CPV-2a (9%), CPV-2b (18%), or CPV-2c (69%) variants was documented. Over the years, we observed a decrease in the frequency of CPV-2a/-2b and a rapid increase of CPV-2c frequency, with a progressive replacement of the European lineage of CPV-2c by the Asian lineage. The observed scenario, besides confirming epidemiological relevance of CPV-2, highlights the occurrence of antigenic variant shifts over time, with a trend toward the replacement of CPV-2a, CPV-2b, and the European lineage of CPV-2c by the emerging Asian CPV-2c lineage. The comparison with other Italian and international sequences suggests the occurrence of viral exchange with other Italian regions and different countries, although the directionality of such viral flows could not be often established with confidence. In several instances, potential CPV-2 introductions led to epidemiological dead ends. However, major, long-lasting clades were also identified, supporting successful infection establishment, local spreading, and evolution. These results, besides demonstrating the need for implementing more effective control measures to prevent viral introductions and minimize circulation, stress the relevance of routine monitoring activities as the only tool to effectively understand CPV-2 epidemiology and evolution, and develop adequate countermeasures.
PubMed: 38420403
DOI: 10.1016/j.heliyon.2024.e26561 -
Animal Microbiome Feb 2024The red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to...
BACKGROUND
The red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted.
METHODS
Using a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately.
RESULTS
There is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane.
CONCLUSION
RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.
PubMed: 38419121
DOI: 10.1186/s42523-024-00299-3 -
Scientific Reports Feb 2024Canine bufavirus (CBuV) was reported in domestic dogs worldwide. We conducted a survey of canine bufavirus in domestic dogs in Thailand from September 2016 to October...
Canine bufavirus (CBuV) was reported in domestic dogs worldwide. We conducted a survey of canine bufavirus in domestic dogs in Thailand from September 2016 to October 2022. Rectal swab samples (n = 531) were collected from asymptomatic dogs and dogs with gastroenteritis signs. The samples were tested for CBuV using PCR with specific primers to the VP1/VP2 gene, and 9.42% (50/531) was CBuV positive. Our findings showed that CBuVs could be detected in both symptomatic and healthy dogs. The Thai CBuVs were found in dogs from different age groups, with a significant presence in those under 1 year (12.60%) and dogs aged 1-5 years (7.34%) (p < 0.05), suggesting a high prevalence of Thai CBuVs in dogs under 5 years of age. We performed complete genome sequencing (n = 15) and partial VP1/VP2 sequencing (n = 5) of Thai CBuVs. Genetic and phylogenetic analyses showed that whole genomes of Thai CBuVs were closely related to Chinese and Italian CBuVs, suggesting the possible origin of Thai CBuVs. The analysis of VP1 and VP2 genes in Thai CBuVs showed that 18 of them were placed in subgroup A, while only 2 belonged to subgroup B. This study is the first to report the detection and genetic characterization of CBuVs in domestic dogs in Thailand. Additionally, surveillance and genetic characterization of CBuVs in domestic animals should be further investigated on a larger scale to elucidate the dynamic, evolution, and distribution of CBuVs.
Topics: Animals; Dogs; Parvoviridae Infections; Thailand; Phylogeny; Parvovirus, Canine; Dog Diseases
PubMed: 38413640
DOI: 10.1038/s41598-024-54914-z -
PloS One 2024Subclinical infection of laboratory animals with one or more of several pathogens affects the results of experiments on animals. Monitoring the health of laboratory...
Immunoinformatics-guided recombinant polypeptide-based enzyme-linked immunosorbent assay for seromonitoring of laboratory animals for minute virus of mice and Kilham rat virus.
Subclinical infection of laboratory animals with one or more of several pathogens affects the results of experiments on animals. Monitoring the health of laboratory animals encompasses routine surveillance for pathogens, including several viruses. This study aimed to explore the development of an alternative assay to the existing ones for detecting infection of mice and rats with the parvoviruses minute virus of mice (MVM) and Kilham rat virus (KRV), respectively. Full-length VP2 and NS1 proteins of these parvoviruses, besides fragments containing multiple predicted epitopes stitched together, were studied for serological detection. The optimal dilution of full-length proteins and antigenic regions containing predicted epitopes for coating, test sera, and conjugate was determined using a checkerboard titration at each step. The assays were evaluated vis-à-vis commercially available ELISA kits. The results showed that an engineered fusion of fragments containing multiple predicted MVM VP2 and NS1 epitopes was better than either of the full-length proteins for detecting antibodies in 90% of the tested sera samples. For KRV ELISA, full-length VP2 was better compared to other individual recombinant protein fragments or combinations thereof for the detection of antibodies in sera. This report is the first description of an ELISA for KRV and an improved assay for MVM. Importantly, our assays could be exploited with small volumes of sera. The results also demonstrate the utility of immunoinformatics-driven polypeptide engineering in the development of diagnostic assays and the potential to develop better tests for monitoring the health status of laboratory animals.
Topics: Mice; Animals; Rats; Minute Virus of Mice; Immunoinformatics; Parvovirus; Enzyme-Linked Immunosorbent Assay; Animals, Laboratory; Antibodies, Viral; Peptides; Epitopes
PubMed: 38412152
DOI: 10.1371/journal.pone.0298742 -
JAMA Network Open Feb 2024Sepsis is a leading cause of pediatric mortality. Little attention has been paid to the association between viral DNA and mortality in children and adolescents with...
IMPORTANCE
Sepsis is a leading cause of pediatric mortality. Little attention has been paid to the association between viral DNA and mortality in children and adolescents with sepsis.
OBJECTIVE
To assess the association of the presence of viral DNA with sepsis-related mortality in a large multicenter study.
DESIGN, SETTING, AND PARTICIPANTS
This cohort study compares pediatric patients with and without plasma cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), human herpesvirus 6 (HHV-6), parvovirus B19 (B19V), BK polyomavirus (BKPyV), human adenovirus (HAdV), and torque teno virus (TTV) DNAemia detected by quantitative real-time polymerase chain reaction or plasma IgG antibodies to CMV, EBV, HSV-1, or HHV-6. A total of 401 patients younger than 18 years with severe sepsis were enrolled from 9 pediatric intensive care units (PICUs) in the Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network. Data were collected from 2015 to 2018. Samples were assayed from 2019 to 2022. Data were analyzed from 2022 to 2023.
MAIN OUTCOMES AND MEASURES
Death while in the PICU.
RESULTS
Among the 401 patients included in the analysis, the median age was 6 (IQR, 1-12) years, and 222 (55.4%) were male. One hundred fifty-four patients (38.4%) were previously healthy, 108 (26.9%) were immunocompromised, and 225 (56.1%) had documented infection(s) at enrollment. Forty-four patients (11.0%) died in the PICU. Viral DNAemia with at least 1 virus (excluding TTV) was detected in 191 patients (47.6%) overall, 63 of 108 patients (58.3%) who were immunocompromised, and 128 of 293 (43.7%) who were not immunocompromised at sepsis onset. After adjustment for age, Pediatric Risk of Mortality score, previously healthy status, and immunocompromised status at sepsis onset, CMV (adjusted odds ratio [AOR], 3.01 [95% CI, 1.36-6.45]; P = .007), HAdV (AOR, 3.50 [95% CI, 1.46-8.09]; P = .006), BKPyV (AOR. 3.02 [95% CI, 1.17-7.34]; P = .02), and HHV-6 (AOR, 2.62 [95% CI, 1.31-5.20]; P = .007) DNAemia were each associated with increased mortality. Two or more viruses were detected in 78 patients (19.5%), with mortality among 12 of 32 (37.5%) who were immunocompromised and 9 of 46 (19.6%) who were not immunocompromised at sepsis onset. Herpesvirus seropositivity was common (HSV-1, 82 of 246 [33.3%]; CMV, 107 of 254 [42.1%]; EBV, 152 of 251 [60.6%]; HHV-6, 253 if 257 [98.4%]). After additional adjustment for receipt of blood products in the PICU, EBV seropositivity was associated with increased mortality (AOR, 6.10 [95% CI, 1.00-118.61]; P = .049).
CONCLUSIONS AND RELEVANCE
The findings of this cohort study suggest that DNAemia for CMV, HAdV, BKPyV, and HHV-6 and EBV seropositivity were independently associated with increased sepsis mortality. Further investigation of the underlying biology of these viral DNA infections in children with sepsis is warranted to determine whether they only reflect mortality risk or contribute to mortality.
Topics: Adolescent; Humans; Male; Child; Infant; Child, Preschool; Female; DNA, Viral; Cohort Studies; Epstein-Barr Virus Infections; Herpesvirus 4, Human; DNA Viruses; Sepsis; Herpesvirus 1, Human; Cytomegalovirus Infections
PubMed: 38407904
DOI: 10.1001/jamanetworkopen.2024.0383 -
Viruses Feb 2024Canine parvovirus (CPV) is a single-stranded DNA virus that can cause typical hemorrhagic enteritis, and it is one of the common canine lethal viruses. In previous...
Canine parvovirus (CPV) is a single-stranded DNA virus that can cause typical hemorrhagic enteritis, and it is one of the common canine lethal viruses. In previous studies, we screened the Food and Drug Administration (FDA)'s drug library and identified nitazoxanide (NTZ), which has anti-CPV capabilities. To investigate the potential antiviral mechanisms, we first reconfirmed the inhibitory effect of NTZ on the CPV by inoculating with different doses and treating for different lengths of time. Then, the differences in the transcription levels between the 0.1%-DMSO-treated virus group and the NTZ-treated virus group were detected using RNA-seq, and a total of 758 differential expression genes (DEGs) were finally identified. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the DEGs revealed that these genes are involved in a variety of biological processes and/or signaling pathways, such as cell cycle, mitosis and cell proliferation and differentiation. A protein-protein interaction (PPI) analysis further identified hub genes associated with cell cycle and division among the DEGs. In addition, the expression levels of some of the enriched genes were detected, which were consistent with the high-throughput sequencing results. Moreover, when the cell cycle was regulated with cell cycle checkpoint kinase 1 (Chk1) inhibitor MK-8776 or Prexasertib HCl, both inhibitors inhibited the CPV. In summary, the transcriptome differential analysis results presented in this paper lay the foundation for further research on the molecular mechanism and potential targets of NTZ anti-CPV.
Topics: Animals; Dogs; Gene Expression Profiling; Nitro Compounds; Thiazoles; Parvoviridae Infections; Parvovirus, Canine; Computational Biology; Transcriptome
PubMed: 38400057
DOI: 10.3390/v16020282 -
Viruses Jan 2024Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet,...
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of overlapping genes likely to encode a functional protein in human parvovirus B19 (genus ), using an experimentally validated software, Synplot2. Synplot2 detected an open reading frame, X, conserved in all erythroparvoviruses, which overlaps the VP1 capsid gene and is under highly significant selection pressure. In a related virus, human parvovirus 4 (genus ), Synplot2 also detected an open reading frame under highly significant selection pressure, ARF1, which overlaps the VP1 gene and is conserved in all tetraparvoviruses. These findings provide compelling evidence that the X and ARF1 proteins must be expressed and functional. X and ARF1 have the exact same location (they overlap the region of the VP1 gene encoding the phospholipase A2 domain), are both in the same frame (+1) with respect to the VP1 frame, and encode proteins with similar predicted properties, including a central transmembrane region. Further studies will be needed to determine whether they have a common origin and similar function. X and ARF1 are probably translated either from a polycistronic mRNA by a non-canonical mechanism, or from an unmapped monocistronic mRNA. Finally, we also discovered proteins predicted to be expressed from a frame overlapping VP1 in other species related to parvovirus B19: porcine parvovirus 2 (Z protein) and bovine parvovirus 3 (X-like protein).
Topics: Humans; Parvovirus B19, Human; Capsid; Capsid Proteins; Open Reading Frames; Parvovirus; RNA, Messenger
PubMed: 38399966
DOI: 10.3390/v16020191