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1.
Emerg Infect Dis ; 29(4): 848-850, 2023 04.
Article in English | MEDLINE | ID: mdl-36918374

ABSTRACT

We retrospectively screened oropharyngeal and rectal swab samples originally collected in California, USA, for Chlamydia trachomatis and Neisseria gonorrhoeae testing for the presence of monkeypox virus DNA. Among 206 patients screened, 17 (8%) had samples with detectable viral DNA. Monkeypox virus testing from mucosal sites should be considered for at-risk patients.


Subject(s)
Chlamydia Infections , Gonorrhea , Mpox (monkeypox) , Humans , California/epidemiology , Chlamydia Infections/diagnosis , Chlamydia Infections/epidemiology , Chlamydia trachomatis/genetics , Chlamydia trachomatis/isolation & purification , DNA , Gonorrhea/diagnosis , Monkeypox virus/genetics , Monkeypox virus/isolation & purification , Neisseria gonorrhoeae/genetics , Neisseria gonorrhoeae/isolation & purification , Retrospective Studies , Mpox (monkeypox)/diagnosis
2.
Mol Cancer ; 21(1): 154, 2022 07 28.
Article in English | MEDLINE | ID: mdl-35902864

ABSTRACT

BACKGROUND: Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage. METHODS: We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model. RESULTS: Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia. CONCLUSIONS: EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity.


Subject(s)
Epstein-Barr Virus Infections , Nasopharyngeal Neoplasms , DNA-Binding Proteins , Epstein-Barr Virus Infections/complications , Epstein-Barr Virus Infections/epidemiology , Epstein-Barr Virus Infections/genetics , Genome-Wide Association Study , Genotype , Herpesvirus 4, Human/genetics , Humans , Nasopharyngeal Carcinoma/diagnosis , Nasopharyngeal Carcinoma/genetics , Nasopharyngeal Neoplasms/diagnosis , Nasopharyngeal Neoplasms/genetics , Nasopharyngeal Neoplasms/pathology , Viral Proteins
3.
J Clin Microbiol ; 60(5): e0017822, 2022 05 18.
Article in English | MEDLINE | ID: mdl-35465708

ABSTRACT

The ability to distinguish between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, responses to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. This assay had 95 to 100% agreement with WGS for 502 upper respiratory tract swab samples collected between 26 April 2021 and 1 August 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Multiplex Polymerase Chain Reaction , Mutation , Real-Time Polymerase Chain Reaction , Reverse Transcription , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
4.
Clin Infect Dis ; 72(9): e291-e295, 2021 05 04.
Article in English | MEDLINE | ID: mdl-32965474

ABSTRACT

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in blood, also known as RNAemia, has been reported, but its prognostic implications are poorly understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with coronavirus disease 2019 (COVID-19) clinical severity. METHODS: An analytical cross-sectional study was performed in a single-center tertiary care institution and included consecutive inpatients and outpatients with confirmed COVID-19. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included intensive care unit (ICU) admission, invasive mechanical ventilation, and 30-day all-cause mortality. RESULTS: Paired nasopharyngeal and plasma samples were included from 85 patients. The median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; P = .04). Comorbidities were frequent including obesity (37.6%), hypertension (30.6%), and diabetes mellitus (22.4%). RNAemia was detected in 28/85 (32.9%) of patients, including 22/28 (78.6%) who required hospitalization. In models adjusted for age, RNAemia was detected more frequently in individuals who developed severe disease including ICU admission (32.1 vs 14.0%; P = .04) and invasive mechanical ventilation (21.4% vs 3.5%; P = .02). All 4 deaths occurred in individuals with detectable RNAemia. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days. CONCLUSIONS: This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Cross-Sectional Studies , Hospitalization , Humans , Middle Aged , RNA, Viral
5.
Emerg Infect Dis ; 27(10): 2720-2723, 2021.
Article in English | MEDLINE | ID: mdl-34296992

ABSTRACT

We report persistent severe acute respiratory syndrome coronavirus 2 infection in a patient with HIV/AIDS; the virus developed spike N terminal domain and receptor binding domain neutralization resistance mutations. Our findings suggest that immunocompromised patients can harbor emerging variants of severe acute respiratory syndrome coronavirus 2.


Subject(s)
Acquired Immunodeficiency Syndrome , COVID-19 , Humans , Mutation , Protein Binding , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
7.
J Clin Microbiol ; 59(8): e0085921, 2021 Jul 19.
Article in English | MEDLINE | ID: mdl-34037430

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase PCR (RT-qPCR) to detect three nonsynonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2-positive specimens from our San Francisco Bay Area population. Between 1 December 2020 and 1 March 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K plus N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing of a validation subset of 229 specimens and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed the rapid emergence of the L452R variant in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.


Subject(s)
COVID-19 , SARS-CoV-2 , Epidemiological Monitoring , Genotype , Humans , Reverse Transcriptase Polymerase Chain Reaction
8.
Clin Chem ; 68(1): 204-213, 2021 12 30.
Article in English | MEDLINE | ID: mdl-34605900

ABSTRACT

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen in blood has been described, but the diagnostic and prognostic role of antigenemia is not well understood. This study aimed to determine the frequency, duration, and concentration of nucleocapsid antigen in plasma and its association with coronavirus disease 2019 (COVID-19) severity. METHODS: We utilized an ultrasensitive electrochemiluminescence immunoassay targeting SARS-CoV-2 nucleocapsid antigen to evaluate 777 plasma samples from 104 individuals with COVID-19. We compared plasma antigen to respiratory nucleic acid amplification testing (NAAT) in 74 individuals with COVID-19 from samples collected ±1 day of diagnostic respiratory NAAT and in 52 SARS-CoV-2-negative individuals. We used Kruskal-Wallis tests, multivariable logistic regression, and mixed-effects modeling to evaluate whether plasma antigen concentration was associated with disease severity. RESULTS: Plasma antigen had 91.9% (95% CI 83.2%-97.0%) clinical sensitivity and 94.2% (84.1%-98.8%) clinical specificity. Antigen-negative plasma samples belonged to patients with later respiratory cycle thresholds (Ct) when compared with antigen-positive plasma samples. Median plasma antigen concentration (log10 fg/mL) was 5.4 (interquartile range 3.9-6.0) in outpatients, 6.0 (5.4-6.5) in inpatients, and 6.6 (6.1-7.2) in intensive care unit (ICU) patients. In models adjusted for age, sex, diabetes, and hypertension, plasma antigen concentration at diagnosis was associated with ICU admission [odds ratio 2.8 (95% CI 1.2-6.2), P=.01] but not with non-ICU hospitalization. Rate of antigen decrease was not associated with disease severity. CONCLUSIONS: SARS-CoV-2 plasma nucleocapsid antigen exhibited comparable diagnostic performance to upper respiratory NAAT, especially among those with late respiratory Ct. In addition to currently available tools, antigenemia may facilitate patient triage to optimize intensive care utilization.


Subject(s)
Antigens, Viral/blood , COVID-19 Testing/methods , COVID-19 , Coronavirus Nucleocapsid Proteins/blood , COVID-19/diagnosis , Electrochemical Techniques , Hospitalization , Humans , Immunoassay , Luminescent Measurements , Nucleocapsid , Phosphoproteins/blood , SARS-CoV-2 , Sensitivity and Specificity
9.
BMC Neurol ; 19(1): 263, 2019 Oct 31.
Article in English | MEDLINE | ID: mdl-31672142

ABSTRACT

BACKGROUND: Progressive multifocal leukoencephalopathy (PML) is a rapidly developing demyelinating disease in the cerebral white matter and is often caused by JC polyomavirus (JCV). PML after lung transplantation is rare and has a poor prognosis, with no established therapies. Reducing the patient's immunosuppressant doses, thereby restoring immunity, could be used to treat PML. However, some patients develop immune reconstitution inflammatory syndrome (IRIS) with this treatment, an immune-induced inflammatory response to JCV that results in serious neuronal damage. We herein report a case of a 60-year-old female who suffered from PML 5 years after lung transplantation, had worsened brain lesions thought to be related to PML-IRIS at the time of immunosuppressant reduction, and missed treatment opportunities. CASE PRESENTATION: A 60-year-old female developed PML 5 years after lung transplantation. Fluid-attenuated inversion recovery and diffusion-weighted brain magnetic resonance imaging (MRI) revealed multiple high-signal lesions, mainly in the cerebral white matter. Polymerase chain reaction found 0.32 million copies/mL of JCV in the cerebrospinal fluid. Thus, she was given a diagnosis of PML. Mycophenolate mofetil and tacrolimus dosages were reduced, and CD4-positive cell counts and the blood concentration of each immunosuppressant were monitored. Mefloquine was also orally administered at a daily dose of 275 mg for 3 days and was then administered at a dose of 275 mg per week. Although the patient's CD4-positive cell counts increased and her immune system recovered, her symptoms and brain MRI findings worsened. We suspected PML progression or a transition to PML-IRIS. Steroid pulse therapy to suppress the inflammatory lesions was not possible but was retrospectively indicated. The patient rapidly began to exhibit akinetic mutism and died 4 months after the onset of neurologic symptoms. CONCLUSIONS: When neurologic symptoms and abnormal brain MRI findings are noted during immune recovery, it is often difficult to distinguish between progressed PML and PML-IRIS. However, the pathogenesis of brain lesions usually involves inflammation and immune-reactive mechanisms for JCV. Steroid pulse therapy, which can reduce inflammation, should thus be administered in organ transplantation cases with differential diagnoses including PML-IRIS.


Subject(s)
Immune Reconstitution Inflammatory Syndrome , Leukoencephalopathy, Progressive Multifocal , Lung Transplantation , Brain/diagnostic imaging , Brain/pathology , Female , Humans , Immunocompromised Host , Immunosuppressive Agents/administration & dosage , Immunosuppressive Agents/adverse effects , Immunosuppressive Agents/therapeutic use , JC Virus , Middle Aged
11.
Environ Toxicol ; 31(12): 1710-1719, 2016 Dec.
Article in English | MEDLINE | ID: mdl-26183440

ABSTRACT

Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used therapeutic agents; however, their pharmacological actions raise concerns about potential risks to the reproductive health of aquatic vertebrates. In the present study, a medaka ovulation assay was applied as an in vitro model to evaluate NSAID-induced antiovulatory activity. We first tested five NSAIDs, including diclofenac sodium (DCF), ketoprofen (KP), salicylic acid (SA), mefenamic acid (MA), and acetylsalicylic acid (ASA) for their antiovulatory activities toward the follicles isolated from the ovaries of spawning females. Of all the chemicals tested, DCF had the highest antiovulatory activity, with the concentration that caused 50% inhibition (IC50) (101 µM). MA was the second most potent inhibitor following DCF, but KP, SA, or ASA had little inhibitory effect on the ovulation of the follicles. The in vitro antiovulatory activity of five NSAIDs showed good correlation with data published on the inhibitory activity on human COX-2. Second, we selected DCF and SA as the most and least potent NSAIDs, respectively, and examined the effects on reproduction of intact fish in order to evaluate whether the ovulation assay was a reasonable predictor of potential reproductive effects in fish. Females exposed to DCF showed a concentration-dependent decrease in the number of spawned eggs and an increment in the gonadosomatic index (GSI), possibly due to an anovulation in the females. In contrast, neither fecundity nor the GSI of females decreased at up to 20 mg/L of SA, at which acute lethality to medaka was induced. In conclusion, the medaka ovulation assay reflected the potency of NSAID-induced antiovulatory activity and may thus serve as an in vitro model for the prediction of NSAID-induced reproductive toxicity. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1710-1719, 2016.


Subject(s)
Anti-Inflammatory Agents, Non-Steroidal/toxicity , Oryzias/physiology , Ovary/drug effects , Reproduction/drug effects , Water Pollutants, Chemical/toxicity , Animals , Aspirin/toxicity , Diclofenac/toxicity , Female , Humans , Ketoprofen/toxicity , Mefenamic Acid/toxicity , Ovary/cytology , Ovulation/drug effects , Ovum/drug effects , Ovum/physiology , Salicylic Acid/toxicity
12.
Appl Environ Microbiol ; 80(4): 1394-402, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24334665

ABSTRACT

Insertion sequences (ISs) are the simplest transposable elements and are widely distributed in bacteria; however, they also play important roles in genome evolution. We recently identified a protein called IS excision enhancer (IEE) in enterohemorrhagic Escherichia coli (EHEC) O157. IEE promotes the excision of IS elements belonging to the IS3 family, such as IS629, as well as several other families. IEE-mediated IS excision generates various genomic deletions that lead to the diversification of the bacterial genome. IEE has been found in a broad range of bacterial species; however, among sequenced E. coli strains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC pathogenic E. coli strains isolated from domestic animals and found that IEE is distributed in specific lineages of enterotoxigenic E. coli (ETEC) strains of serotypes O139 or O149 isolated from swine. The iee gene is located within integrative elements that are similar to SpLE1 of EHEC O157. All iee-positive ETEC lineages also contained multiple copies of IS629, a preferred substrate of IEE, and their genomic locations varied significantly between strains, as observed in O157. These data suggest that IEE may have been transferred among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative elements. In addition, IS629 is actively moving in the ETEC O139 and O149 genomes and, as in EHEC O157, is promoting the diversification of these genomes in combination with IEE.


Subject(s)
DNA Transposable Elements , Enterotoxigenic Escherichia coli/genetics , Enterotoxigenic Escherichia coli/isolation & purification , Escherichia coli Proteins/genetics , Animals , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Enterotoxigenic Escherichia coli/classification , Genotype , Molecular Sequence Data , Sequence Analysis, DNA , Serotyping , Swine
13.
Genome Biol Evol ; 16(1)2024 01 05.
Article in English | MEDLINE | ID: mdl-38109923

ABSTRACT

Several hundred disease-causing mutations are currently known in domestic dogs. Breeding management is therefore required to minimize their spread. Recently, genetic methods such as direct-to-consumer testing have gained popularity; however, their effects on dog populations are unclear. Here, we aimed to evaluate the influence of genetic testing on the frequency of mutations responsible for canine degenerative myelopathy and assess the changes in the genetic structure of a Pembroke Welsh corgi population from Japan. Genetic testing of 5,512 dogs for the causative mutation in superoxide dismutase 1 (SOD1) (c.118G>A (p.E40K)) uncovered a recent decrease in frequency, plummeting from 14.5% (95/657) in 2019 to 2.9% (24/820) in 2022. Weir and Cockerham population differentiation (FST) based on genome-wide single-nucleotide polymorphism (SNP) of 117 selected dogs detected the SNP with the highest FST located in the intron of SOD1 adjacent to the c.118G>A mutation, supporting a selection signature on SOD1. Further genome-wide SNP analyses revealed no obvious changes in inbreeding levels and genetic diversity between the 2019 and 2022 populations. Our study highlights that genetic testing can help inform improved mating choices in breeding programs to reduce the frequency of risk variants and avoid inbreeding. This combined strategy could decrease the genetic risk of canine degenerative myelopathy, a fatal disease, within only a few years.


Subject(s)
Spinal Cord Diseases , Superoxide Dismutase , Dogs , Animals , Superoxide Dismutase-1/genetics , Superoxide Dismutase/genetics , Inbreeding , Mutation , Spinal Cord Diseases/genetics , Spinal Cord Diseases/veterinary
14.
J Clin Microbiol ; 51(11): 3700-10, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23985916

ABSTRACT

Antiviral therapy for cytomegalovirus (CMV) plays an important role in the clinical management of solid organ and hematopoietic stem cell transplant recipients. However, CMV antiviral therapy can be complicated by drug resistance associated with mutations in the phosphotransferase UL97 and the DNA polymerase UL54. We have developed an amplicon-based high-throughput sequencing strategy for detecting CMV drug resistance mutations in clinical plasma specimens using a microfluidics PCR platform for multiplexed library preparation and a benchtop next-generation sequencing instrument. Plasmid clones of the UL97 and UL54 genes were used to demonstrate the low overall empirical error rate of the assay (0.189%) and to develop a statistical algorithm for identifying authentic low-abundance variants. The ability of the assay to detect resistance mutations was tested with mixes of wild-type and mutant plasmids, as well as clinical CMV isolates and plasma samples that were known to contain mutations that confer resistance. Finally, 48 clinical plasma specimens with a range of viral loads (394 to 2,191,011 copies/ml plasma) were sequenced using multiplexing of up to 24 specimens per run. This led to the identification of seven resistance mutations, three of which were present in <20% of the sequenced population. Thus, this assay offers more sensitive detection of minor variants and a higher multiplexing capacity than current methods for the genotypic detection of CMV drug resistance mutations.


Subject(s)
Cytomegalovirus/genetics , DNA, Viral/genetics , DNA-Directed DNA Polymerase/genetics , Drug Resistance, Viral , High-Throughput Nucleotide Sequencing/methods , Mutation, Missense , Phosphotransferases (Alcohol Group Acceptor)/genetics , Viral Proteins/genetics , Adolescent , Adult , Aged , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Cytomegalovirus/drug effects , Cytomegalovirus/isolation & purification , Cytomegalovirus Infections/virology , DNA, Viral/chemistry , Female , Humans , Male , Microbial Sensitivity Tests/methods , Middle Aged , Sensitivity and Specificity , Young Adult
15.
J Mol Diagn ; 25(7): 490-501, 2023 07.
Article in English | MEDLINE | ID: mdl-37068736

ABSTRACT

Plasma Epstein-Barr virus (EBV) DNA is an established biomarker for endemic nasopharyngeal carcinoma. However, existing real-time quantitative PCR (qPCR) assays are limited by poor interlaboratory reproducibility. This is a barrier to biomarker integration into staging systems and management. It was hypothesized that EBV digital PCR (dPCR) would have similar sensitivity but improved precision relative to qPCR. Using the World Health Organization EBV standard and patient specimens, the NRG-HN001 BamHI-W qPCR, two commercial EBNA-1 qPCR assays, and two laboratory-developed dPCR assays amplifying the BamHI-W, EBNA-1, and EBER targets were compared. Testing was conducted in the North American reference laboratory for the NRG-HN001 randomized trial. The EBV dPCR assays achieved similar performance compared with qPCR. Although dPCR does not require quantitation standards, different dPCR thresholding algorithms yielded significant qualitative and quantitative variation. This was most evident with low levels of EBV DNA. No-template control-informed thresholding (ddpcRquant) mitigated false-positive/false-negative findings. The NRG-HN001 BamHI-W qPCR and laboratory-developed BamHI-W droplet dPCR offered higher sensitivity, lower limit of blank, higher precision at low plasma EBV DNA levels (≤1500 IU/mL), and higher overall agreement with clinical specimens versus single-copy qPCR/dPCR targets (EBNA-1/EBER). These data confirm the rationale for using the BamHI-W target to define prognostic thresholds and indicate that both qPCR and dPCR methods harmonized to the World Health Organization standard can provide the necessary analytical performance.


Subject(s)
Epstein-Barr Virus Infections , Nasopharyngeal Neoplasms , Humans , Nasopharyngeal Carcinoma/diagnosis , Nasopharyngeal Carcinoma/genetics , Herpesvirus 4, Human/genetics , Real-Time Polymerase Chain Reaction/methods , Epstein-Barr Virus Infections/diagnosis , Reproducibility of Results , DNA, Viral/analysis , Biomarkers , Nasopharyngeal Neoplasms/diagnosis , Nasopharyngeal Neoplasms/genetics
16.
IDCases ; 33: e01881, 2023.
Article in English | MEDLINE | ID: mdl-37680215

ABSTRACT

As part of an epidemiologic survey, we screened remnant samples collected for STI testing for mpox virus. We identified two cases of presumed MPXV infection in pregnant, heterosexual cisgender women. Here, we describe their pregnancy and birth outcomes. Both patients required induction of labor and experienced labor complicated by chorioamnionitis.

17.
J Clin Virol ; 164: 105493, 2023 07.
Article in English | MEDLINE | ID: mdl-37220710

ABSTRACT

BACKGROUND: Despite the sharp increase in mpox (formerly monkeypox) incidence and the wide geographic spread of mpox during the 2022 outbreak, the community prevalence of infection remains poorly characterized. This study is a retrospective epidemiologic survey to estimate mpox prevalence. METHODS: Samples obtained for sexually transmitted infection (STI) testing from April to September 2022 in the public hospital and clinic system of San Mateo County, California were screened for mpox virus (MPXV) using polymerase chain reaction. RESULTS: 16/1,848 samples from 11/1,645 individuals were positive for MPXV by qPCR. 4/11 individuals with positive MPXV testing were cisgender women, 2 of whom were pregnant at the time of sample collection. Both deliveries were complicated by chorioamnionitis. Anorectal and oropharyngeal samples were the most likely to be positive for MPXV (4/60 anorectal samples and 4/66 oropharyngeal samples compared with 5/1,264 urine samples and 3/445 vaginal samples). CONCLUSIONS: Our study is one of the first epidemiologic surveys for MPXV infection outside of sexual health/STI clinic settings. Relatively high rates of MPXV from oropharyngeal and anorectal samples reinforces the importance of MPXV testing at various anatomic sites, particularly if patients are presenting with non-lesional symptoms (pharyngitis, proctitis). However, the United States Food and Drug Administration (FDA) has not yet authorized non-lesional MPXV testing. The identification of MPXV in women in our cohort suggests that the rates of mpox in women may have previously been underestimated and highlights the risk of pregnancy complications associated with mpox.


Subject(s)
Mpox (monkeypox) , Pregnancy , Humans , Female , Prevalence , Retrospective Studies , Ambulatory Care Facilities , California/epidemiology , Monkeypox virus
18.
J Clin Virol ; 162: 105444, 2023 05.
Article in English | MEDLINE | ID: mdl-37043903

ABSTRACT

BACKGROUND: SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts. METHODS: This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern. RESULTS: Initial valid results were obtained from 95.8% [95% confidence interval (CI): 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI: 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5. CONCLUSIONS: This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2/genetics , Biological Assay , Mutation , Oligonucleotides
19.
Expert Opin Drug Saf ; 21(10): 1303-1313, 2022 Oct.
Article in English | MEDLINE | ID: mdl-35418260

ABSTRACT

BACKGROUND: A recent 3-year post-marketing surveillance (PMS) study reaffirmed the safety and effectiveness of linagliptin in linagliptin-naïve Japanese patients with type 2 diabetes (T2D). We present further analyses from this study by body mass index (BMI). RESEARCH DESIGN AND METHODS: Safety and effectiveness were assessed across BMI subgroups (<25, 25 to <30, and ≥30 kg/m2). RESULTS: Data were available for 876, 566, and 201 patients in the BMI subgroups, respectively. Incidence of adverse drug reactions [ADR] with linagliptin was 11.42%, 11.31%, 10.45%, respectively. The most common ADR of special interest was hepatic disorders (n [%]: 6 [0.68], 7 [1.24], and 3 [1.49], respectively). Additional use of glucose-lowering drugs (GLDs) increased with BMI (15.0%, 19.1%, 24.4% of patients; P < 0.001). In the overall population, HbA1c change (adjusted mean %±SE) until week 156 was -0.71±0.04, -0.68±0.04 and -0.74±0.09. In patients receiving linagliptin with no additional GLDs, HbA1c changes were -0.58%±0.04, -0.62%±0.04, and -0.77%±0.11. CONCLUSIONS: In this study of linagliptin in Japanese patients with T2D, across BMI subgroups no new safety concerns were observed. The proportion of patients with additional GLD use increased with baseline BMI. Decreases in HbA1c were observed in all subgroups, including in patients with no additional GLD use. CLINICALTRIALS.GOV: NCT01650259.


Subject(s)
Diabetes Mellitus, Type 2 , Linagliptin , Humans , Body Mass Index , Diabetes Mellitus, Type 2/drug therapy , Glycated Hemoglobin , Japan , Linagliptin/adverse effects , Product Surveillance, Postmarketing
20.
Neurosci Res ; 180: 90-98, 2022 Jul.
Article in English | MEDLINE | ID: mdl-35257837

ABSTRACT

Recent evidence suggests that soluble amyloid-ß oligomers (AßOs) act as a key factor in the pathogenetic mechanism of Alzheimer's disease (AD). AßOs induce neurotoxic and synaptotoxic effects probably through binding to certain receptors, however it remains unclarified which receptors are most critically involved. In addition, dysregulation in glutamatergic signaling is implicated in AD. In this study, we used a rat primary cortical neuron model to investigate AßO-induced aberrations of synaptic proteins and binding of extracellular AßOs to candidate receptors in the glutamatergic system. Immunocytochemical analyses showed that both presynaptic (SNAP-25, synapsin I) and postsynaptic (spinophilin, homer 1b/c) proteins appeared to aberrantly dislocate from synapses upon AßO treatment. Double immunofluorescence staining of AßO-treated neurons without permeabilization pretreatment revealed that extracellular AßOs exist over neuronal soma and neurites and clearly colocalized with GluN1 and GluN2B subunits of NMDA receptors and metabotropic glutamate receptor 1 (mGluR1), but not with NMDA GluN2A subunits and mGluR5. AßO treatment altered neither total protein levels nor intracellular localizations of these receptors. These results suggest that extracellular AßOs specifically bind to both NMDA receptors containing GluN2B subunits and mGluR1. It is likely that binding of AßOs to these receptors induces various pathological responses, consequently leading to synaptic disruptions. Our study thus highlights the important roles of GluN2B-containing NMDA receptors and mGluR1 receptors in the synapse pathology in AD.


Subject(s)
Alzheimer Disease , Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Animals , Neurons/metabolism , Rats , Receptors, Metabotropic Glutamate , Receptors, N-Methyl-D-Aspartate/metabolism , Synapses/physiology
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