Transport of viral specimens

Co-circulation of seasonal influenza A(H1N1)pdm09, A(H3N2) and B/Victoria lineage viruses with further genetic diversification, EU/EEA, 2022/23 influenza season

BackgroundInfluenza viruses can cause large seasonal epidemics with high healthcare impact and severity as they continually change their virological properties such as genetic makeup over time.AimWe aimed to monitor the characteristics of circulating influenza viruses over the 2022/23 influenza season in the EU/EEA countries. In addition, we wanted to compare how closely the circulating viruses resemble the viral components selected for seasonal influenza vaccines, and whether the circulating viruses had acquired resistance to commonly used antiviral drugs.MethodsWe performed a descriptive analysis of the influenza virus detections and characterisations reported by National Influenza Centres (NIC) from the 30 EU/EEA countries from week 40/2022 to week 39/2023 to The European Surveillance System (TESSy) as part of the Global Influenza Surveillance and Response System (GISRS).ResultsIn the EU/EEA countries, the 2022/23 influenza season was characterised by co-circulation of A(H1N1)pdm09, A(H3N2) and B/Victoria-lineage viruses. The genetic evolution of these viruses continued and clade 6B.1A.5a.2a of A(H1N1)pdm09, 3C.2a1b.2a.2b of A(H3N2) and V1A.3a.2 of B/Victoria viruses dominated. Influenza B/Yamagata-lineage viruses were not reported.DiscussionThe World Health Organization (WHO) vaccine composition recommendation for the northern hemisphere 2023/24 season reflects the European virus evolution, with a change of the A(H1N1)pdm09 component, while keeping the A(H3N2) and B/Victoria-lineage components unchanged.

Ammonium sulfate denatures transport medium less dependent on guanidinium isothiocyanate and enables SARS-CoV-2 RNA and antigen detection compatibility

Introduction

Rapid identification of infected individuals through viral RNA or antigen detection followed by effective personal isolation is usually the most effective way to prevent the spread of a newly emerging virus. Large-scale detection involves mass specimen collection and transportation. For biosafety reasons, denaturing viral transport medium has been extensively used during the SARS-CoV-2 pandemic. However, the high concentrations of guanidinium isothiocyanate (GITC) in such media have raised issues around sufficient GITC supply and laboratory safety. Moreover, there is a lack of denaturing transport media compatible with SARS-CoV-2 RNA and antigen detection.

Methods

Here, we tested whether supplementing media containing low concentrations of GITC with ammonium sulfate (AS) would affect the throat-swab detection of SARS-CoV-2 or a viral inactivation assay targeting coronavirus and other enveloped and non-enveloped viruses. The effect of adding AS to the media on RNA stability and its compatibility with SARS-CoV-2 antigen detection were also tested.

Results and discussion

We found that adding AS to the denaturing transport media reduced the need for high levels of GITC, improved SARS-COV-2 RNA detection without compromising virus inactivation, and enabled the denaturing transport media compatible with SARS-CoV-2 antigen detection.

Common laboratory organic solvents are better medium for molecular detection of RNA viruses using PCR

PURPOSE

The unavailability of recommended viral transport medium during epidemics of respiratory viral infections is a substantial healthcare concern. It may prompt the use of alternatives, which may give rise to results with questionable validity. The present study was carried out to assess and validate the utility of commonly available solvents in the hospital/healthcare set-ups which may be used as ready and economical alternatives to commercial VTMs.

METHODS

To evaluate the readily available solvents as an alternative to VTM, cell culture supernatant of pH1N1 2009 isolate with HA titres of 1:4 and extracted viral RNA of SARS-CoV-2 were spiked in a 1:10 ratio in ethanol, acetone, methanol and were compared to commercially available VTM for detection of influenza virus by real time RT-PCR (qRT-PCR). The tubes were kept at room temperature 24 h, 48 h and 72 h. Ct values of the various solvents at different time points were compared and statistical analysis was performed using Python.

RESULTS

The Ct values of the Influenza and SARS-CoV2 viral genes in each solvent were maintained for 3 days at room temperatures, suggesting viral samples were stably preserved in the solvent for 3 days.

CONCLUSION

Methanol was found to be the most promising solvent for increasing the stability of viral RNA thereby enhancing the molecular diagnosis of the concerned pathogen.

Assessment of Strategies for Preserving Swine Viral RNA Targets in Diagnostic Specimens

Successful downstream molecular analyses of viral ribonucleic acid (RNA) in diagnostic laboratories, e.g., reverse transcription-quantitative polymerase chain reaction (RT-qPCR) or next-generation sequencing, are dependent on the quality of the RNA in the specimen. In swine specimens, preserving the integrity of RNA requires proper sample handling at the time the sample is collected on the farm, during transport, and in the laboratory until RNA extraction is performed. Options for proper handling are limited to maintaining the cold chain or using commercial specimen storage matrices. Herein, we reviewed the refereed literature for evidence that commercial specimen storage matrices can play a role in preserving swine viral RNA in clinical specimens. Refereed publications were included if they compared RNA detection in matrix-treated vs. untreated samples. At present, the small number of refereed studies and the inconsistency in reported results preclude the routine use of commercial specimen storage matrices. For example, specimen storage matrices may be useful under specific circumstances, e.g., where it is mandatory to render the virus inactive. In a broader view, statistically sound side-by-side comparisons between specimens, viral RNA targets, and storage conditions are needed to establish if, when, and how commercial specimen storage matrices could be used in diagnostic medicine.

Screening and Stability Evaluation of Freeze-Dried Protective Agents for a Live Recombinant Pseudorabies Virus Vaccine

Infection of pigs with the pseudorabies virus (PRV) causes significant economic losses in the pig industry. Immunization with live vaccines is a crucial aspect in the prevention of pseudorabies in swine. The TK/gE/gI/11k/28k deleted pseudorabies vaccine is a promising alternative for the eradication of epidemic pseudorabies mutant strains. This study optimized the lyophilization of a heat-resistant PRV vaccine to enhance the quality of a live vaccine against the recombinant PRV rHN1201TK-/gE-/gI-/11k-/28k-. The A4 freeze-dried protective formulation against PRV was developed by comparing the reduction in virus titer after lyophilization and after seven days of storage at 37 °C. The formulation contains 1% gelatin, 5% trehalose, 0.5% poly-vinylpyrimidine (PVP), 0.5% thiourea, and 1% sorbitol. The A4 freeze-dried vaccine demonstrated superior protection and thermal stability. It experienced a freeze-dried loss of 0.31 Lg post-freeze-drying and a heat loss of 0.42 Lg after being stored at a temperature of 37 °C for 7 consecutive days. The A4 freeze-dried vaccine was characterized through XRD, FTIR, and SEM analyses, which showed that it possessed an amorphous structure with a consistent porous interior. The trehalose component of the vaccine formed stable hydrogen bonds with the virus. Long-term and accelerated stability studies were also conducted. The A4 vaccine maintained viral titer losses of less than 1.0 Lg when exposed to 25 °C for 90 days, 37 °C for 28 days, and 45 °C for 7 days. The A4 vaccine had a titer loss of 0.3 Lg after storage at 2-8 °C for 24 months, and a predicted shelf life of 6.61 years at 2-8 °C using the Arrhenius equation. The A4 freeze-dried vaccine elicited no side effects when used to immunize piglets and produced specific antibodies. This study provides theoretical references and technical support to improve the thermal stability of recombinant PRV rHN1201TK-/gE-/gI-/11k-/28k- vaccines.

From cold chain to ambient temperature: transport of viral specimens- a review

The diagnosis of an aetiology is dependent on the collection, transport, and storage of the infectious sample. The transport of the sample plays a crucial role in the chain of diagnosis. It is important to maintain the biological integrity of the pathogen during the transport of the sample to achieve an accurate diagnosis. This is important, particularly for labile organisms like viruses that are inactivated easily compared to other microorganisms. Many transport media have been utilised to ensure the integrity of the virus during transport. While most of the transport media are focused on preserving the infectious properties of the virus, progress has been made to develop virus transport media to inactivate the virus and obtain the stability of the viral nucleic acid, enabling better molecular diagnosis of the virus aetiologies. This review summarises the various media used for the transport of virus samples and focuses on the need to develop virus transport media that inactivates the virus and preserves the viral nucleic acid.

Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics

Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.

Investigating the survival of herpes simplex virus on toothbrushes and surrogate phallic devices

BACKGROUND

Herpes simplex virus-1 (HSV-1) is a member of the alphaherpesvirus (alphaherpesvirinae) subfamily, allowing it to affect a wide range of hosts. Herpes simplex virus-1 affects 3.7 billion people, or 67% of the population, under the age of 50. With a vast number of people infected by the virus, everyday objects are often contaminated with this agent. In this study we determined how long HSV-1 can remain viable on contaminated fomites.

METHODS

Fomites were selected for their use near potentially contaminated orifices and variable frequency of sanitization. Toothbrushes and surrogate phallic devices (SPDs) were cut, sterilized, and contaminated. After contaminating the fomites, we collected samples over a 24 h period, then used plaque assays to determine viral titers at prescribed time points.

RESULTS

The quantity of replication-competent virus present appears to decrease significantly 2 h post-contamination, then steadily declines over time, nearing zero at 24 h.

CONCLUSIONS

Our findings suggest that different surfaces influence HSV-1 survival. Proper cleaning must be performed for these types of fomites, especially if shared in an environment where someone with active genital or oral herpes lesions uses one of these fomites shortly after someone else.

Alternate Approach in Storing and Shipment of SARS-CoV-2 RNA Samples with the Use of FTA Cards

Shipment of COVID-19 specimens within the country or overseas at long distances requires cold chain facility using dry ice and triple packing to prevent the risk of COVID-19 infection to the personnel involved in sample transport. The present study aimed to utilize FTA card technology as an alternate means of sample transport and storage across the country. Twenty-one SARS-CoV-2 lab confirmed samples with different Ct value (High, medium & low) were used to detect viral load in samples loaded on FTA card and further compared with VTM samples. The SARS-CoV-2 RNA was detected by rRT-PCR after storing for 14 days at 4 °C and 37 °C. The present study evaluated the utility of FTA cards for preserving the SARS CoV-2 RNA for 14-day period. A significant difference (P < 0.05) was observed in the cycle threshold (ΔCt 4–5) values obtained from FTA and VTM viral samples but it did not affect the positivity. The SARS-CoV-2 RNA could be recovered efficiently from FTA sample stored at 4 °C and 37 °C for 14 days. Thus, FTA cards could be an alternate option for transporting the samples at ambient temperature for a long time.

Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens

Background

Saliva samples may be an easier, faster, safer, and cost-saving alternative to NPS samples, and can be self-collected by the patient. Whether SARS-CoV-2 RT-qPCR in saliva is more accurate than in nasopharyngeal swaps (NPS) is uncertain. We evaluated the accuracy of the RT-qPCR in both types of samples, assuming both approaches were imperfect.

Methods

We assessed the limit of detection (LoD) of RT-qPCR in each type of sample. We collected paired NPS and saliva samples and tested them using the Berlin Protocol to detect SARS-CoV-2 envelope protein (E). We used a Bayesian latent class analysis (BLCA) to estimate the sensitivity and specificity of each test, while accounting for their conditional dependence.

Results

The LoD were 10 copies/mL in saliva and 100 copies/mL in NPS. Paired samples of saliva and NPS were collected in 412 participants. Out of 68 infected cases, 14 were positive only in saliva. RT-qPCR sensitivity ranged from 82.7% (95% CrI: 54.8, 94.8) in NPS to 84.5% (50.9, 96.5) in saliva. Corresponding specificities were 99.1 (95% CrI: 95.3, 99.8) and 98.4 (95% CrI: 92.8, 99.7).

Conclusions

SARS-CoV-2 RT-qPCR test in saliva specimens has a similar or better accuracy than RT-qPCR test in NPS. Saliva specimens may be ideal for surveillance in general population, particularly in children, and in healthcare or other personnel in need of serial testing.

Stability of enveloped and nonenveloped viruses in hydrolyzed gelatin liquid formulation

BACKGROUND

The thermal stability of viruses in gelatin liquid formulations for medical research and application is poorly understood and this study aimed to examine the thermal stability of 4 enveloped and nonenveloped DNA and RNA viruses in hydrolyzed gelatin liquid formulations.

METHODS

Bovine herpesvirus (BHV) was used as a model virus to examine the molecular weight (MW), concentration and gelatin type and to optimize virus stability in liquid formulations at 25 °C and 4 °C. Using the model virus liquid formulation, the stability of multiple enveloped and nonenveloped RNA and DNA viruses, including parainfluenza virus, reovirus (RV), BHV, and adenovirus (AdV), was monitored over up to a 30-week storage period.

RESULTS

The BHV model virus was considered stable after 3 weeks in hydrolyzed gelatin (MW: 4000) with a 0.8 LRV (log10 reduction value) at 25 °C or a 0.2 LRV at 4 °C, compared to the stabilities observed in higher MW gelatin (60,000 and 160,000) with an LRV above 1. Based on the gelatin type, BHV in alkaline-treated hydrolyzed gelatin samples were unexpectantly more stable than in acid-treated hydrolyzed gelatin sample. All four viruses exhibited stability at 4 °C for at least 8 weeks, BHV or AdV remained stable for over 30 weeks of storage, and at 25 °C, AdV and RV remained stable for 8 weeks.

CONCLUSION

The results demonstrated that 5% of 4000 MW hydrolyzed gelatin formulation can act as a relevant stabilizer for the thermal stability of viruses in medical research and application.

Molecular characterization of the S1 gene in GI-17 and GI-13 type isolates of avian infectious bronchitis virus (IBV) in Costa Rica, from 2016 to 2019

Avian infectious bronchitis is one of the most important respiratory diseases affecting poultry production worldwide. The etiological agent of this disease is the avian infectious bronchitis virus (IBV). We analyzed 14 isolates of IBV obtained from poultry farms in Costa Rica, from 2016 through 2019. We sequenced the S1 region of the genome and the sequences obtained were submitted to GenBank. Phylogenetic analyses showed that the isolates obtained during 2016-2017 belong to the GI-17 lineage and are related to the Georgia 13-type Ga-13/14255/14 and CK/CR/1160/16 variants, with a 96.90-100% nucleotide sequence identity and a 92.25-100% amino acid sequence identity. The main differences were detected in the RBD and HVR-3 regions, where a series of mutations eliminate an N-glycosylation site in 10 out of 11 isolates. The isolates obtained during 2018-2019 belong to the GI-13 lineage and are closely related to the 4/91 vaccine variant, with over 98% sequence identity at the nucleotide and amino acids levels. Variations were detected in the RBD and HVR regions, with a possible N-glycosylation site detected in isolate CK/CR/0632/19. These results indicate that a GA13-like pathogenic variant circulated during the 2016-2017 period and that the 4/91 variant was detected after the introduction of the vaccine. The variations shown in both the GA13-like and 4/91 isolates examined, reveal the need for continuous surveillance of IBV in Costa Rica, to detect new variants that may be introduced to the country or develop during outbreaks. This information is highly relevant for vaccination planning and disease management programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-022-00762-2.

Highly sensitive and ultra-rapid antigen-based detection of SARS-CoV-2 using nanomechanical sensor platform

The rapid spread of COVID-19 including recent emergence of new variants with its extreme range of pathologies create an urgent need to develop a versatile sensor for a rapid, precise, and highly sensitive detection of SARS-CoV-2. Herein, we report a microcantilever-based optical detection of SARS-CoV-2 antigenic proteins in just few minutes with high specificity by employing fluidic-atomic force microscopy (f-AFM) mediated nanomechanical deflection method. The corresponding antibodies against the target antigens were first grafted on the gold-coated microcantilever surface pre-functionalized with EDC-NHS chemistry for a suitable antibody-antigen interaction. Rapid detection of SARS-CoV-2 nucleocapsid (N) and spike (S1) receptor binding domain (RBD) proteins was first demonstrated at a clinically relevant concentration down to 1 ng/mL (33 pM) by real-time monitoring of nanomechanical signal induced by antibody-antigen interaction. More importantly, we further show high specific detection of antigens with nasopharyngeal swab specimens from patients pre-determined with qRT-PCR. The results take less than 5 min (swab to signal ≤5 min) and exhibit high selectivity and analytical sensitivity (LoD: 100 copies/ ml; 0.71 ng/ml of N protein). These findings demonstrate potential for nanomechanical signal transduction towards rapid antigen detection for early screening of SARS-CoV-2 and its related mutants.

Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids

Objective: The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Our goal is to reinforce testing capabilities and identify weaknesses that could arise in resource-limited environments that do not have well-controlled cold chains. Method: The sensitivity of qRT-PCR analysis was studied in four VTM for synthetic single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) simulants of the SARS-CoV-2 genome. Results: The sensitivity and reproducibility of qRT-PCR for the synthetic ssRNA and dsDNA were found to be highly sensitive to VTM with the best results observed for ssRNA in HBSS and PBS-G. Surprisingly, the presence of epithelial cellular material with the ssRNA increased the sensitivity of the qRT-PCR assay. Repeated freeze-thaw cycling decreased the sensitivity of the qRT-PCR with two noted exceptions. Conclusions: The choice of VTM is critically important to defining the sensitivity of COVID-19 molecular diagnostics assays and this study suggests they can impact upon the stability of the SARS-CoV-2 viral genome. This becomes increasingly important if the virus structure is destabilised before analysis, which can occur due to poor storage conditions. This study suggests that COVID-19 testing performed with glycerol-containing PBS will produce a high level of stability and sensitivity. These results are in agreement with clinical studies reported for patient-derived samples.

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is influenced by the type of transport medium: Implications for diagnosis and monitoring

It is unclear if the use of a molecular transport medium (MTM) containing guanidine isothiocyanate (GITC) would be advantageous over the CDC recommended, commonly used viral transport medium (VTM). We retested 70 SARS-CoV2 cases by RT-PCR in varying stages of follow-up using MTM and VTM in parallel and found discrepant results of RNase P, E and N genes. Majority (81%) patients tested positive with MTM as compared with VTM (27.1%). Even patients who were sampled 3 weeks after diagnosis demonstrated a significant discrepancy in the positivity rates between MTM vs VTM raising concerns about the clinical utility of VTM.

Take-home kits to detect respiratory viruses among healthcare personnel: Lessons learned from a cluster randomized clinical trial

BACKGROUND

Health care personnel (HCP) working in outpatient settings routinely interact with patients with acute respiratory illnesses. Absenteeism following symptom development and lack of staff trained to obtain samples limit efforts to identify pathogens among infected HCP.

METHODS

The Respiratory Protection Effectiveness Clinical Trial assessed respiratory infection incidence among HCP between 2011 and 2015. Research assistants obtained anterior nasal and oropharyngeal swabs from HCP in the workplace following development of respiratory illness symptoms and randomly while asymptomatic. Participants received take-home kits to self-collect swabs when absent from work. Samples mailed to a central laboratory were tested for respiratory viruses by reverse transcription polymerase chain reaction.

RESULTS

Among 2,862 participants, 3,467 swabs were obtained from symptomatic participants. Among symptomatic HCP, respiratory virus was detected in 904 of 3,467 (26.1%) samples. Self-collected samples by symptomatic HCP at home had higher rates of viral detection (40.3%) compared to 24% obtained by trained research assistants in the workplace (P < .001).

CONCLUSIONS

In this randomized clinical trial, take-home kits were an easily implemented, effective method to self-collect samples by HCP. Other studies have previously shown relative equivalence of self-collected samples to those obtained by trained healthcare workers. Take-home kit self-collection could diminish workforce exposures and decrease the demand for personnel protective equipment worn to protect workers who collect respiratory samples.

DETECTION OF DEER ATADENOVIRUS A DNA IN DAM AND OFFSPRING PAIRS OF ROCKY MOUNTAIN MULE DEER (ODOCOILEUS HEMIONUS HEMIONUS) AND ROCKY MOUNTAIN ELK (CERVUS CANADENSIS NELSONI)

Adenovirus hemorrhagic disease affects primarily mule deer (Odocoileus hemionus), white-tailed deer (Odocoileus virginianus), Rocky Mountain elk (Cervus canadensis nelsoni), and moose (Alces alces) in their first year of life. The method by which the causative virus, Deer atadenovirus A, is maintained in the environment and transmitted to neonates is unknown. In this study, we investigated the potential transmission of the virus from dam to offspring in Rocky Mountain mule deer (Odocoileus hemionus hemionus) and elk in western Wyoming, US. We sampled dams before parturition during placement of vaginal implant transmitters and at parturition and sampled neonates during capture in their first days of life. We also tested for the virus in mortalities submitted for pathologic examination and laboratory analysis. We detected viral DNA in samples from all time points tested but did not find a connection between positive dams and offspring mortalities associated with adenovirus hemorrhagic disease. Although we did not find direct evidence of transmission events between dams and offspring, asymptomatic animals shedding of Deer atadenovirus A, are a likely source of infection in neonates.

Recommendations for respiratory syncytial virus surveillance at national level

Respiratory syncytial virus (RSV) is a common cause of acute lower respiratory tract infections and hospitalisations among young children and is globally responsible for many deaths in young children, especially in infants aged <6 months. Furthermore, RSV is a common cause of severe respiratory disease and hospitalisation among older adults. The development of new candidate vaccines and monoclonal antibodies highlights the need for reliable surveillance of RSV. In the European Union (EU), no up-to-date general recommendations on RSV surveillance are currently available. Based on outcomes of a workshop with 29 European experts in the field of RSV virology, epidemiology and public health, we provide recommendations for developing a feasible and sustainable national surveillance strategy for RSV that will enable harmonisation and data comparison at the European level. We discuss three surveillance components: active sentinel community surveillance, active sentinel hospital surveillance and passive laboratory surveillance, using the EU acute respiratory infection and World Health Organization (WHO) extended severe acute respiratory infection case definitions. Furthermore, we recommend the use of quantitative reverse transcriptase PCR-based assays as the standard detection method for RSV and virus genetic characterisation, if possible, to monitor genetic evolution. These guidelines provide a basis for good quality, feasible and affordable surveillance of RSV. Harmonisation of surveillance standards at the European and global level will contribute to the wider availability of national level RSV surveillance data for regional and global analysis, and for estimation of RSV burden and the impact of future immunisation programmes.

Recommendations for developing a feasible and sustainable national surveillance strategy for respiratory syncytial virus that will enable harmonisation and data comparison at the European level.https://bit.ly/3rWUOOI

Prolonged Unfrozen Storage and Repeated Freeze-Thawing of SARS-CoV-2 Patient Samples Have Minor Effects on SARS-CoV-2 Detectability by RT-PCR

Reliable transportation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patient samples from a swabbing station to a diagnostics facility is essential for accurate results. Therefore, cooling or freezing the samples is recommended in case of longer transportation times. In this study, SARS-CoV-2 detectability by RT-PCR was assessed after prolonged unfrozen storage or repetitive freeze-thawing of SARS-CoV-2 samples. SARS-CoV-2–positive patient swabs stored in viral transport medium were exposed to different temperatures (4°C, 25°C, and 35°C) and to repetitive freeze-thawing, to assess the effect of storage conditions on RT-PCR detection. SARS-CoV-2 RNA was still reliably detected by RT-PCR after 21 days of storage in viral transport medium, even when the samples had been stored at 35°C. The maximum observed change in cycle threshold value per day was 0.046 (±0.019) at 35°C, and the maximum observed change in cycle threshold value per freeze-thaw cycle per day was 0.197 (±0.06). Compared with storage at 4°C, viral RNA levels deviated little but significantly when stored at 25°C or 35°C, or after repeated freeze-thawing. The results of this study indicate that viral RNA levels are relatively stable at higher temperatures and repetitive freeze-thawing.

Criticality of In-House Preparation of Viral Transport Medium in Times of Shortage During COVID-19 Pandemic

Objective

With the COVID-19 pandemic, there have been supply challenges necessitating that laboratories must prepare their own viral transport medium (VTM), which provides stability for clinical specimens for diagnostic viral testing.

Methods

Within a veteran affairs medical center clinical laboratory, VTM was prepared with a Hanks Balanced Salt Solution (HBSS) 500 mL bottle with phenol red, sterile heat-inactivated fetal bovine serum (FBS), gentamicin sulfate (50 mg/mL), and amphotericin B (250 μg/mL). An antimicrobial mixture was made of 50 mL each of amphotericin B and gentamicin sulfate. Ten mL of FBS and 2 mL of the antimicrobial mixture were mixed into the HBSS bottle, from which 3 mL aliquots were made. Sterility and efficacy check were assessed. These preparations were conducted at our VAMC’s clinical laboratory to assure adequate VTM supply during the COVID-19 shortage.

Results

The VTM was successfully prepared in-house, supporting uninterrupted testing for the facility and other affiliated medical facilities/centers and community living centers.

Conclusion

This quality assurance/improvement report represents the first published manuscript on feasible VTM preparation exclusively within a clinical microbiology laboratory during the COVID-19 pandemic.

Evaluation of transport media for laboratory detection of SARS-CoV-2 in upper respiratory tract swab specimens

The reduced availability of commercial swabs and transport media for testing and administrative demands for increased testing capacity during the coronavirus disease 2019 (COVID-19) public health emergency has seriously challenged national laboratory testing programs, forcing many to use nontraditional collection devices, often without typical analytical assessment of their suitability in testing. Five common transport media (four commercial and one in-house) were evaluated for their suitability in the collection of nasopharyngeal swab specimens for subsequent molecular detection of severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2). Results suggest that these transport media provide dependable temporal stability of the SARS-CoV-2 virus without significant analytical interference of molecular assays. These findings are not only important for addressing critical laboratory supply chain shortages of transport media in the current COVID-19 health crisis but also for future pandemic planning, when again supplies of commercially available transport media might be depleted.

Sampling and detection of corona viruses in air: A mini review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a strain of coronaviruses that causes coronavirus disease 2019 (COVID-19). In these days, the spread of the SARS-CoV-2 virus through the air has become a controversial topic among scientists. Various organizations provide standard methods for monitoring biological agents in the air. Nevertheless, there has been no standard recommended method for sampling and determination of viruses in air. This manuscript aimed at reviewing published papers for sampling and detection of corona viruses, especially SARS-Cov-2 as a global health concern. It was found that SARS-Cov 2 was present in some air samples that were collected from patient's rooms in hospitals. This result warrants its airborne transmission potential. However, due to the fact that in the most reviewed studies, sampling was performed in the patient's room, it seems difficult to discriminate whether it is airborne or is transmitted through respiratory droplets. Moreover, some other disrupting factors such as patient distance from the sampler, using protective or oxygen masks by patients, patient activities, coughing and sneezing during sampling time, air movement, air conditioning, sampler type, sampling conditions, storage and transferring conditions, can affect the results. About the sampling methods, most of the used samplers such as PTFE filters, gelatin filers and cyclones showed suitable performance for trapping SARS-Co and MERS-Cov viruses followed by PCR analysis.

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium

As the coronavirus disease 2019 (COVID-19) pandemic sweeps across the world, the availability of viral transport medium (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA has demonstrated stability, we posited that phosphate-buffered saline (PBS) may be a viable transport medium, as an alternative to VTM, for clinical real-time quantitative PCR (qPCR) testing. The intra-individual reliability and interindividual reliability of SARS-CoV-2 qPCR were assessed in clinical endotracheal secretion samples transported in VTM or PBS to evaluate the stability of the qPCR signal for three viral targets (N gene, ORF1ab, and S gene) when samples were stored in these media at room temperature for up to 18 hours. We report that the use of PBS as a transport medium allows high intra-individual and interindividual reliability, maintains viral stability, and compares with VTM in the detection of the three SARS-CoV-2 genes through 18 hours of storage. This study establishes PBS as a clinically useful medium that can be readily deployed for transporting and short-term preservation of specimens containing SARS-CoV-2. Use of PBS as a transport medium has the potential to increase testing capacity for SARS-CoV-2, aiding more widespread screening and early diagnosis of COVID-19.

Pathogenic viruses: Molecular detection and characterization

Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization.

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The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health.

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PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation.

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Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia.

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Development of local capacity to rapidly identify new viruses is very important.

Avian Influenza Virus Sample Types, Collection, and Handling

Successful detection of avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel immunodiffusion tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; oropharyngeal swabs from gallinaceous poultry and cloacal swabs from waterfowl are the preferred specimens for most diagnostic tests, although it is optimal to collect swabs from both locations, if possible. In addition to collecting the appropriate sample for the tests to be performed, selecting the right materials for sample collection (i.e., type of swab) is very important. This chapter will outline the collection of different specimen types and procedures for proper specimen handling.

Using noninvasive metagenomics to characterize viral communities from wildlife

Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.

INFLUÊNCIA DAS CONDIÇÕES DE ARMAZENAMENTO DO VÍRUS INFLUENZA NA DETECÇÃO POR RT-qPCR E ISOLAMENTO VIRAL

Resumo A infecção de suínos pelo vírus influenza causa perdas significativas na suinocultura e a doença tem implicações consideráveis para a saúde pública. Dessa forma, a rápida detecção viral em amostras biológicas de suínos é importante para a vigilância da influenza. Para o diagnóstico, as condições de manutenção das amostras biológicas (modo de acondicionamento, temperatura e período de acondicionamento), desde a colheita das amostras de suínos até o envio ao laboratório, podem interferir negativamente na detecção viral. Neste estudo foi analisada a viabilidade de uma amostra do vírus influenza A H1N1/2009 isolada de suínos, mantida em diferentes modos de acondicionamento (meio comercial UTM, meio in house VTM e sem meio de manutenção) e diferentes temperaturas (4, 23 e 37 °C) por um período de até 120 horas. As amostras foram avaliadas por RT-qPCR e isolamento em ovos embrionados. Foram observados efeitos significativos (p<0,05) para o modo e período de acondicionamento e da interação entre esses dois fatores com a carga viral. Dessa forma, as amostras biológicas enviadas para diagnóstico de influenza devem ser armazenadas, preferencialmente, em meio de manutenção viral a 4 °C e o tempo decorrido entre a colheita da amostra e a chegada ao laboratório deve ser de, no máximo, três dias.

Oral Viral Infections: Diagnosis and Management

This article focuses on common viral infections in the oral cavity with associated systemic manifestations. Discussed are the clinical features, histopathology, diagnosis, treatment, and prevention of viral infections in oral cavity. This will be a useful aid for general practitioners and other dental personnel wanting to expand their pathologic knowledge. This article discusses herpes simplex, varicella zoster, mononucleosis, cytomegalovirus, enteroviruses, rubeola, rubella, mumps, and human papillomavirus. After reviewing this topic, the dentist or hygienist will minimally be competent to diagnose the appropriate oral cavity viral infectious diseases and help patients get the appropriate care they need.

Assessment of a swab collection method without virus transport medium for PCR diagnosis of coxsackievirus infections

Classically, detection of human enterovirus (EV) infections is based on virus isolation in tissue culture, proper sample collection and handling that optimizes virus viability. Samples are collected in virus transport medium (VTM) to ensure virus stability. High sensitivity and rapid results have made polymerase chain reaction (PCR) analysis increasingly popular for routine diagnosis. The PCR method enables simple sample collection and storage for EV diagnostics, which may eventually allow self-sampling at home. Our aim was to test a modification of the conventional clinical swab sample collection method for molecular diagnosis of EV infection. We compared swabs (cotton or synthetic) without VTM and the classical standard synthetic swabs with VTM. Effects of storage temperature (+4 ^°C or -80 ^°C) and duration were studied. EV-RNA could be detected by reverse transcriptase and nested PCR in both swab types without VTM. Differences depended on the storage duration and temperature. Optimum conditions were immediate processing or storage at -80 ^°C. Storage without VTM at +4 ^°C for longer periods is not advisable. We conclude that swabs without VTM can be considered for clinical EV-diagnostics based on PCR, and ultimately for epidemiological sample collection.

Rapid detection of infectious bursal disease by loop-mediated isothermal amplification for field analysis

Infectious bursal disease (IBD) is an immunosuppressive, acute and highly contagious illness of growing-poultry stock infected with infectious bursal disease virus (IBDV). It is common in Pakistan, causing potential economic losses throughout the year. The objective of the study is to propose a rapid, sensitive and specific diagnostic tool, and compare it with existing commonly used reverse transcriptase polymerase chain reaction (RT-PCR) method for IBDV. Different primers were used for RT-PCR and reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) to target the IBD virus. RT-LAMP primers showed prodigious specificity without cross reaction to the other animal pathogens. Moreover, RT-LAMP was found to have 10 times higher selectivity for IBDV identification as compared to RT-PCR. RT-LAMP detected 9.2% more field samples than RT-PCR. Sequences of PCR products were determined and phylogenetic analysis of research isolates revealed its maximum similarity with indigenous and Indian IBDV isolates. RT-LAMP was found to be simple, specific, less laborious and a better technique as compared to RT-PCR for quick analysis. In general, RT-LAMP was declared positive on observing turbidity or adding fluorescence staining reagent such as SYBR Green I. The options of direct use of field sample homogenate and viewing directly the peaks in the graph shown on a monitor/laptop have made it much more convenient and time saving than gel based RT-PCR.

Prolonged intermittent virus shedding during an outbreak of canine influenza A H3N2 virus infection in dogs in three Chicago area shelters: 16 cases (March to May 2015)

OBJECTIVE To estimate an appropriate isolation period for dogs infected with canine influenza A H3N2 virus on the basis of the duration of virus shedding. DESIGN Retrospective case series. ANIMALS 16 dogs, from 3 Chicago area shelters, naturally infected with canine influenza A H3N2 virus. PROCEDURES Medical records of 16 affected dogs were reviewed. Nasal swab specimens from each dog had been tested periodically for a minimum of 15 days following an initial positive real-time reverse transcriptase PCR (rRT-PCR) assay result for influenza A virus shedding. Amplicons were purified, quantified, and sequenced by the Sanger DNA sequencing technique. Virus isolation and sequence results of canine influenza A H3N2 virus from nasal swab specimens were obtained in conjunction with signalment, description of clinical signs, type of treatment, and outcome. RESULTS Viruses from each dog were identified as canine influenza A H3N2 virus on the basis of DNA sequencing. The interval between first and last positive rRT-PCR assay results ranged from 13 to 24 days, whereas the time interval from first reported clinical signs to last positive assay results ranged from 15 to 26 days. Isolation of canine influenza A H3N2 virus was successful in the late shedding period from nasal swab specimens of 4 dogs at 15 and 20 days after the first positive rRT-PCR assay result and 18 to 20 days after the first clinical signs. Clinical signs resolved for all dogs that remained in the shelters during the testing period. CONCLUSIONS AND CLINICAL RELEVANCE Dogs infected with H3N2 virus should be isolated for a period of ≥ 21 days following onset of illness. Even when resolution of clinical signs occurs sooner than 21 days, shedding of H3N2 virus may persist.

Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus

Tembusu virus (TMUV) is a mosquito-borne flavivirus which threatens both poultry production and public health. In this study we developed a complete open reading frame alignment-based rRT-LAMP method for the universal detection of TUMV. To prevent false-positive results, the reaction was supplemented with uracil DNA glycosylase (UDG) to eliminate carryover contamination. The detection limit of the newly developed UDG-rRT-LAMP for TMUV was as low as 100 copies/reaction of viral RNA and 1 × 10^0.89 − 1 × 10^1.55 tissue culture infectious dose/100 μL of viruses. There were no cross-reactions with other viruses, and the reproducibility of the assay was confirmed by intra- and inter-assay tests with variability ranging from 0.22–3.33%. The new UDG-rRT-LAMP method for TMUV produced the same results as viral isolation combined with RT-PCR as the “gold standard” in 96.88% of cases for 81 clinical samples from subjects with suspected TMUV infection. The addition of UDG can eliminate as much as 1 × 10⁻¹⁶ g/reaction of contaminants, which can significantly reduce the likelihood of false-positive results during the rRT-LAMP reaction. Our result indicated that our UDG-rRT-LAMP is a rapid, sensitive, specific, and reliable method that can effectively prevent carryover contamination in the detection of TMUV.

Homotypic Dengue Virus Reinfections in Nicaraguan Children

BACKGROUND

Infection with any of the 4 related dengue virus serotypes (DENV-1-4) is thought to result in lifelong immunity to homotypic reinfection (ie, reinfection with the same serotype).

METHODS

Archived serum samples collected as part of an ongoing pediatric dengue cohort study in Nicaragua were tested for DENV by real-time reverse transcription polymerase chain reaction. Samples were collected from 2892 children who presented with an acute febrile illness clinically attributed to a non-DENV cause (hereafter, "C cases"). Test results were added to a database of previously identified symptomatic dengue cases in the cohort to identify repeat infections.

RESULTS

Four patients with homotypic DENV reinfections were identified and confirmed among 29 repeat DENV infections (13.8%) with serotype confirmation. Homotypic reinfections with DENV-1, DENV-2, and DENV-3 occurred 325-621 days after the initial infection. Each patient experienced 1 symptomatic dengue case and 1 DENV-positive C case, and 2 patients presented with symptomatic dengue during their second infection. These DENV-positive C cases did not elicit long-lived humoral immune responses, despite viremia levels of up to 6.44 log10 copies per mL of serum.

CONCLUSIONS

We describe the first set of virologically confirmed homotypic DENV reinfections. Such cases challenge the current understanding of DENV immunity and have important implications for modeling DENV transmission.

Avian influenza infection dynamics under variable climatic conditions, viral prevalence is rainfall driven in waterfowl from temperate, south-east Australia

Understanding Avian Influenza Virus (AIV) infection dynamics in wildlife is crucial because of possible virus spill over to livestock and humans. Studies from the northern hemisphere have suggested several ecological and environmental drivers of AIV prevalence in wild birds. To determine if the same drivers apply in the southern hemisphere, where more irregular environmental conditions prevail, we investigated AIV prevalence in ducks in relation to biotic and abiotic factors in south-eastern Australia. We sampled duck faeces for AIV and tested for an effect of bird numbers, rainfall anomaly, temperature anomaly and long-term ENSO (El-Niño Southern Oscillation) patterns on AIV prevalence. We demonstrate a positive long term effect of ENSO-related rainfall on AIV prevalence. We also found a more immediate response to rainfall where AIV prevalence was positively related to rainfall in the preceding 3-7 months. Additionally, for one duck species we found a positive relationship between their numbers and AIV prevalence, while prevalence was negatively or not affected by duck numbers in the remaining four species studied. In Australia largely non-seasonal rainfall patterns determine breeding opportunities and thereby influence bird numbers. Based on our findings we suggest that rainfall influences age structures within populations, producing an influx of immunologically naïve juveniles within the population, which may subsequently affect AIV infection dynamics. Our study suggests that drivers of AIV dynamics in the northern hemisphere do not have the same influence at our south-east Australian field site in the southern hemisphere due to more erratic climatological conditions.

Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam

Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Re) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Re of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia.

IMPORTANCE

EV-A71 is one of many viruses that cause HFMD, a common syndrome that largely affects infants and children. HFMD usually causes only mild illness with no long-term consequences. Occasionally, however, severe infection may arise, especially in very young children, causing neurological complications and even death. EV-A71 is highly contagious and is associated with the most severe HFMD cases, with large and frequent epidemics of the virus recorded worldwide. Although major advances have been made in the development of a potential EV-A71 vaccine, there is no current prevention and little is known about the patterns and dynamics of EV-A71 spread. In this study, we utilize full-length genome sequence data obtained from HFMD patients in Viet Nam, a geographical region where the disease has been endemic since 2003, to characterize the phylodynamics of this important emerging virus.

Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics

Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens.

Performance evaluation of Puritan® universal transport system (UniTranz-RT™) for preservation and transport of clinical viruses

The ability of a non-propagating microbial transport medium to maintain the viability of clinically relevant viruses was compared to a similar commercial medium to establish performance equivalence. Two dilutions of stock of test viruses, namely adenovirus (AdV), cytomegalovirus (CMV), echovirus Type 30 (EV), herpes simplex virus (HSV) types 1 and 2, influenza A, parainfluenza 3 (PIV), respiratory syncytial virus (RSV), and varicella zoster virus (VZV), were spiked into Puritan® Medical Products Company Universal Transport System (UniTranz-RT™) and BD(TM) Universal Viral Transport System (UVT) and incubated at 4 °C and room temperature (RT) for up to 72 hr. Post incubation assessment of recovery of AdV, EV, HSV-2, PIV, and VZV from UniTranz-RT™ and UVT using shell vial assays followed by immunofluorescence staining demonstrated statistically significant differences between both transport media. In general, significantly higher recoveries of AdV, EV, and VZV were found from UniTranz-RT™ than UVT whereas HSV-2 and PIV were recovered better from UVT than UniTranz-RT™, under specific test conditions. The recovery of HSV-1, influenza A, PIV, and RSV showed no significant differences between transport media. Sulforhodamine B-based assay analysis of UniTranz-RT™ lots prior to and at expiration exhibited no cytotoxicity. The overall results of the study validate the full performance of UniTranz-RT™ as a viral transport medium and establish its effectiveness on par with the UVT.

Performance evaluation of two microbial transport media designed for preservation and transport of Chlamydiae, Mycoplasma and Ureaplasma

The ability of a non-propagating transport device (test device) to maintain the viability of clinically relevant bacteria was compared with a similar commercial device (predicate device) to establish performance equivalence. Test bacteria, namely Chlamydia trachomatis, Chlamydia pneumoniae, Mycoplasma hominis, Mycoplasma pneumoniae and Ureaplasma urealyticum, were inoculated into the test [Puritan Medical Products Universal Transport System (UniTranz-RT(TM))] and predicate (BD Universal Viral Transport System) devices, and incubated at 4 °C and room temperature for up to 72 h. Bacterial viability was assessed at selected time points post-incubation using shell vial assays followed by immunofluorescence staining (for Chlamydia) or by standard culture techniques (for Mycoplasma and Ureaplasma). Results indicated that the Chlamydia strains were equally stable in both test and predicate devices through 72 h storage, at both test temperatures. Quantifiable levels of Mycoplasma and Ureaplasma were recovered from the test and predicate devices throughout the storage period. Low-temperature storage improved bacterial viability when compared with room temperature storage. In addition, the predicate device demonstrated slightly improved performance versus the test device in the context of Mycoplasma and Ureaplasma following 72 h storage. The overall results of the study confirmed the full performance of UniTranz-RT(TM) as a microbial transport medium and established equal performance with the predicate device.

Avian influenza virus sample types, collection, and handling

Successful detection of avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel precipitin tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; although it is optimal to collect both oropharyngeal and cloacal swabs, oropharyngeal swabs should be collected from gallinaceous poultry and cloacal swabs should be collected from waterfowl. In addition to collecting the appropriate sample for the tests to be performed, selecting the right materials for sample collection (i.e., type of swab) is very important. This chapter outlines the collection of different specimen types and procedures for proper specimen handling.

Factors affecting the success of influenza laboratory diagnosis

Influenza is one of the most common human infectious diseases, and has profound health and economic consequences. The laboratory diag- nosis of influenza virus infections plays an important role in the global surveillance of influenza. Therefore, there is a growing demand for highly sensitive and rapid methods for detecting influenza. The performance of particular diagnostic methods is affected by various factors. In this study, we assess the effects of patients' age and time to diagnosis on the probability of detecting influenza using four diagnostic methods (virus isolation, rapid test, RT-PCR and real-time RT-PCR). We examined 3,546 samples from central and eastern Slovakia during the influenza seasons from 2005-2006 to 2010-2011. In general, the probability of influenza detection significantly decreased with the time from onset of illness to sample collection (T1) as well as with patients' age (AGE). On the contrary, time from sample collection to delivery (T2) did not play a role in the prob- ability of influenza detection. As judged by odds ratios, the virus isolation method was most sensitive to T1, followed by the rapid test and RT-PCR methods. For the effect of AGE, the rapid test and virus isolation methods were more sensitive than PCR-based methods. The effects of T1 and AGE were independent of each other. Laboratories which participate in inifluenza surveillance should use several methods to enable rapid and accurate influenza A and B virus detection.

Evaluation of two different swab transport systems in the detection of avian influenza virus excretion from infected Pekin ducks (Anas platyrhynchos)

The role of wild birds in the epidemiology and ecology of influenza A viruses has long been recognised (Alexander, 2007a). As a result of the emergence of a H5N1 highly pathogenic avian influenza (HPAI) virus and the apparent role of wild birds in its spread across Asia, Europe and Africa, avian influenza (AI) wild bird surveillance has been implemented in many countries including, since February 2006, a mandatory programme in the European Union (CEC, 2006a). In the present study the detection of virus excreted from Pekin ducks (Anas platyrhynchos) infected experimentally with A/mallard/England/2126/07 (H3N6) was investigated over a fourteen day period post-infection using cloacal and oropharyngeal swabs, with (wet) and without (dry) viral transport medium which were collected from each duck in alternating order. For influenza A virus matrix gene RNA detection, wet oropharyngeal swabs were significantly more sensitive than dry oropharyngeal on days 4-5 after infection. For cloacal samples, dry swabs were equivalent or superior to wet swabs throughout the study. Although differences in detection between dry and wet swabs were observed, the qualitative bird-level results were unaffected, meaning that the infection status of individual birds was correctly determined.

Feasibility of an antiviral clinical trial requiring cross-country shipment of conjunctival adenovirus cultures and recovery of infectious virus

PURPOSE

Accurate and timely laboratory diagnosis of adenovirus from conjunctival cultures is essential to ensure appropriate enrollment, and detection of residual infectious virus is essential to evaluate antiviral efficacy in any multicenter national clinical trial. As part of a feasibility study, we investigated those variables that might affect the successful recovery of infectious adenovirus from patient conjunctival cultures after cross-country shipment.

MATERIALS AND METHODS

Simulated adenovirus conjunctival cultures were prepared in viral transport media to evaluate the effect of four variables (adenovirus serotype, initial concentration, initial storage temperature [-20 degrees C, 0 degrees C, 20 degrees C], and preshipment storage times [1-5 days]) on the recovery of infectious adenovirus by a central laboratory in St. Paul, MN, following air shipment from Pittsburgh, PA. Upon arrival, the internal temperatures of the containers were recorded, and the samples were cultured on A549 cells using standard tube and/or shell vial culture.

RESULTS

Overall, adenovirus was recovered in 352/354 (99.4%) of the samples when the initial titer was greater than 1.0 PFU/ml. Adenovirus serotype, initial storage temperature, and preshipment storage times had no adverse effect on virus recovery.

CONCLUSIONS

Simulated conjunctival samples could successfully be shipped cross-country at ambient temperatures to a commercial laboratory for adenovirus isolation by culture. Having demonstrated feasibility, a clinical trial was subsequently carried out that confirmed the ease of shipment and recovery of infectious adenovirus from conjunctival cultures.

Avian influenza virus sample types, collection, and handling

Successful detection of the avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel precipitin tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; oropharyngeal swabs should be collected from poultry, and cloacal swabs should be collected from waterfowl. This chapter will outline the collection of different specimen types and procedures for proper specimen handling.

Coinfection of avian influenza virus (H9N2 subtype) with infectious bronchitis live vaccine

Avian influenza virus of H9N2 subtype is pathotyped as a non-highly pathogenic virus. However, frequent incidences of avian influenza of high mortality that are caused by H9N2 viruses have been observed in broiler chicken farms in Iran and some other Asian countries. Coinfections or environmental factors may be involved in such cases. Infectious microorganisms have been implicating in taking part in the cases of coinfection. We studied the effect of experimental coinfection of H9N2 avian influenza virus with infectious bronchitis live vaccine, which is used extensively in chicken farms in Iran. Clinical signs, gross lesions, viral shedding and mortality rate of the experimentally infected birds were examined. Coinfection of infectious bronchitis live vaccine and H9N2 avian influenza virus led to an extension of the shedding period of H9N2 virus, increasing the severity of clinical signs and mortality rates, causing macroscopic lesions in the embryos.

Evaluation of sampling technique and transport media for the diagnostics of adenoviral eye infections. Adenovirus sampling and transport

BACKGROUND

Human adenoviruses (HAdV) may cause pharyngoconjunctival fever, follicular conjunctivitis or epidemic keratoconjunctivitis (EKC). Especially, outbreaks of the latter may lead to severe economic losses when preventive measures are implemented too late. Thus, a safe sampling method, proper specimen transport conditions and a fast and sensitive diagnostic technique is mandatory.

METHODS

Two commercially available virus transport systems (VTS) were compared with two NaCl-moisturised sampling devices, one of which comprises Dacron-tipped plastic-shafted swabs and the other a cotton-tipped wood-shafted swab, available in most ophthalmologists' offices. Downstream methods for specific detection of HAdV included direct immunofluorescence assay (IFA) of conjunctival swabs, virus isolation by cell culture and quantitative real-time polymerase chain reaction (qPCR). Furthermore, the influence of application of local anaesthetics prior to swabbing on subsequent detection of HAdV was investigated.

RESULTS

Application of local anaesthetics had a positive influence on the amount of swabbed cells, thus increasing the chance of obtaining positive results by IFA. Neither isolation of HAdV by cell culture nor by qPCR was negatively influenced by this pretreatment. Surprisingly, both commercially available VTS performed significantly worse than the NaCl-moisturised swabs. This was shown with regard to virus recovery rates in cell culture as well as viral genome copy numbers in the qPCR.

CONCLUSIONS

Based on our results, the following recommendations are provided to improve sampling, transport and diagnostic techniques regarding conjunctival swabs for diagnosis of human adenovirus infection: (1) application of local anaesthetics, (2) NaCl-moisturised VTS for shipment of specimens, and (3) detection of HAdV by qPCR. The latter method proved to be superior to virus isolation by cell culture, including subsequent identification by IFA, because it is faster, more sensitive and allows simultaneous handling of a number of samples. Hence, countermeasures to prevent further virus spread in an outbreak situation can be implemented earlier, thus reducing the number of subsequent adenoviral infections.

Advances in the diagnosis of respiratory virus infections

Background: Advances have been made in selecting sensitive cell lines for isolation, in early detection of respiratory virus growth in cells by rapid culture assays, in production of monoclonal antibodies to improve many tests such as immunofluorescence detection of virus antigens in nasopharyngeal aspirates, in highly sensitive antigen detections by time-resolved fluoroimmunoassays (TR-FIAs) and biotin-enzyme immunoassays (BIOTH-E), and, finally, in the polymerase chain reaction (PCR) detection of respiratory virus DNA or RNA in clinical specimens. All of these advances have contributed to new or improved possibilities for the diagnosis of respiratory virus infections.

Objectives and study design: This review summarizes our experiences during the last 15 years in the development of diagnostic tests for respiratory virus infections, and in use of these tests in daily diagnostic work and in epidemiological studies.

Results: Immunofluorescence tests based on monoclonal antibodies, all-monoclonal TR-FIAs, and biotin-enzyme immunoassays (EIAs) have about the same sensitivities and specificities. They compare well with the sensitivity of virus culture. PCR followed by liquid-phase hybridization is a sensitive method for detecting adenovirus DNA and enterovirus and rhinovirus RNA in clinical specimens. IgG EIA on paired acute and convalescent phase sera is the most sensitive serological test for respiratory virus infections and is a valuable reference method when evaluating the sensitivity of new diagnostic tests. The IgG avidity test can distinguish primary infections from re-infections at least in respiratory syncytial virus (RSV) infections. IgM antibody assays, on the other hand, had low sensitivities in our studies.

Conclusions: The choice of diagnostic methods for respiratory virus infections depends on the type and location of the laboratory, the number of specimens tested, and the previous experience of the laboratory. Virus culture, whenever possible, should be the basic diagnostic method; the results, including identification of the virus, should be available no more than 24 h later than the results of rapid diagnostic tests. In small laboratories, especially in hospitals where specimen transportation is well organized, immunofluorescence may be the best choice for antigen detection with the provision that an experienced microscopist and a good UV microscope are available. If the laboratory receives a large number of specimens and has previous experience with EIAs, then biotin-EIAs or TR-FIAs may be the most practical techniques. Their advantages include the stability of the antigens in clinical samples since intact, exfoliated epithelial cells are not required, treatment of specimens is practical, testing of large numbers of specimens is possible, and reading the printed test result is less subjective than reading fluorescence microscopy. The larger role of PCR in the diagnosis of respiratory virus infections depends on future developments such as practical methods to extract DNA or RNA and to purify the extracts from nonspecific inhibitors, plus further improvements to minimize cross-contamination. Group-specific detection of enteroviruses and rhinoviruses is an example of the potential for PCR technology. In experienced laboratories. EIA IgG antibody tests should be available. Recombinant antigens may be a useful part of such assays.

Nonsusceptibility of primate cells to Taura syndrome virus

Primate cells commonly used to test for viruses of the Picornaviridae family are not susceptible to infection by Taura syndrome virus of penaeid shrimp.

Taura syndrome virus (TSV), a pathogen of penaeid shrimp and member of the family Dicistroviridae, was recently reported to have the ability to infect primate cells. We independently retested this hypothesis. Three lines of primate cells FRhK-4, MA-104, and BGMK, which are highly susceptible to infection by human picornaviruses, were challenged with TSV. Viral replication was assayed by real-time reverse transcription–polymerase chain reaction using cell media samples collected on days 0, 4, and 7 postchallenge. By day 7, genome copy numbers had decreased 25%–99%. No cytopathic effect was observed after 7 days. An in situ hybridization assay, with gene probes specific for detection of TSV, was negative for TSV in challenged cells. The infectivity of residual virus in the cell culture media at day 7 was confirmed by bioassay using TSV-free indicator shrimp (Litopenaeus vannamei). TSV did not infect the primate cells tested, and no evidence of zoonotic potential was found.