Optical imaging spectroscopy for rapid, primary screening of SARS-CoV-2: a proof of concept.

Effective testing is essential to control the coronavirus disease 2019 (COVID-19) transmission. Here we report a-proof-of-concept study on hyperspectral image analysis in the visible and near-infrared range for primary screening at the point-of-care of SARS-CoV-2. We apply spectral feature descriptors, partial least square-discriminant analysis, and artificial intelligence to extract information from optical diffuse reflectance measurements from 5 µL fluid samples at pixel, droplet, and patient levels. We discern preparations of engineered lentiviral particles pseudotyped with the spike protein of the SARS-CoV-2 from those with the G protein of the vesicular stomatitis virus in saline solution and artificial saliva. We report a quantitative analysis of 72 samples of nasopharyngeal exudate in a range of SARS-CoV-2 viral loads, and a descriptive study of another 32 fresh human saliva samples. Sensitivity for classification of exudates was 100% with peak specificity of 87.5% for discernment from PCR-negative but symptomatic cases. Proposed technology is reagent-free, fast, and scalable, and could substantially reduce the number of molecular tests currently required for COVID-19 mass screening strategies even in resource-limited settings.

Feasibility and Accuracy of HIV Testing of Children by Caregivers Using Oral Mucosal Transudate HIV Tests.

BACKGROUND: Children encounter multiple barriers in accessing facilities. HIV self-testing using oral mucosal transudate (OMT) tests has been shown to be effective in reaching hard-to-reach populations. We evaluated the feasibility and accuracy of caregivers conducting HIV testing using OMTs in children in Zimbabwe. METHODS: We offered OMTs to caregivers (>18 years) living with HIV to test children (2-18 years) living in their households. All caregivers were provided with manufacturer instructions. In Phase 1 (January-December 2018, 9 clinics), caregivers additionally received a demonstration by a provider using a test kit and video. In Phase 2 (January-May 2019, 3 clinics), caregivers did not receive a demonstration. We collected demographic data and assessed caregiver's ability to perform the test and interpret results. Caregiver performance was assessed by direct observation and scored using a predefined checklist. Factors associated with obtaining a full score were analyzed using logistic regression. RESULTS: Overall 400 caregivers (83.0% female, median age 38 years) who were observed tested 786 children (54.6% female, median age 8 years). For most tests, caregivers correctly collected oral fluid [87.1% without provider demonstrations (n = 629) and 96.8% with demonstrations (n = 157), P = 0.002]. The majority correctly used a timer (90.3% without demonstrations and 96.8% with demonstrations, P = 0.02). In multivariate logistic regression caregivers who obtained a full score for performance were more likely to have received a demonstration (odds ratio 4.14, 95% confidence interval: 2.01 to 8.50). CONCLUSIONS: Caregiver-provided testing using OMTs is a feasible and accurate HIV testing strategy for children. We recommend operational research to support implementation at scale.

Evaluation of adenovirus amplified detection of immunochromatographic test using tears including conjunctival exudate in patients with adenoviral keratoconjunctivitis.

BACKGROUND: We evaluated a novel silver amplification immunochromatography test for rapid detection of adenovirus (AdV) antigen equipped with an automated reader system using tears including conjunctival exudate in patients with adenoviral keratoconjunctivitis. METHODS: Two kinds of immunochromatographic (IC) kits, a conventional IC kit for conjunctival scrapings (control kit) and an IC kit using tears including conjunctival exudate collected by pressing a filter paper strip on the conjunctiva (test kit), were tested on 90 patients who attended Migita Eye Clinic with suspected adenoviral conjunctivitis. The results of the test kits were automatically obtained by a specific reader, which was based on silver amplification immunochromatography system, in 15 min. The detection of AdV was confirmed by real-time polymerase chain reaction (PCR) method, and typing was performed by direct sequencing. Comparative dilution assay was carried out with the two kits, using AdV type 3 and type 54 strains. RESULTS: The sensitivity of the control kit and test kit was 89.8% and 98.3%, respectively. The specificity of both kits was 100%. A significant difference in the sensitivities of the two IC kits against PCR positivity was observed (P < 0.01). A significant correlation was found between AdV DNA copy numbers on a logarithmic scale obtained with the two tests (P < 0.01). The sensitivity of the test kit was 32-64-fold higher than that of the control kit without silver amplification for both AdV types. CONCLUSIONS: These results suggest that this novel amplified AdV detection kit using tears including conjunctival exudate is useful, because it decreases patients' discomfort from specimen collection and its sensitivity is significantly higher than that of the conventional IC kit.

Multiplex Droplet Digital PCR Assay for Quantification of Human T-Cell Leukemia Virus Type 1 Subtype c DNA Proviral Load and T Cells from Blood and Respiratory Exudates Sampled in a Remote Setting.

During human T-cell leukemia virus type 1 (HTLV-1) infection, the frequency of cells harboring an integrated copy of viral cDNA, the proviral load (PVL), is the main risk factor for progression of HTLV-1-associated diseases. Accurate quantification of provirus by droplet digital PCR (ddPCR) is a powerful diagnostic tool with emerging uses for monitoring viral expression. Current ddPCR techniques quantify HTLV-1 PVL in terms of whole genomic cellular material, while the main targets of HTLV-1 infection are CD4+ and CD8+ T cells. Our understanding of HTLV-1 proliferation and the amount of viral burden present in different compartments is limited. Recently a sensitive ddPCR assay was applied to quantifying T cells by measuring loss of germ line T-cell receptor genes as method of distinguishing non-T-cell from recombined T-cell DNA. In this study, we demonstrated and validated novel applications of the duplex ddPCR assay to quantify T cells from various sources of human genomic DNA (gDNA) extracted from frozen material (peripheral blood mononuclear cells [PBMCs], bronchoalveolar lavage fluid, and induced sputum) from a cohort of remote Indigenous Australians and then compared the T-cell measurements by ddPCR to the prevailing standard method of flow cytometry. The HTLV-1 subtype c (HTLV-1c) PVL was then calculated in terms of extracted T-cell gDNA from various compartments. Because HTLV-1c preferentially infects CD4+ T cells, and the amount of viral burden correlates with HTLV-1c disease pathogenesis, application of this ddPCR assay to accurately measure HTLV-1c-infected T cells can be of greater importance for clinical diagnostics and prognostics as well as monitoring therapeutic applications.

Bovine Herpesvirus 4 in Parana State, Brazil: case report, viral isolation, and molecular identification.

Bovine Herpesvirus 4 (BoHV-4) is a member of Gammaherpesvirinae sub-family and belongs to genus Rhadinovirus . This virus has been associated with different clinical manifestations and research activity has put forward a strong correlation among virus infection, postpartum metritis, and abortion. The goal of this work was to characterize a virus strain isolate from a cow's uterine outflow. From swabs drawn of uterine secretion, a virus strain was isolated and characterized by its cytopathology, morphology, and molecular biology approaches. In culture there was CPE development, characterized mainly by long strands with several small balloons along them, radiated from infected cells. Electron microscopy analysis revealed virus particles that had icosahedrical capsid symmetry surrounded by a loose envelope, typical of a herpesvirus. A 2,571 bp PCR product after Hind III digestion generated four fragments, whose base pair composition were 403, 420, 535, and 1,125 bp. Restriction enzymes Hind III and Bam HI generated the expected diagnostic bands as well as a 2,350 bp hypermolar fragment as a result of Bam HI treatment to demonstrate that agent was a bovine herpesvirus 4, appertaining to DN-599 group.

Bovine Herpesvirus 4 in Parana State, Brazil: case report, viral isolation, and molecular identification

Bovine Herpesvirus 4 (BoHV-4) is a member of Gammaherpesvirinae sub-family and belongs to genus Rhadinovirus. This virus has been associated with different clinical manifestations and research activity has put forward a strong correlation among virus infection, postpartum metritis, and abortion. The goal of this work was to characterize a virus strain isolate from a cow’s uterine outflow. From swabs drawn of uterine secretion, a virus strain was isolated and characterized by its cytopathology, morphology, and molecular biology approaches. In culture there was CPE development, characterized mainly by long strands with several small balloons along them, radiated from infected cells. Electron microscopy analysis revealed virus particles that had icosahedrical capsid symmetry surrounded by a loose envelope, typical of a herpesvirus. A 2,571 bp PCR product after HindIII digestion generated four fragments, whose base pair composition were 403, 420, 535, and 1,125 bp. Restriction enzymes HindIII and BamHI generated the expected diagnostic bands as well as a 2,350 bp hypermolar fragment as a result of BamHI treatment to demonstrate that agent was a bovine herpesvirus 4, appertaining to DN-599 group.

Viral genomes in the pericardial fluid and in peri- and epicardial biopsies from a German cohort of patients with large to moderate pericardial effusions.

The aetiology of pericardial effusion has been generally assessed by clinical work-up only, which leaves a large cohort of patients with "idiopathic" effusions virtually undiagnosed. In accordance with the ESC guidelines, this contribution intends to change this attitude. After therapeutic or diagnostic pericardiocentesis of 259 patients with large to moderate pericardial effusions, pericardial fluid, epicardial and pericardial biopsies, and blood samples were analysed by PCR for cardiotropic microbial agents. Cytology, histology, immunohistology of tissue and fluids and laboratory tests were performed. Of the 259 patients, 35 % suffered from an autoreactive aetiology, 28 % suffered from a malignant and 14 % from an infectious cause. Investigating all samples by PCR, we identified viral genomes in 51 (19.7 %) patients, parvovirus B19 (B19 V) being identified in 25 and Epstein-Barr virus (EBV) in 19 cases. In patients with a sole infectious aetiology (n = 36), B19 V was detected in 21 and EBV in 10 cases. When differentiating with regard to the material investigated for the presence of cardiotropic viruses, parvovirus B19 was most often detected in the epicardium and EBV was most frequently detected in the pericardial fluid independent from the final diagnostic categorisation. Bacterial cultures including tests for tuberculosis were all negative. Molecular techniques improve sensitivity, specificity and diagnostic accuracy for the underlying aetiology in pericarditis patients with effusion. The identification of specific viral signatures will help to understand pathogenetic mechanisms in pericarditis and allow to tailor an adequate therapy beyond antiphlogistic treatment.

Comparison of the etiology of viral respiratory illnesses in inner-city and suburban infants.

BACKGROUND: The risk of developing childhood asthma has been linked to the severity and etiology of viral respiratory illnesses in early childhood. Since inner-city infants have unique environmental exposures, we hypothesized that patterns of respiratory viral infections would also be distinct. METHODS: We compared the viral etiology of respiratory illnesses in 2 groups: a cohort of 515 infants from 4 inner-city areas and a cohort of 285 infants from mainly suburban Madison, Wisconsin. Nasal secretions were sampled during periods of respiratory illness and at 1 year of age and were analyzed for viral pathogens by multiplex polymerase chain reaction. RESULTS: Overall, inner-city infants had lower rates of viral detection. Considering specific viruses, sick urban infants had lower rates of detectable rhinovirus or respiratory syncytial virus infection and higher rates of adenovirus infection. Every urban site had a higher proportion of adenovirus-positive samples associated with illnesses (10%-21%), compared with Madison (6%). CONCLUSIONS: These findings provide evidence that inner-city babies have different patterns of viral respiratory illnesses than babies who grow up in a more suburban location. These findings raise important questions about the etiology of virus-negative illnesses in urban infants and the possibility of long-term consequences of early life infections with adenovirus in this population.

Identification of viral and atypical bacterial pathogens in children hospitalized with acute respiratory infections in Hong Kong by multiplex PCR assays.

Acute respiratory tract infection is a leading cause of hospital admission of children. This study used a broad capture, rapid and sensitive method (multiplex PCR assay) to detect 20 different respiratory pathogens including influenza A subtypes H1, H3, and H5; influenza B; parainfluenza types 1, 2, 3, and 4; respiratory syncytial virus (RSV) groups A and B; adenoviruses; human rhinoviruses; enteroviruses; human metapneumoviruses; human coronaviruses OC43, 229E, and SARS-CoV; Chlamydophila pneumoniae; Legionella pneumophila; and Mycoplasma pneumoniae; from respiratory specimens of 475 children hospitalized over a 12-month period for acute respiratory tract infections. The overall positive rate (47%) was about twice higher than previous reports based on conventional methods. Influenza A, parainfluenza and RSV accounted for 51%, and non-cultivable viruses accounted for 30% of positive cases. Influenza A peaked at March and June. Influenza B was detected in January, February, and April. Parainfluenza was prevalent throughout the year except from April to June. Most RSV infections were found between February and September. Adenovirus had multiple peaks, whereas rhinovirus and coronavirus OC43 were detected mainly in winter and early spring. RSV infection was associated with bronchiolitis, and parainfluenza was associated with croup; otherwise the clinical manifestations were largely nonspecific. In general, children infected with influenza A, adenovirus and mixed viruses had higher temperatures. In view of the increasing concern about unexpected outbreaks of severe viral infections, a rapid multiplex PCR assay is a valuable tool to enhance the management of hospitalized patients, and for the surveillance for viral infections circulating in the community.

Absence of surface expression of feline infectious peritonitis virus (FIPV) antigens on infected cells isolated from cats with FIP.

Feline infectious peritonitis virus (FIPV) positive cells are present in pyogranulomas and exudates from cats with FIP. These cells belong mainly to the monocyte/macrophage lineage. How these cells survive in immune cats is not known. In this study, FIPV positive cells were isolated from pyogranulomas and exudates of 12 naturally FIPV-infected cats and the presence of two immunologic targets, viral antigens and MHC I, on their surface was determined. The majority of the infected cells were confirmed to be cells from the monocyte/macrophage lineage. No surface expression of viral antigens was detected on FIPV positive cells. MHC I molecules were present on all the FIPV positive cells. After cultivation of the isolated infected cells, 52+/-10% of the infected cells re-expressed viral antigens on the plasma membrane. In conclusion, it can be stated that in FIP cats, FIPV replicates in cells of the monocyte/macrophage lineage without carrying viral antigens in their plasma membrane, which could allow them to escape from antibody-dependent cell lysis.

The use of the OraSure collection device for hepatitis virus testing in health care settings.

Oral mucosal transudate (OMT) has levels of IgG and IgA that, although lower than in serum, are of the same specificity as serum. Blood can be a difficult sample to take especially from persons with an aversion to the process or with poor veins. There is also a small exposure risk to the phlebotomist. OMT has been shown to be useful in screening for a range of bloodborne viruses, however, the ELISA assays need to be modified, usually by increasing test volumes and incubation times and/or by modifying the substrate. A number of commercial serum kits have been modified successfully in this way. The major roles for these assays are for epidemiology or for screening high risk populations. If used for screening, it is imperative that any positive is confirmed by a serum test. The use of OMT samples using the OraSure(R) collection device, which is FDA approved and with which we have the most experience, has increased in recent years in community health care settings, with positive feedback from users.

Vascular transfer of adenovirus is augmented by nitric oxide in the rat heart.

Reversible opening of the endothelial barrier remains a major obstacle when hearts are transfected via the coronary system. Our aim was to establish an experimental system permitting the continuous analysis of vascular transfer of virus in the intact heart. Isolated saline-perfused rat hearts were inverted and covered with a latex cap to collect interstitial transudate (IT) on the pericardial surface. Adenovirus (10(9) pfu/ml) was stably labeled with rhodamine fluorescent dye. Analysis of IT and coronary perfusate revealed that under baseline conditions, adenovirus in the IT reached 75% of its vascular concentration within 3 min. The nitric oxide-donors S-nitroso-N-acetyl penicillamine (SNAP) and bradykinin (BK) were the most effective substances to increase total IT volume and adenoviral interstitial concentration. Perfusion with 9% serum markedly reduced IT volume flow and delayed the SNAP/BK effect. Our findings demonstrate that SNAP and BK effectively increased coronary transfer of adenovirus suggesting that the inverted isolated heart is a suitable model to optimize vascular transfer of virus under standardized conditions.

Detection of HIV-RNA in aqueous humor and subretinal fluid in an HIV carrier with rhegmatogenous retinal detachment.

BACKGROUND: Although human immunodeficiency virus (HIV)-related ocular complexes are commonly observed in acquired immune deficiency syndrome (AIDS) patients, it has not been previously reported that HIV had already invaded the ocular tissues of HIV carriers. CASE: A 56-year-old woman was diagnosed as having rhegmatogenous retinal detachment with a retinal tear in the 6-o'clock position in her right eye. No signs of ocular manifestations except the retinal detachment were observed. A blood examination revealed that she was already infected with HIV-1, and she was categorized as an HIV carrier. OBSERVATIONS: Aqueous humor and subretinal fluid samples were obtained at the time of surgery for rhegmatogenous retinal detachment. Reverse-transcription polymerase chain reaction and Southern blotting at three regions of the HIV, LTR, gag, and env, confirmed the HIV infection in both aqueous humor and subretinal fluid. During the approximately 2-year follow-up after surgery, the patient did not show any signs of retinitis, uveitis, or other ocular manifestations. CONCLUSIONS: This is the first report to reveal that HIV can invade the eye in the early stage of HIV infection. This infection may be related to HIV-related ocular complexes, which suppress the local immunological response.

Effect of adenovirus type 1 and influenza A virus on Streptococcus pneumoniae nasopharyngeal colonization and otitis media in the chinchilla.

Considerable evidence has implicated respiratory tract virus potentiation of bacterial adherence, colonization, and superinfection as a significant factor contributing to the pathogenesis of otitis media (OM). Influenza A and B viruses, adenovirus, and respiratory syncytial virus are the primary respiratory tract viruses associated with this disease. Investigations have established a dramatic increase in the development of experimental OM in chinchillas co-inoculated with influenza A virus and Streptococcus pneumoniae (Spn). The mechanism underlying this phenomenon was suggested to involve, in part, viral compromise of eustachian tube mucosal integrity and function. This study was designed to assess and compare the effect of adenovirus and influenza A virus infection on adherence, the kinetics of colonization, and invasion of the middle ear by Spn in the chinchilla model of OM. Cohorts were inoculated intranasally with adenovirus type 1 or influenza A virus, and then inoculated intranasally 7 days later with Spn 6A. All cohorts were observed over a 14-day period after challenge with Spn, and the incidence and severity of OM were assessed by several methods, including culture of the nasopharynx and middle ear effusions. The data indicated that influenza A virus promotes a significant increase in nasopharyngeal colonization by Spn, an increased incidence and severity of OM, and a sustained presence of Spn in the effusions. Adenovirus infection, however, did not enhance colonization by Spn or result in an increased incidence or severity of OM.

Viral RNA in middle ear mucosa and exudates in patients with chronic otitis media with effusion.

OBJECTIVE: To evaluate viral and cytokine signaling correlates of the persistent inflammation associated with chronic otitis media with effusion (OME). DESIGN: Prospective study. METHOD: Reverse transcriptase-polymerase chain reaction targeting RNA viruses frequently associated with OME (respiratory syncytial virus and parainfluenza virus type 3, the proinflammatory cytokines interleukin 8 and interleukin 1beta, and RANTES [regulated upon activation, normal T cell expressed and secreted]) was performed on mucosal biopsy samples and on samples of the liquid and cellular compartments of inflammatory exudates obtained from 26 children (49 ears) with infected middle ears. Ribonucleic acid extracted from rapidly frozen samples was reverse transcribed by Moloney murine leukemia virus reverse transcriptase and amplified for 35 cycles using previously validated primers. Amplicons were evaluated by molecular size after agarose gel electrophoresis with ethidium bromide. RESULTS: Most children had evidence of the presence of an RNA virus in at least one specimen. Respiratory syncytial virus was present in 40% and parainfluenza virus type 3 in 8% of effusions. Interleukin 8 messenger RNA was present in 21% of inflammatory exudates but never in cells from the mucosal biopsy samples. CONCLUSIONS: Our data support a viral contribution to the cause of OME and suggest that the inflammatory cytokines observed derive more from cells in the inflammatory exudate than from those in the middle ear mucosa.

Absence of HHV-8 DNA sequences in malignant mesothelioma.

Human herpesvirus 8 (HHV-8) associated primary effusion lymphomas arise and grow in the body cavities as effusions, but it is not known whether the lining of body cavities and mesothelium derived malignancies are potential targets of HHV-8 infection. We examined a series of 13 diffuse malignant mesotheliomas and four mesothelial cell rich effusion samples of non-neoplastic aetiology from non-immunodepressed patients using the polymerase chain reaction to detect HHV-8 specific sequences. HHV-8 amplification products were absent in diffuse malignant mesotheliomas and in non-neoplastic effusions samples. These results suggest that HHV-8 has a selective tropism among body cavity based tumours, being confined to primary effusion lymphomas.

Comparative field evaluation of HIV rapid diagnostic assays using serum, urine, and oral mucosal transudate specimens.

BACKGROUND: Comparative field utility of selected HIV-1 assays using homologous collections of serum, urine and oral mucosal transudate (OMT) was determined in adult populations from a tuberculosis hospital and STD clinic in Djibouti, East Africa. STUDY DESIGN: Enzyme immunoassay with confirmatory Western blot was performed on all serum specimens for comparison with rapid, instrument-free assays (SUDS HIV-1, Murex: TestPack HIV-1/2. Abbott; and COMBAIDS HIV 1 + 2, SPAN Diagnostics) using various specimen sources. Delayed (48 h post-collection) testing was also performed on urine. Sensitivity and specificity for the rapid assays, in descending order, were as follows: serum SUDS HIV-1 assay (100%, 98.3%), serum COMBAIDS HIV-1/2 assay (98.4%, 99.6%), and OMT SUDS HIV-1 assay (98.4%, 94.5%). RESULTS: The OMT EIA optical density cutoff value was modified resulting in an improved specificity from 89.1 to 99.6%, however, sensitivity decreased from 100 to 98.5%. Urine EIA and rapid assays demonstrated unacceptable test performance for use as a screening test.

Kaposi's sarcoma-associated herpesvirus: a lymphotropic human herpesvirus associated with Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease.

Despite extensive epidemiological evidence suggesting that Kaposi's sarcoma (KS) has an infectious origin, a specific viral association with KS had not been documented until recently, when two novel DNA fragments were identified in KS lesional tissue from a patient with the acquired immunodeficiency syndrome (AIDS). These fragments belong to a previously unidentified human herpesvirus, called KS-associated herpesvirus (KSHV), or human herpesvirus 8. Although this virus is generally absent from normal control tissues, inflammatory conditions, and a variety of tumors, it is present in most AIDS- as well as non-AIDS-related KS lesions, suggesting that it is not simply an opportunistic infection in human immunodeficiency virus (HIV)-infected patients. Furthermore, this virus is consistently present in a specific type of non-Hodgkin's lymphoma, frequently although not exclusively occurring in patients with AIDS (namely, the primary effusion lymphomas, previously called body cavity-based lymphomas). KSHV is also present in a significant proportion of cases of AIDS- and non-AIDS-related multicentric Castleman's disease. Sequence analysis has led to the identification of genes in the KSHV genome that may have important pathobiological functions, and experimental approaches have been developed to isolate, grow and transmit KSHV in vitro. An understanding of KSHV is important for evaluating its role in the pathogenesis of Kaposi's sarcoma, primary effusion lymphomas, and multicentric Castleman's disease, and to help develop better methods for the prevention and treatment of these diseases.

Conjunctival scrapings and impression cytology in chronic conjunctivitis. Correlation with microbiology.

To assess the utility of exfoliative cytology in the diagnosis of chronic conjunctivitis, we compared its findings with microbiological examination and established the correlation between cytology and microbiology in 32 patients with conjunctivitis lasting four weeks or more, with a nonspecific clinical picture. The material for cytology was collected by scraping and by imprint of the ocular surface on Millipore filter paper. The specimens were stained with Giemsa. Material for bacterial culture and fluorescent antibody test for viruses and Chlamydia were obtained at the same time. In 12 patients neutrophils predominated in cytology, in six eosinophils were found and in four there were more lymphocytes. One patient had a basophilic intracytoplasmic inclusion specific for Chlamydia infection. In eight patients coagulase-negative Staphylococcus species and in one Staphylococcus aureus were isolated, in two the fluorescent antibody test for Chlamydia was positive and in three for viruses. In all patients with a positive bacterial culture, a predominance of neutrophils was observed. All patients with a positive test for viruses had lymphocytosis in conjunctival scrapings. In two patients microbiology detected Chlamydia, but characteristic intracytoplasmic inclusions were observed only in one. Scrapings gave more specific results, that correlated well with microbiology in bacterial and viral infection, whereas the results of impression cytology showed minor metaplastic changes of epithelial cells that were nonspecific for the type of inflammation. Cytology remains a useful non-invasive tool and is an adjunct to clinical and microbiological examination. It proved especially helpful in allergic conjunctivitis.