Multiplex detection of herpesviruses in tear fluid using the "stair primers" PCR method: prospective study of 93 patients

Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal Conjunctiva

Our study aims are: (1) to evaluate phenotypically normal canine conjunctival and orbital tissue and tissue from canine lobular orbital adenomas (CLOAs) for the presence of viral genomic material and (2) phylogenetically classify detected DNA viruses to determine if a DNA virus is associated with CLOAs. A total of 31 formalin fixed paraffin embedded CLOA tissue samples, 4 papillomas or sarcoid, and 10 fresh clinically normal conjunctival tissues were included in this study. Genomic DNA was isolated from all samples and sequencing libraries were prepared. The libraries were molecularly indexed and pooled and viral DNA was enriched via targeted sequence capture utilizing ViroCap. The libraries were sequenced on the Illumina HiSeq platform and compared to known viral DNA reference genomes to identify viral DNA. Carnivore parvovirus was identified in 6.4% and 20% of CLOA tissue and normal conjunctival samples, respectively. This study showed that conjunctival tissue from healthy dogs and CLOAs uncommonly harbor DNA viruses, and no DNA virus was associated with these tumors. Further studies are needed to evaluate the etiologic cause of CLOAs.

Keep Eyes on COVID-19: Ophthalmic Symptoms and Potential Transmission of SARS-CoV-2 through the Oculus

In December 2019, a new coronavirus disease 2019 (COVID-19) emerged and rapidly spread globally, posing a worldwide health emergency. The pathogen causing this pandemic was identified as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It is well known that SARS-CoV-2 transmits via respiratory droplets and close contact with infected individuals or contaminated items. In addition to these two major transmission routes, other modes of transmission have not been confirmed. Considering that some COVID-19 patients have presented with ocular discomforts and positive SARS-CoV-2 RNA in ocular surfaces, as well as the discovery of the SARS-CoV-2 receptors, angiotensin-converting enzyme 2, and transmembrane protease, serine 2, in the oculus, the ocular surface is now thought to be a possible alternative route of SARS-CoV-2 transmission and a replication site. This review summarizes the evidence connecting COVID-19 with ocular tissues, ocular symptoms during SARS-CoV-2 infection, the potential role of the conjunctiva in SARS-CoV-2 transmission, and the physiopathological mechanisms. Appropriate precautions in ophthalmology departments, including innovative complete and effective patient management plans, protective personal equipment, hand hygiene, and strict personal distance intervals, are essential to effectively minimize the spread of SARS-CoV-2 and control the pandemic.

Role of plasmonics in detection of deadliest viruses: a review

Viruses have threatened animal and human lives since a long time ago all over the world. Some of these tiny particles have caused disastrous pandemics that killed a large number of people with subsequent economic downturns. In addition, the quarantine situation itself encounters the challenges like the deficiency in the online educational system, psychiatric problems and poor international relations. Although viruses have a rather simple protein structure, they have structural heterogeneity with a high tendency to mutation that impedes their study. On top of the breadth of such worldwide worrying issues, there are profound scientific gaps, and several unanswered questions, like lack of vaccines or antivirals to combat these pathogens. Various detection techniques like the nucleic acid test, immunoassay, and microscopy have been developed; however, there is a tradeoff between their advantages and disadvantages like safety in sample collecting, invasiveness, sensitivity, response time, etc. One of the highly resolved techniques that can provide early-stage detection with fast experiment duration is plasmonics. This optical technique has the capability to detect viral proteins and genomes at the early stage via highly sensitive interaction between the biological target and the plasmonic chip. The efficiency of this technique could be proved using commercialized techniques like reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) techniques. In this study, we aim to review the role of plasmonic technique in the detection of 11 deadliest viruses besides 2 common genital viruses for the human being. This is a rapidly moving topic of research, and a review article that encompasses the current findings may be useful for guiding strategies to deal with the pandemics. By investigating the potential aspects of this technique, we hope that this study could open new avenues toward the application of point-of-care techniques for virus detection at early stage that may inhibit the progressively hygienic threats.

Microbes of the human eye: Microbiome, antimicrobial resistance and biofilm formation

BACKGROUND

The review focuses on the bacteria associated with the human eye using the dual approach of detecting cultivable bacteria and the total microbiome using next generation sequencing. The purpose of this review was to highlight the connection between antimicrobial resistance and biofilm formation in ocular bacteria.

METHODS

Pubmed was used as the source to catalogue culturable bacteria and ocular microbiomes associated with the normal eyes and those with ocular diseases, to ascertain the emergence of anti-microbial resistance with special reference to biofilm formation.

RESULTS

This review highlights the genetic strategies used by microorganisms to evade the lethal effects of anti-microbial agents by tracing the connections between candidate genes and biofilm formation.

CONCLUSION

The eye has its own microbiome which needs to be extensively studied under different physiological conditions; data on eye microbiomes of people from different ethnicities, geographical regions etc. are also needed to understand how these microbiomes affect ocular health.

Multiplex Solid-Phase Real-Time Polymerase Chain Reaction without DNA Extraction: A Rapid Intraoperative Diagnosis Using Microvolumes

PURPOSE

Current polymerase chain reaction (PCR) methods for the diagnosis of infections are time consuming and require large sample volume and skilled technicians. We developed a novel, easy-to-use, and rapid (processing time, 1 minute; total time, 33 minutes) multiplex real-time PCR test (Direct Strip PCR) that did not require DNA extraction to detect 9 pathogens that could cause uveitis in 20-μl samples.

DESIGN

Multicenter prospective evaluation of a diagnostic PCR test.

PARTICIPANTS

A total of 511 participants (patients with infectious uveitis and controls) were examined at 18 institutes worldwide.

METHODS

After validation, intraocular fluid samples were subjected to etiologic or exclusive diagnosis, including intraoperative rapid diagnosis.

MAIN OUTCOME MEASURES

The concordance and correlations between Direct Strip PCR and quantitative PCR (qPCR) results.

RESULTS

Direct Strip PCR exhibited rapid detection, good repeatability and specificity, long storage stability, and detection ability equal to that of qPCR. It also showed low interinstitutional variability compared with qPCR, even when PCR beginners used various real-time PCR machines. The Direct Strip PCR for 9 pathogens exhibited high concordance against the qPCR (positive concordance rate, 98.8%-100%; negative concordance rate, 99.8%-100%; κ coefficient, 0.969-1.000; P < 0.001-0.031). Additionally, results obtained using Direct Strip PCR and qPCR were highly correlated (ρ = 0.748; P < 0.001). This assay was used for rapid intraoperative diagnosis.

CONCLUSIONS

The Direct Strip PCR test may improve the prognosis of various infectious diseases because it facilitates rapid etiologic evaluation at the first hospital visit and can be used for intraoperative diagnosis.

A new era of uveitis: impact of polymerase chain reaction in intraocular inflammatory diseases

Uveitis is a sight-threatening intraocular inflammatory disorder which may occur from both infectious and non-infectious or autoimmune causes. The frequency of infectious uveitis and autoimmune uveitis varies depending on countries and regions. According to a nationwide survey conducted by the Japanese Ocular Inflammation Society, infectious and non-infectious uveitis accounted for 16.4 and 50.1% of new patients, respectively while the remaining 33.5% of new uveitis cases were not classified or were idiopathic uveitis. Infectious uveitis is particularly important because it causes tissue damage to the eye and may result in blindness unless treated. However, it can be treated if the pathogenic microorganisms are identified promptly and accurately. Remarkable advancements in molecular and immunological technologies have been made in the last decade, and the diagnosis of infectious uveitis has been greatly improved by the application of molecular and immunological investigations, particularly polymerase chain reaction (PCR). PCR performed on a small amount of ocular samples provides a prompt, sensitive, and specific molecular diagnosis of pathogenic microorganisms in the eye. This technology has opened a new era in the diagnosis and treatment of uveitis, enabling physicians to establish new clinical entities of uveitis caused by infectious microorganisms, identify pathogens in the eyes of many patients with uveitis, and determine prompt diagnosis and appropriate therapy. Here we review the PCR process, new PCR tests specialized for ocular diseases, microorganisms detected by the PCR tests, diseases in the eye caused by these microorganisms, and the clinical characteristics, diagnosis, and therapy of uveitis.

Dry eye disease and microbial keratitis: is there a connection?

Dry eye is a common ocular surface disease of multifactorial etiology characterized by elevated tear osmolality and inflammation leading to a disrupted ocular surface. The latter is a risk factor for ocular surface infection, yet overt infection is not commonly seen clinically in the typical dry eye patient. This suggests that important innate mechanisms operate to protect the dry eye from invading pathogens. This article reviews the current literature on epidemiology of ocular surface infection in dry eye patients and laboratory-based studies on innate immune mechanisms operating at the ocular surface and their alterations in human dry eye and animal models. The review highlights current understanding of innate immunity in dry eye and identifies gaps in our knowledge to help direct future studies to further unravel the complexities of dry eye disease and its sequelae.

Role of human herpes virus 6 in corneal inflammation alone or with human herpesviruses

PURPOSE

: The purpose of this study was to determine the association of human herpes virus 6 (HHV-6) and/or other human herpesviruses in corneal inflammation using polymerase chain reaction (PCR).

METHODS

: We collected tear films, conjunctival smears, and a corneal button of inflamed cornea, and the presence of HHV-6 and other herpesviruses in these samples were assessed by a nested PCR.

RESULTS

: In tear films collected from 3 of 9 patients with dendritic keratitis, HHV-6 DNA was positive twice, together with herpes simplex virus (HSV) or varicella zoster virus DNA most often, during the acute phase of the disease. Two other patients in this group were either positive for HSV-1 and varicella zoster virus or for HSV-1 and Epstein-Barr virus DNA but negative for HHV-6. When another 12 patients' smear samples from corneal ulcer or keratouveitis were examined, 9 were positive for HHV-6 DNA. Of these, 4 were positive for HSV-1 simultaneously, whereas the remaining 5 patients were negative for HSV-1. One patient's smear was positive for HSV-1 but not for HHV-6. In the corneal button, both HSV and HHV-6 DNAs were positive by nested PCR. HHV-6 was also positive by nested PCR in the conjunctival swab obtained from the contralateral inflamed eye of the patient.

CONCLUSIONS

: In 22 patients with corneal inflammation, HHV-6 was positive in 14 of 22 patients and HSV-1 was found in 9 of those patients. These data indicated that the association of HHV-6 with disease was more frequent than with other herpesviruses and that HHV-6 may be another sole causative agent for corneal inflammation.

Ocular herpes simplex virus type 1: is the cornea a reservoir for viral latency or a fast pit stop?

PURPOSE

To present a review supporting and refuting evidence from mouse, rabbit, nonhuman primate, and human studies of herpes simplex virus type 1 (HSV-1) concerning corneal latency.

METHODS

More than 50 research articles on HSV-1 published in peer-reviewed journals were examined.

RESULTS

Infectious HSV-1 has been found in mouse denervated tissues and in tissues with negative cultures from the corresponding ganglion. However, the different mouse strains have shown varied responses to different strains of HSV, making it difficult to relate such findings to humans. Rabbit studies provide excellent evidence for HSV-1 corneal latency including data on HSV-1 migration from the cornea into the corneoscleral rim and on the distribution of HSV-1 DNA in the cornea. However, the available methods for the detection of infectious HSV-1 may not be sensitive enough to detect low-level infection. Infectious HSV-1 has been successfully isolated from the tears of nonhuman primates in the absence of detectable corneal lesions. The recurrence of corneal ulcers in nonhuman primates before the appearance of infectious HSV-1 in tears suggests that the origin of the HSV-1 is the cornea, rather than the trigeminal ganglion. Human studies presented evidence of both ganglion and corneal latency.

CONCLUSIONS

Understanding HSV-1 disease progression and the possibility of corneal latency could lead to more effective treatments for herpetic keratitis. However, it is unlikely that operational latency in the cornea will be definitively proven unless a new method with higher sensitivity for the detection of infectious virus is developed.

Usefulness of Herpes Consensus PCR methodology to routine diagnostic testing for herpesviruses infections in clinical specimens

The purposes of the study were to assess the usefulness of simultaneously amplifying herpes simplex virus 1 and 2, varicella-zoster virus, cytomegalovirus, Epstein-Barr virus and human herpesvirus 6 DNA in various clinical specimens and to analyze clinical events in patients presenting positive results. A total of 763 clinical samples obtained from 758 patients, including 115 cerebrospinal fluids, 102 aqueous fluids, 445 swabs from genital (152), oro-facial (138) and other (155) skin lesions, 96 eye swabs and 5 bronchoalveolar lavages, were tested by using the Consensus polymerase chain reaction methodology. The clinical files of the patients were consulted retrospectively. 171 of the 758 patients (22.5%) were positive for at least one of the six target viruses: herpes simplex virus 1 (n = 95), varicella-zoster virus (n = 40), herpes simplex virus 2 (n = 21), herpes simplex virus 1 plus herpes simplex virus 2 (n = 8), cytomegalovirus (n = 4), Epstein-Barr virus (n = 1), human herpesvirus 6 (n = 1), and herpes simplex virus 1 plus human herpesvirus 6 (n = 1). The Consensus methodology enabled the rapid and accurate detection of herpesviruses in various clinical specimens and provided a reliable tool in the diagnosis of herpetic infections.

Epidemiology of Epstein-Barr virus, cytomegalovirus, and Kaposi's sarcoma-associated herpesvirus infections in peripheral blood leukocytes revealed by a multiplex PCR assay

A multiplex polymerase chain reaction (PCR) has been developed for the simultaneous detection of Epstein-Barr virus (EBV), cytomegalovirus (CMV), and Kaposi's sarcoma-associated herpesvirus (KSHV) in a clinical sample. Primers of multiplex PCR were designed to amplify specific regions of the EBV EBNA1, CMV IE2, and KSHV LANA genes. This multiplex PCR assay was found to have detection sensitivities of 1-10 copies of purified viral DNA cloned into the plasmid. To assess diagnostic and pre-clinical applications with this method, we utilized KSHV-positive primary effusion lymphoma (PEL) cells, EBV-positive Burkitt's lymphoma cells, CMV-infected fibroblast cells, and clinically prepared peripheral blood leukocytes (PBLs) that had been infected with viruses. We found that this multiplex PCR assay has high sensitivity and specificity for simultaneous detection of EBV, CMV, and KSHV genomes in a single amplification from a clinical material. Using this multiplex PCR assay, we investigated the prevalence of EBV, CMV, and KSHV in PBL samples from normal Japanese randomly selected. KSHV, EBV, and CMV genomes were detected in samples from 2 (0.2%), 377 (39.5%), and 27 (2.8%) of the 953 blood donors, respectively. Interestingly, both EBV and CMV genomes were detected in samples from all KSHV-positive donors.

Cytomegalovirus antibodies in tear fluid of patients with retinitis

The diagnosis of cytomegalovirus retinitis (CMV-R) is difficult and usually based on clinical criteria or invasive diagnostic procedures. The purpose of this study was to investigate a possible association between CMV-R and specific anti-CMV antibodies in tears. Paired tear and serum samples were obtained from 96 individuals, which included 20 children with congenital CMV infection and chorioretinitis, 56 adults with retinitis with clinical signs suggestive of viral infection, and 20 healthy control subjects, and were tested for CMV antibodies using ELISA. The prevalence of anti-CMV antibodies in tears was found to be 80% (16/20) in children, 35% (20/56) in adults, and 5% (1/20) in control subjects. Furthermore, high antibody levels were detected in 35% (7/20) of children and 10.7% (6/56) of adults with retinitis, and were not found in control subjects. There was a strong association between high tear levels of anti-CMV antibodies and active ocular infection. No correlations were found between tear and serum antibodies. ELISA sensitivity was 80% and specificity 95%. Further studies are needed to compare the tear and intraocular levels of CMV-specific antibodies in patients with retinitis to find out if CMV antibody testing in tear fluid could substitute for more invasive diagnostic procedures.

Surveillance sérologique pour les Herpesvirus chez les receveurs de cornée

AIMS

Herpesviruses are ubiquitous viruses, providing circulating antibodies in a wide range of patients. Donor-to-host transmission of Herpes simplex virus via corneal graft has been proven, leading to primary graft failure. However, the serological survey of the corneal recipient for Herpesviruses has not yet been investigated.

METHODS

Circulating antibodies to HSV, VZV, CMV, and EBV were tested in 117 corneal recipients prior to surgery as well as 8 days and 3 months following surgery. Twenty-two patients had a history of corneal herpes. All patients were treated with local steroids, and no patient received systemic immunosuppressive therapy.

RESULTS

No seroconversion was encountered, in particular, no CMV--patient was found CMV+ after grafting. The mean concentration of antibodies significantly decreased after grafting in a few patients. A serological profile of EBV reactivation was detected after surgery in four patients at day 8 and three more patients at 3 months.

CONCLUSIONS

This study shows no significant seroconversion after grafting. However, it shows a postoperative decrease in antibody levels as well as a serological profile of EBV reactivation, possibly related to local steroids or graft immune processes.

Experience from the development of a diagnostic single tube real-time PCR for human caliciviruses, Norovirus genogroups I and II

Detection of caliciviruses requires high mutation tolerance and throughput. The development of a rational simple, single tube reverse transcription-real-time quantitative PCR (QPCR) technique for human noroviruses (NV) is reported here. A dual-probe, triple-primer system (NM system) was used for simultaneous detection and preliminary differentiation of NV genogroups in fecal samples. The design was based on a comprehensive analysis of all 1140 NV sequences available in GenBank. A touch-down amplification protocol improved the frequency of detection. The final QPCR was evaluated with 71 fecal samples from outbreak and sporadic cases in Sweden (1997-2004), all calicivirus-positive by electron microscopy. Up to 56 (79 %) were positive. The method is more rational than NV detection methods described previously, and should be a developmental basis for large-scale routine methods for detection of NV.

Sensitive detection of SARS coronavirus RNA by a novel asymmetric multiplex nested RT-PCR amplification coupled with oligonucleotide microarray hybridization

We have developed a sensitive method for the detection of specific genes simultaneously. First, DNA was amplified by a novel asymmetric multiplex PCR with universal primer(s). Second, the 6-carboxytetramethylrhodamine (TAMRA)-labeled PCR products were hybridized specifically with oligonucleotide microarrays. Finally, matched duplexes were detected by using a laser-induced fluorescence scanner. The usefulness of this method was illustrated by analyzing severe acute respiratory syndrome (SARS) coronavirus RNA. The detection limit was 10(0) copies/microL. The results of the asymmetric multiplex nested reverse transcription-PCR were in agreement with the results of the microarray hybridization; no hybridization signal was lost as happened with applicons from symmetric amplifications. This reliable method can be used to the identification of other microorganisms, screening of genetic diseases, and other applications.

The severe acute respiratory syndrome coronavirus in tears

BACKGROUND

Severe acute respiratory syndrome (SARS) is a new infectious disease that caused a global outbreak in 2003. Research has shown that it is caused by a novel coronavirus. A series of cases is reported where polymerase chain reaction (PCR) testing on tears had demonstrated the presence of the virus. Detection of ocular infection from tears using the PCR technique has been widely used by ophthalmologists to diagnose infections for other viruses.

METHODS

This is a case series report from cases classified as probable or suspect SARS cases. Tear samples were collected from 36 consecutive patients who were suspected of having SARS in Singapore over a period of 12 days (7-18 April 2003), and analysed by PCR using protocols developed by the WHO network of laboratories.

RESULTS

Three patients with probable SARS (one female and two male patients) had positive results from their tear samples. Tear samples were used to confirm SARS in the female patient, who was positive only from her tears. The positive specimens were found in cases sampled early in their course of infection.

CONCLUSIONS

This is the first case series reported with the detection of the SARS coronavirus from tears, and has important implications for the practice of ophthalmology and medicine. The ability to detect and isolate the virus in the early phase of the disease may be an important diagnostic tool for future patients and tear sampling is both simple and easily repeatable. Many healthcare workers are in close proximity to the eyes of patients and this may be a source of spread among healthcare workers and inoculating patients. Ophthalmic practices may need to change as more stringent barrier methods, appropriate quarantine, and isolation measures are vital when managing patients with SARS.

Species identification of all eight human herpesviruses with a single nested PCR assay

There are eight currently known human herpesviruses, all of which are capable of latent persistence and reactivation following primary infection. Herpesvirus induced disease is common, widespread, and associated with significant morbidity, particularly in the immunocompromised human host. Current methods of herpesvirus detection include viral culture and polymerase chain reaction (PCR). A robust PCR method based upon amplification of the highly conserved herpesvirus DNA polymerase gene that is capable of detection of all eight human herpesviruses, including EBV and HHV-6 subtypes, from clinical material is described. Species identification of PCR products is accomplished by either of two methods, chemiluminescent dot blot hybridization and heteroduplex mobility shift assay, both of which allow for simultaneous detection of multiple herpesviruses. This method should prove useful for rapid and accurate species identification of all eight human herpesviruses from clinical material.

A role for arrays in clinical virology: fact or fiction?

Microarrays of DNA probes have at least three roles in clinical virology. These are: firstly, in diagnosis, to recognise the causative agent of an illness; secondly, for molecular typing for (i) patient management, (ii) epidemiological reasons (e.g. investigating routes of transmission), (iii) purposes related to vaccine use; and thirdly, in research, to investigate the interactions between the virus and the host cell. Microarrays intended for syndromic diagnostic purposes require genome specific probes to capture the unknown target viral sequences and thereby reveal the presence of that virus in a test sample. Microarrays intended for typing and patient management, e.g. monitoring antiviral drug resistant mutations require a set of probes representing the important sequence variants of one or more viral genes. Microarrays intended for research into virus–host interactions require probes representative of each individual gene or mRNA of either the virus or the host genome. Diagnostic microarrays are dependent for their utility and versatility on generic, multiplex or random polymerase chain reactions that will amplify any of several (unknown) viral target sequences from a patient sample. In this review, the existing and potential applications of microarrays in virology, and the problems that need to be overcome for future success, are discussed.