qPCR Test Research Articles

Inter‐Laboratory Comparison of qPCR Assays for Piscirickettsia salmonis in Atlantic Salmon (Salmo salar L.) in 11 Chilean Laboratories

ABSTRACTReal‐time PCR (qPCR) testing is an essential component of early detection surveillance systems for Piscirickettsia salmonis infection in Atlantic salmon farms in Chile. Currently, all 11 laboratories in the authorised diagnostic laboratory network use assays based on published protocols. Compared with other P. salmonis qPCR assays, these assays have the advantage of targeting two different genes, that is, the 16S ribosomal gene and the internal transcribed spacer (ITS), potentially allowing for higher diagnostic accuracy. However, variation and lack of harmonisation of qPCR testing systems (e.g., primers/probe, RNA/DNA as target, extraction methods, etc.) may contribute to among‐laboratory variation in qPCR results and an increased frequency of false‐negative and false‐positive results. The purpose of the ring trial reported herein was to compare qPCR results from 11 laboratories in Chile routinely testing Atlantic salmon for P. salmonis as part of a national control program. The panel of 14 samples included duplicates of three concentrations of P. salmonis in a homogenised head kidney, LF89 and EM90 bacteria and two negative controls (blank and a suspension of Flavobacterium psychrophilum). The sample order was randomised across labs, samples were tested blinded and analysed without knowledge of the source lab. Of the laboratories, 8 (72.7%) had at least one incorrect result out of 14 tested samples. Low‐concentration samples (Ct of about 30) were more often incorrectly classified by reverse transcription‐qPCR (RT‐qPCR) (3/6 labs) than by qPCR (0/5). Six (54.5%) labs had at least one false‐positive result indicating that cross‐contamination was likely during sample processing. Affected laboratories are advised to conduct internal investigations to confirm the causes of false‐positive results and recommendations for design and implementation of future ring trials are discussed.

Evaluation of the Vaginal Panel Realtime PCR kit (Vircell, SL) for diagnosing vaginitis: A comparative study with routinely used diagnostics.

Vaginitis is a prevalent clinical disorder associated with several adverse health consequences, prompting women to seek medical care. In this study we evaluate the Vaginal Panel Real-Time PCR kit (qPCR test) against routinely used diagnostics for detection of bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), and trichomoniasis. A total of 1011 vaginal swab specimens were analyzed. The routinely diagnostic methods for BV was Gram stain-based Nugent score. VVC presence was detected by culture, and Candida species were identified using MALDI-TOF MS. Trichomonas vaginalis was identified by culture in a selective medium. Molecular analyses were conducted on the MagXtract® 3200 System and analyzed using the CFX96™ Real-Time PCR Detection System. The sensitivity, specificity, positive predictive value, and negative predictive value of the qPCR test compared to the reference method for BV diagnosis was 93.1%, 88.8%, 90.1% and 92.2%, respectively, with a Kappa value of 0.82. For Candida species, sensitivity, specificity, positive predictive value, and negative predictive value were 96.0%, 98.4%, 95.3%, and 98.7%, respectively. The qPCR test detected 32 additional positive samples for Candida not reported by the routinely used diagnostics. For trichomoniasis, the qPCR test identified T. vaginalis in fifteen specimens, despite no microscopic detection in cultured specimens. Our results demonstrate that the Vaginal Panel Real-Time PCR kit shows optimal concordance with routinely used diagnostics for diagnosing vaginitis. Furthermore, enhancing detection of T. vaginalis. However, further validation studies are necessary to confirm its full diagnostic accuracy. The use of nucleic acid amplification tests (NAATs) provides rapid and accurate diagnosis, crucial for early detection and treatment of vaginitis.

Neuro-leishmaniasis with cauda equina syndrome and cranial nerve palsy: a rare manifestation of recurrent atypical visceral leishmaniasis

BackgroundVisceral leishmaniasis (VL) is a neglected tropical disease primarily affecting Brazil, East Africa, and India, with India accounting for 18% of the global burden. While VL typically presents with systemic symptoms like fever, weight loss, and splenomegaly, it can occasionally manifest atypically, posing significant diagnostic challenges. Neurological presentations of VL are extremely rare, making them difficult to suspect and diagnose. Cases where VL predominantly presents with neurological symptoms are particularly novel, underscoring the need for heightened awareness of such atypical manifestations in endemic regions.Clinical caseA 38-year-old man with history of recurrent atypical VL presented with diffuse lower back pain, progressive tingling, numbness, weakness in the lower extremities, and double vision for one month. Clinical and radiological evaluations suggested cauda equina syndrome and cranial nerve palsy, accompanied by generalized lymphadenopathy, subcutaneous nodules, and skin papules. The differential diagnosis initially included disseminated tuberculosis, histoplasmosis, and lymphoma. Cerebrospinal fluid (CSF) analysis revealed an inflammatory syndrome. Histopathology of lymph node and bone marrow revealed Leishmania amastigotes and subcutaneous nodule and skin biopsy revealed inflammatory cells with granulomas. Furthermore, the qPCR test on DNA from a subcutaneous nodule, lymph node, and CSF was positive for Leishmania kinetoplast DNA. The species was further confirmed as Leishmania donovani through ITS-based PCR amplification and sequencing. Finally, a diagnosis of relapse of VL with lymph node, cutaneous, and neurological involvement, including abducens nerve palsy and cauda equina syndrome, was established. He was treated with combination of liposomal amphotericin B and miltefosine, along with intrathecal hyaluronidase, resulting in significant improvement.ConclusionUnlike previously reported cases with both systemic and neurological symptoms, our patient predominantly presented with neurological manifestations, making this a unique and novel presentation of VL. This case highlights diagnostic challenges and management of atypical VL, emphasizing neurological involvement and successful therapeutic strategies.

Detection of equine parvovirus-hepatitis and efficacy of governmental regulation for equine biologics purity.

In 2018, a new virus, named equine parvovirus-hepatitis (EqPV-H), was discovered in a biologic product that had been administered to horses that subsequently developed clinical signs of equine serum hepatitis (Theiler disease). Further correlation of the virus with the disease sparked federal requirements that all equine biologics be free of EqPV-H. The initial quantitative real-time PCR (qPCR) test for EqPV-H has proved to be sensitive to co-extracted PCR inhibitors in template nucleic acids, causing false-negative results. We investigated the use of digital PCR (dPCR) as a more robust test. Examination of 227 equine biologic product lots available for purchase both before and after regulatory implementation using both detection methods indicated that dPCR is a more reliable platform. Nevertheless, use of the qPCR method for product screening had reduced the fraction of serials with EqPV-H detected from 39.6% prior to regulation to 6.8% after regulatory implementation. Adoption of dPCR testing is an opportunity to further decrease the prevalence of EqPV-H in equine biologics.

A loop-mediated isothermal amplification test for yaws: a multi-country diagnostic accuracy evaluation

To meet the WHO target of eradicating yaws by 2030, highly sensitive and specific diagnostic tools are needed. A multiplex Treponema pallidum-Haemophilus ducreyi loop-mediated isothermal amplification (TPHD-LAMP) test holds promise as a near-patient diagnostic tool for yaws and H ducreyi. We conducted a prospective evaluation in Cameroon, Côte d'Ivoire, Ghana, and the Republic of the Congo to determine the diagnostic accuracy of the TPHD-LAMP test, as well as to assess its acceptability, feasibility, and cost. Active case searching within schools and communities was used to locate participants with clinically suspicious laws-like lesions. Individuals with serologically confirmed active yaws provided paired lesion swabs between March, 2021, and April, 2023. For each participant, one swab was tested with the TPHD-LAMP at a local district laboratory and the other with reference quantitative PCR (qPCR) tests conducted at national reference laboratories. The primary outcome was TPHD-LAMP test sensitivity and specificity compared with qPCR. Laboratory technicians were interviewed using a multiple-choice survey to gauge acceptability and feasibility of the TPHD-LAMP test. Costs of each test were calculated. Of 3085 individuals with at least one suspected yaws lesion, 531 (17%) were serologically confirmed. We enrolled 493 participants with seropositive yaws and a further 32 with negative serology. The sensitivity of the TPHD-LAMP test for detecting T pallidum was 63% (95% CI 56-70) and the specificity was 66% (95% CI 61-71). Sensitivity and specificity for T pallidum improved to 73% (63-82; p=0·0065) and 75% (68-80; p=0·0003), respectively, in H ducreyi-negative samples. Interviews highlighted challenges in user-friendliness and practicality of the TPHD-LAMP test. The cost of the test per sample was one third of that of qPCR, although the TPHD-LAMP test entailed higher costs to establish the assay. This was the first multi-country diagnostic evaluation of a molecular test for yaws. The TPHD-LAMP testing, in its current form, falls short of the WHO target product profile criteria for yaws diagnostics. These findings highlight the importance of assessing new diagnostics in real-world conditions to ensure their suitability for programmatic use. The EDCTP2 programme supported by the EU.

Noninvasive Methods Unveil the Trophic Transmission of the Tapeworm Ligula intestinalis in Gull‐Billed Terns

ABSTRACTRecent developments in microscopic and molecular tools have allowed the implementation of new approaches for assessing parasitic infections in wildlife populations. This is particularly important for the noninvasive detection and quantification of endoparasites in live animals. Here, we combined copromicroscopic (Mini‐FLOTAC) and molecular (qPCR) techniques to detect the infection of the macroparasite Ligula intestinalis (Cestoda, Pseudophyllidea) in fresh droppings of Gull‐billed Terns Gelochelidon nilotica (Charadriiformes, Laridae) breeding in southwestern Spain. Additionally, we sequenced the cytochrome b gene in parasite isolates from Gull‐billed Terns (definitive host) and Common Bleak Alburnus alburnus (second intermediate host) sampled around tern colonies to explore potential genetic differences between the isolates. The qPCR test showed a higher prevalence (18%; in 13/73 samples) than Mini‐FLOTAC (9%; in 8/88 samples), indicating that qPCR was more sensitive for diagnostic purposes than fecal flotation alone. Although the agreement between both techniques was substantial (84.2%) mainly due to the large number of uninfected samples, only Mini‐FLOTAC allowed us to quantify parasite shedding. When combining techniques, the prevalence of infection did not differ between adults and chicks, suggesting frequent trophic transmission from parents to their offspring via food provisioning. Phylogenetic analyses identified four haplotypes in the isolates from Gull‐billed Terns and Bleak, all of which were placed within a European clade composed of tapeworms recovered exclusively from phylogenetically derived cyprinid fish. This, combined with the short lifespan of mature tapeworms, suggests that Gull‐billed Terns became infected after consuming infected fish around their breeding colonies rather than on their West African wintering grounds. Altogether, our results represent the first record of L. intestinalis in Gull‐billed Terns and the first molecular characterization of the parasite in the Iberian Peninsula. This integrative coprodiagnostic protocol can be applied to other host–parasite systems, allowing researchers to study helminth infections in wild populations using a noninvasive approach.

TRP36-ELISA for E. canis detection: Concordance with TaqMan real-time PCR and point-of-care testing

Ehrlichia canis, a widely distributed tick-borne pathogen, requires prompt and accurate diagnosis for effective management. Real-time PCR serves as the reference standard for diagnosing E. canis infection, whereas serological tests are crucial for detecting antibody responses indicative of infection or post-exposure status. Early detection during the acute phase of the disease is essential for optimal treatment and recovery. E. canis Tandem Repeat Protein 36 (TRP36) elicits early acute phase responses. We developed an enzyme-linked immunosorbent assay (ELISA) using recombinant TRP36 to detect IgM and IgG antibodies against E. canis. We assessed the diagnostic agreement, sensitivity, and specificity of the rTRP36-ELISA and a commercial test kit (SNAP 4Dx Plus Test) with TaqMan Real-time PCR (qPCR) using the NCSS 2023 program version 23.0.1. Leftover serum samples from 32 dogs at the Veterinary Teaching Hospital were randomly selected and examined for E. canis infection using qPCR, rTRP36-ELISA, and SNAP 4Dx Plus Test. qPCR detected positive results in 12 (37.5 %), whereas ELISA and SNAP 4Dx Plus detected positive results in 10 (31.25 %) and 13 (40.62 %), respectively. Moderate agreement (κ = 0.545) was observed between rTRP36-ELISA and qPCR, and fair agreement (κ = 0.379) between SNAP 4Dx Plus and qPCR. Substantial agreement (κ = 0.79) was found between rTRP36-ELISA and SNAP 4Dx Plus. Compared to qPCR, the sensitivity and specificity of rTRP36-ELISA were 70 % and 77.27 %, respectively, compared to 53.85 % and 73.86 %, respectively, for SNAP 4Dx Plus. Our findings suggest that TRP36 is a promising antigen for E. canis serodiagnosis, potentially improving sensitivity and specificity.

Development of a forensic DNA research grade test material.

Advancements in forensic DNA typing technology and methods have increased sensitivity and, while beneficial, carry the weight of more challenging profile interpretation. In response, the forensic DNA community has often requested more complex reference materials to address commonly encountered measurement and interpretation issues such as complex DNA mixtures, DNA degradation, and PCR inhibition. The National Institute of Standards and Technology (NIST) released Research Grade Test Material 10235: Forensic DNA Typing Resource Samples to support the forensic DNA community. Components include three single source samples, two degraded samples, and three mixture samples. As part of the Research Grade Test Material (RGTM) process, automated methods for bottling, alternative sample tube types, and the addition of carrier RNA for stabilizing low-quantity samples were investigated. Both internal and external testing demonstrate the stability of the material over time at 4°C through qPCR testing. In the development of a data portal, users have been allowed to anonymously upload results and compare their data with NIST and others. This report describes the preparation and stability of this material.

A Novel Trichinella spiralis Galectin Strengthens the Macrophage ADCC Killing of Larvae via Driving M1 Polarization.

Galectin recognizes β-galactosides through its carbohydrate recognition domains (CRDs). This study aimed to determine the biological features of a novel Trichinella spiralis galectin (galactoside-binding lectin family protein, TsGLFP) and its role in driving macrophage M1 polarization and enhancing ADCC killing of larvae. TsGLFP belongs to the galectin family and has two CRDs. The complete TsGLFP cDNA sequence was cloned and then expressed in Escherichia coli BL21. The results of qPCR, Western blot, and indirect immunofluorescence tests (IIFTs) revealed that TsGLFP was expressed in various stages of T. spiralis worms and principally localized at the cuticle and around the female embryos of the nematode. rTsGLFP had the function of agglutinating mouse erythrocytes, and this agglutination activity could be inhibited by lactose. After the mouse macrophage RAW264.7 was incubated with rTsGLFP, the expression level of the M1 genes (iNOS, IL-6, and TNF-α) and NO production were obviously increased. After incubating macrophages with rTsGLFP, there was a noticeable rise in the expression levels of p-IκB-α and p-NF-κB p65. Additionally, rTsGLFP enhanced the macrophage's ability to kill newborn larvae by ADCC cytotoxicity. When the macrophages were pretreated with the specific p-NF-κB p65 inhibitor PDTC, and then stimulated with rTsGLFP, the expression levels of iNOS, NO, and p-NF-κB p65 and the macrophages' ADCC cytotoxicity were distinctly decreased. These findings indicated that rTsGLFP enhanced the macrophage ADCC killing of larvae by driving M1 polarization through activating the NF-κB pathway.

A-251 Simplification of Molecular Diagnostics for Sexually Transmitted Infection Point-of-Care Testing

Abstract Background HPV-caused cancers contribute to a large disease burden, accounting for 5% of all cancers. It is estimated that over 700,000 people develop HPV-related cancers each year with the majority being cervical cancer. The burden of this disease is disproportionately carried by low-income countries with the highest rates of HPV cervical infections primarily found in sub-Saharan Africa, Latin America, Eastern Europe, and South-East Asia. Many regions in low-resource countries lack adequate access to sensitive point-of-care screening tools, preventing timely diagnosis and treatment. Current low-cost methods, such as Pap smears and visual inspection using acetic acid suffer from low sensitivity, specificity, and reproducibility which limit their effectiveness as a screening modality. Many countries use nucleic acid amplification tests (NAATs) to identify key HPV infections which may progress towards cervical cancer. However, the expenditure for NAAT-capable equipment and reagents are cost-prohibitive for rural and underserved communities. To reduce screening barriers, we developed an isothermal HPV molecular test that can detect all 14 cancer-causing HPV strains using a novel amplification methodology combined with G-quadruplex DNAzyme colorimetric detection. Methods We developed a novel isothermal amplification technique that is related to loop-mediated isothermal amplification (LAMP) but uses modified looped primers to enable exponential amplification at 60°C for 1 hour. The modified primers only require two binding sites compared to 4-6 in LAMP. To detect the amplified products, we used G-quadruplex peroxidase-like DNAzyme probes which reduce ABTS to produce a visually interpreted result. Analytical validation evaluated the method’s limit of detection, specificity, and accuracy. As proof of concept in a relevant matrix, clinical cervical brushings collected ThinPrep Pap media were tested with the new method and compared to an FDA-approved reference qPCR test. Results Repeated experiments demonstrate that the lowest detectable HPV DNA concentration was approximately 1000 genomic copies/µL with no amplification with other pathogens. As proof of concept, the comparison to the reference standard demonstrated high accuracy. Conclusions The application of our assay is intended as a near-patient screening tool with further evaluation by a clinician for confirmation. With an accurate and rapid screening tool, we envision low-resource regions across the world will have the tools to rapidly detect and treat cervical cancers in their early stages.

Spore PCR and qPCR Methods for Rapid Detection of Five Colletotrichum Species Responsible for Pepper Anthracnose in Korea

Pepper anthracnose, caused by <i>Colletotrichum</i> spp., leads to a decrease in the quantity of pepper fruit production. Molecular diagnosis is crucial for rapid identification of pathogens and determination of fungicide resistance. However, the traditional process of isolating the pathogen, extracting genomic DNA, and analyzing the gene sequence is time-consuming, which delays rapid diagnosis. In this study, we introduced a method using conidia of <i>Colletotrichum</i> spp. instead of genomic DNA, eliminating the need for DNA extraction or special processing for diagnosis. To elucidate this method, sensitivity was assessed through polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR) tests using internal transcribed spacer-based primer pairs. Both PCR and qPCR tests showed that detection is feasible with just one conidia, with over 1,000 conidia yielding results comparable to approximately 1 pg of genomic DNA. For amplifying the cytochrome b gene for quinone-outside inhibitor fungicide susceptibility testing, detection from a single conidium is achievable, but a stable PCR product is obtained by increasing the number of cycles to 35. Additionally, the addition of 10% grinding fresh chili pepper paste to V8-Juicea gar medium, which is known for inducing conidia rapidly from the isolates, resulted in 3.2 to 6.0 times more conidia compared to the commonly used potato dextrose agar medium, enhancing the potential for swift testing. Taken together, this study presents a direct utilization of pepper anthracnose conidia through PCR or qPCR, offering a valuable technique for amplifying target genes, such as the minimum conidial amount and barcode genes, for molecular identification of anthracnose disease in pepper through PCR and qPCR analysis.

Assessment of real-time PCR test in oral fluid samples for screening the serotypes of Actinobacillus pleuropneumoniae circulating in swine herds

Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, causing remarkable economic losses in the global swine industry. The diversity of A. pleuropneumoniae is generally determined through serotype identification, which is commonly employed for control strategies and surveillance. However, serological methods currently in use still have significant limitations. This study explores the use of real-time polymerase chain reaction (qPCR) to detect circulating serotypes of A. pleuropneumoniae in non-diseased swine herds through testing of oral fluids.The study included three A. pleuropneumoniae-positive and three A. pleuropneumoniae-negative farms located in Quebec, Canada. Tonsil brushings, microbiological growths, and oral fluids were analyzed using qPCR to detect A. pleuropneumoniae and its distinct serotypes. Serological tests were performed using the LPS ELISA available at that time. In negative farms the absence of A. pleuropneumoniae and any serotype confirmed the specificity of the method. Positive farms, on the other hand, confirmed also the sensitivity of the analysis, with oral fluid samples consistently yielding positive results for the serotypes identified by ELISA.The qPCR test conducted on oral fluids offers a noninvasive and cost-effective method for monitoring, complementing traditional serological techniques. It provides qualitative information about serotype distribution, facilitating proactive surveillance and control strategies.

Antiviral potential of phenolic compounds against HSV-1: In-vitro study

Background This in vitro study aimed to investigate the effect of several phenolic compounds, including doxorubicin, quercetin, and resveratrol, on HSV-1 infection. Methods The cytotoxicity of the drugs was assessed on Vero cells using the MTT assay. HSV-1 was treated with the drugs, and the supernatants were collected at various time points. TCID50% and qPCR tests were conducted on the supernatants to determine viral titration post-inoculation. Results The TCID50% assay showed significant changes in viral titration for acyclovir, doxorubicin, and quercetin at most concentrations ( p-value < .05), while no significant changes were observed for resveratrol. The qPCR results demonstrated that drug-treated HSV-1 exhibited a significant reduction in DNA titers at various time points compared to non-treated HSV-1 infected Vero cells, except doxorubicin (0.2 µM) and acyclovir (5 µm). However, over time, DNA virus levels gradually increased in the drug-treated groups. Notably, at certain concentrations of doxorubicin and quercetin-treated groups, virus titer significantly declined, similar to acyclovir. Conclusions Our findings suggest that quercetin at concentrations of 62 and 125 µM significantly reduced HSV-1 infectivity, as well as these two concentrations of quercetin showed a significant difference in virus reduction compared with acyclovir (10 µM) at certain time points. The anti-inflammatory properties of quercetin, in contrast to acyclovir, make it a potential candidate for anti HSV-1 treatment in life-threatening conditions such as Herpes encephalitis. Additionally, doxorubicin, an anticancer drug, showed meaningful inhibition of HSV-1 at non-toxic concentrations of 2 and 8 µM, suggesting its potential interference with HSV-1 in viral-oncolytic therapy in cancer treatment.

Shuanghuanglian volatile oil exerts antipyretic, anti-inflammatory, and antibacterial synergistic effects through multiple pathways

Ethnopharmacological relevanceTraditional Chinese Medicine (TCM) has a rich history spanning 2000 years. Shuanghuanglian, a traditional Chinese herbal formula composed of three botanicals, is primarily used to treat colds, respiratory infections (including bacterial pneumonia), and pharyngitis. Previous research has found that the volatile oil of Shuanghuanglian is crucial for its efficacy. However, there is a lack of studies investigating its mechanisms. Aim of the studyThis study aims to explore the antibacterial and anti-inflammatory mechanisms of Shuanghuanglian volatile oil and its potential to enhance the antibacterial effects when used in conjunction with antibiotics. MethodsDetermination of the GC-MS fingerprint of SVO using Gas Chromatography-Mass Spectrometry (GC-MS), The antibacterial effects of SVO on multidrug-resistant Klebsiella pneumoniae (MDR-KP) were assessed by detecting MIC, checkerboard method assay, time-kill curves, resistance growth curves, transcriptome sequencing analysis, scanning electron microscopy(SEM), purification, and quantitative analysis of extracellular polysaccharides(EPS). In vivo part, an MDR-KP induced mouse pneumonia model was established to evaluate the mitigating effects of SVO on mouse pneumonia, using comprehensive network pharmacology and bioinformatics to identify genes related to bacterial pneumonia and potential targets of SVO. Validation was performed through molecular docking, qPCR, and ELISA tests. ResultsSVO modulates the expression of MDR-KP mRNA for wecB, wecC, murA, murD, murE, murF, inhibiting the synthesis of O-antigen polysaccharides and peptidoglycans, thereby compromising bacterial cell wall integrity and affecting the synthesis of biofilms. These actions not only exhibit antibacterial effects but also enhance antibacterial activity, restoring the sensitivity of CEF to MDR-KP. SVO suppresses the biological activity of PTGS2, reducing the production of Prostaglandin E2 (PGE2), thereby exerting antipyretic and anti-inflammatory effects, providing new insights for the development of natural non-steroidal anti-inflammatory drugs (NSAIDs). ConclusionsOur research indicates that SVO exerts antipyretic, anti-inflammatory, and antibacterial synergistic effects through multiple pathways.

Diversity and risk assessment of Phytophthora spp. found on plant roots in native plant nurseries and interstate shipping nurseries in California

For many nurseries it is difficult to diagnose Phytophthora-infected plants in time to prevent disease incursion and spread, especially if the infection occurs on roots and causes no or limited symptoms on aerial plant parts. Rapid, accurate, and specific diagnostic methods can facilitate the identification and removal of infected plants. This study was conducted to investigate if specific nursery types within California are more likely to have different Phytopthora species and which hosts are more likely to test positive for a Phytophthora species using immunological and molecular diagnostic tools. From Fall 2016 to Spring 2019, we collected 1,180 root samples from 15 nurseries, each in California, that fell into one of three distinct plant-sourcing categories. Plant roots were tested with Phytophthora-specific ImmunoStrips, and positives samples were identified to species-level by qPCR and sequencing. Of the 1,180 samples collected, 262 (22%) were found positive for infection by a Phytophthora sp. and 152 of these samples (58%) could be diagnosed to the species level. Hosts belonging to the genera Ceanothus (Rhamnaceae), Arctostaphylos (Ericaceae), and Salvia (Lamiaceae) tested positive for Phytophthora spp. most often. A total of 18 Phytophthora species were detected from the root samples, most frequently over the course of this study. Despite its high rate of false positives (30%), the ImmunoStrip® Phytophthora assay is useful as a preliminary screening tool for in-field diagnosis of root infection. qPCR testing of positive ImmunoStrip® tests allows for more accurate detection and facilitates species assignment.

A multiplexed real‐time PCR assay for simultaneous quantification of human immunodeficiency virus and Hepatitis B virus for low‐and‐middle‐ income countries

Due to shared routes of transmission, including sexual contact and vertical transmission, HIV-HBV co-infection is common, particularly in sub-Saharan Africa. Measurement of viral load (VL), for both HIV and HBV, plays a critical role for determining their infectious phase and monitoring response to antiviral therapy. Implementation of viral load testing in clinical settings is a significant challenge in resource-limited countries, notably because of cost and availability issues. We designed HIV and HBV primers for conserved regions of the HIV and HBV genomes that were specifically adapted to viral strains circulating in West Africa that are HIV-1 subtype CRF02AG and HBV genotype E. We first validated two monoplex qPCR assays for individual quantification and, then developed a multiplex qPCR for simultaneous quantification of both viruses. HIV RNA and HBV DNA amplification was performed in a single tube using a one-step reverse transcription-PCR reaction with primers and probes targeting both viruses. Performance characteristics such as the quantification range, sensitivity, and specificity of this multiplex qPCR assay were compared to reference qPCR tests for both HIV and HBV viral load quantification. The multiplex assay was validated using clinical samples from co- or mono-infected patients and gave comparable viral load quantification to the HIV and HBV reference test respectively. The multiplex qPCR demonstrated an overall sensitivity of 71.25 % [68.16–74.3] for HBV and 82 % [78.09–85.90] for HIV and an overall specificity of 100 % [94.95–100] for both viruses. Although the overall sensitivities of the HIV and HBV assays were lower than the commercial comparator assays, the sensitivity in the clinical decision range of >1000 copies/mL for HIV was 80 % [71.26–88.73] and >1000 IU/mL for HBV was 100 % [95.51–100] which indicates the test results can be used to guide treatment decisions. This in-house developed multiplex qPCR assay represents a useful diagnostic tool as it can be performed on affordable "open" real-time PCR platforms currently used for HIV or SARS-Cov-2 infection surveillance in Mali.

Development and Application of a Portable Environmental DNA Test for the Detection of Rafetus swinhoei in Viet Nam

ABSTRACTSwinhoe's (or Yangtze) giant softshell turtle (Rafetus swinhoei) is a large, critically endangered freshwater turtle and considered among the rarest species in the world. As of 2024, only two individuals have been confirmed to remain alive, one at the Suzhou Zoo in China and one in Xuan Khanh Lake, Viet Nam. The only hope for the long‐term survival of R. swinhoei is finding additional, as yet undiscovered, animals that have thus far eluded detection by traditional survey methods. In recent years, numerous studies have been published on the use of environmental DNA (eDNA) for species detection and monitoring. This method takes advantage of the persistence of DNA in the environment, such as in water, soil, and air. An organism's DNA is shed into the environment through urine, feces, and the sloughing of skin. Species‐specific quantitative polymerase chain reaction (qPCR) testing can be used to detect eDNA in samples collected from the environment. eDNA trials to detect R. swinhoei were initiated by the Asian Turtle Program and Washington State University in 2013. To expand the use of eDNA for species detection by conservationists, we developed and validated a first‐of‐its‐kind innovative point‐of‐detection (POD) qPCR platform for the rapid, onsite detection of R. swinhoei from water samples. Here we show that the portable eDNA test kit can be used for the successful detection of R. swinhoei in a large body of water and that pooling filters may be a useful strategy to reduce test costs and improve detection efficiency. Use of this test can expand the search for R. swinhoei in unexplored and understudied lakes, reservoirs, and other bodies of water where this species may be present and could inform field surveys utilizing eDNA for other threatened species that are rare in nature.

Identification and Validation of STC1 Act as a Biomarker for High-Altitude Diseases and Its Pan-Cancer Analysis.

High-altitude diseases, including acute mountain sickness (AMS), high-altitude cerebral edema (HACE), and high-altitude pulmonary edema (HAPE), are closely related to an individual's ability to adapt to hypoxic environments. However, specific research in this field is relatively limited, and further biomarker research and clinical trials are needed to clarify the exact role and potential therapeutic applications of key genes in high-altitude diseases. This study focuses on the role of the STC1 gene in high-altitude diseases and explores its expression patterns in different types of cancer. By using gene expression data analysis and functional experiments, we identified STC1 as a key gene affecting the development of altitude sickness. In addition, we also conducted expression and mutation analysis on STC1 in various cancer samples and found significant differences in the expression of this gene in 13 types of malignant tumors, which is associated with the hypoxic state in the tumor microenvironment. In addition, STC1 is significantly associated with patient prognosis and influences tumor immunity by mediating six types of immune cells (CD8+T cells, CD4+T cells, neutrophils, macrophages, monocytes, and B cells) in the tumor microenvironment. The expression and diagnostic value of STC1 were confirmed through GEO datasets and qPCR testing, indicating consistency with the results of bioinformatics analysis. These results indicate that STC1 is not only an important factor in the adaptive response to high-altitude diseases but may also play a role in the adaptation of cancer to low-oxygen environments. Our research provides a new perspective and potential targets for the discovery of biomarkers for high-altitude diseases and cancer treatment.

Humans seropositive for Trypanosoma cruzi co-infected with intestinal helminths have higher infectiousness, parasitaemia and Th2-type response in the Argentine Chaco

BackgroundThe Gran Chaco ecoregion is a well-known hotspot of several neglected tropical diseases (NTDs) including Chagas disease, soil-transmitted helminthiasis and multiparasitic infections. Interspecific interactions between parasite species can modify host susceptibility, pathogenesis and transmissibility through immunomodulation. Our objective was to test the association between human co-infection with intestinal parasites and host parasitaemia, infectiousness to the vector and immunological profiles in Trypanosoma cruzi-seropositive individuals residing in an endemic region of the Argentine Chaco.MethodsWe conducted a cross-sectional serological survey for T. cruzi infection along with an intestinal parasite survey in two adjacent rural villages. Each participant was tested for T. cruzi and Strongyloides stercoralis infection by serodiagnosis, and by coprological tests for intestinal parasite detection. Trypanosoma cruzi bloodstream parasite load was determined by quantitative PCR (qPCR), host infectiousness by artificial xenodiagnosis and serum human cytokine levels by flow cytometry.ResultsThe seroprevalence for T. cruzi was 16.1% and for S. stercoralis 11.5% (n = 87). We found 25.3% of patients with Enterobius vermicularis. The most frequent protozoan parasites were Blastocystis spp. (39.1%), Giardia lamblia (6.9%) and Cryptosporidium spp. (3.4%). Multiparasitism occurred in 36.8% of the examined patients. Co-infection ranged from 6.9% to 8.1% for T. cruzi-seropositive humans simultaneously infected with at least one protozoan or helminth species, respectively. The relative odds of being positive by qPCR or xenodiagnosis (i.e. infectious) of 28 T. cruzi-seropositive patients was eight times higher in people co-infected with at least one helminth species than in patients with no such co-infection. Trypanosoma cruzi parasite load and host infectiousness were positively associated with helminth co-infection in a multiple regression analysis. Interferon-gamma (IFN-γ) response, measured in relation to interleukin (IL)-4 among humans infected with T. cruzi only, was 1.5-fold higher than for T. cruzi-seropositive patients co-infected with helminths. The median concentration of IL-4 was significantly higher in T. cruzi-seropositive patients with a positive qPCR test than in qPCR-negative patients.ConclusionsOur results show a high level of multiparasitism and suggest that co-infection with intestinal helminths increased T. cruzi parasitaemia and upregulated the Th2-type response in the study patients.Graphical

Human Herpesvirus 6-A Rare Aetiologic Agent for CNS Infections in Immunocompetent Individuals or an Underestimation?

Background: Human herpesvirus 6 (HHV-6) is considered a ubiquitous virus, with many countries reporting a seroprevalence of more than 80-90% among the general population. However, this virus is unique among herpesviruses in its ability to integrate into the genetic material of the host's cells. Thus, there are three ways by which HHV-6 can cause an active infection-primary infection, reactivation of a latent acquired infection, or activation of iciHHV-6 (inherited chromosomally integrated HHV-6). Whole blood quantitative polymerase chain reaction (qPCR) is very useful in distinguishing between iciHHV-6 and primary infection/reactivation. Our aim is to assess the role of HHV-6 in the aetiology of central nervous system (CNS) infections in adults and children, to describe all HHV-6-positive cases in an attempt to determine the susceptible population and to identify potential risk factors that can be linked to HHV-6 meningoencephalitis. Methods: We performed a retrospective study involving patients that were admitted to Prof. Dr. Matei Bals National Institute of Infectious Diseases, Bucharest, Romania, with a diagnosis of meningitis or encephalitis. We only selected the clinical records of patients that had a multiplex PCR Biofire® FilmArray® meningitis/encephalitis panel. Results: We report a 5% HHV-6 positivity in the cerebrospinal fluid (CSF) of patients with CNS infections tested with a commercial multiplex PCR M/E (meningitis/encephalitis) panel. Additionally, 2% to 4% of the total study population (n = 100) had active HHV-6 infections, which denotes 40 to 80% of the HHV-6-positive samples. We did not observe any statistically significant correlation between HHV-6 positivity in the CSF and variables such as age, sex, or comorbidities, including obesity, diabetes, hypertension, immunosuppression, or oncologic disease. Therefore, no risk factors could be linked with HHV-6 positivity in the CSF. Conclusions: although multiplex qualitative PCR is highly useful for providing rapid results and identifying nearly every pathogen that can cause meningitis/encephalitis, we have to be aware of this type of test's limitations. All patients with HHV-6 detectable in their CSF via a multiplex PCR test should also undergo qPCR testing from both CSF and blood to prevent over-diagnosing HHV-6 CNS infections, to avoid unnecessary antiviral treatments, and ensure the accurate identification of the true diagnosis.