Effect of swab matrix, storage time, and temperature on detection of avian influenza virus RNA in swab samples

SARS-CoV-2 emergency use authorization published sensitivity differences do not correlate with positivity rate in a hospital/reference laboratory setting

During the first year of the COVID-19 pandemic skyrocketing demand for testing in the United States, coupled with supply chain issues, necessitated the use of multiple SARS-CoV-2 molecular testing platforms at many health centers. At our institution these platforms consisted of 8 ordered services for sample triage, using 9 emergency use authorized (EUA) SARS-CoV-2 RNA nucleic acid amplification tests resulting in 10 possible ordered service/EAU combinations. Here we review the results of the first ∼2.9 million samples tested and note the variability in positivity rates. We conclude that differences in reported limit of detection did not translate to differences in positivity rate or show correlation to discordant results observed. This highlights the importance of balancing patient testing capacity needs with the desire to have more sensitive tests.

Effects of swab pool size and transport medium on the detection and isolation of avian influenza viruses in ostriches

Background

Rigorous testing is a prerequisite to prove freedom of notifiable influenza A virus infections in commercially farmed ostriches, as is the isolation and identification of circulating strains. Pooling 5 ostrich tracheal swabs in a 50 % v/v phosphate-buffered saline (PBS): glycerol transport medium (without antibiotics) is the current standard practice to increase reverse transcription real time PCR (RT-rtPCR) testing throughput and simultaneously reduce the test costs. In this study we investigated whether doubling ostrich tracheal swabs to 10 per pool would affect the sensitivity of detection of H5N8 high pathogenicity avian influenza virus (HPAIV) and H7N1 low pathogenicity avian influenza virus (LPAIV) by quantitative RT-rtPCR, and we also compared the effect of a protein-rich, brain heart infusion broth (BHI) virus transport media containing broad spectrum antimicrobials (VTM) on the efficacy of isolating the H5N8 and H7N1 viruses from ostrich tracheas, since the historical isolation success rate from these birds has been poor.

Results

Increasing the ostrich swabs from 5 to 10 per pool in 3 mls of transport medium had no detrimental effect on the sensitivity of the RT-rtPCR assay in detecting H5N8 HPAIV or H7N1 LPAIV; and doubling of the swab pool size even seemed to improve the sensitivity of virus detection at levels that were statistically significant (p less than or equal to 0.05) in medium and low doses of spiked H5N8 HPAIV and at high levels of spiked H7N1 LPAIV. On virus isolation, more samples were positive when swabs were stored in a protein-rich viral transport medium supplemented with antimicrobials in PBS: glycerol (10/18 vs. 7/18 for H5N8 HPAI); although the differences were not statistically significant, overall higher virus titres were detected (10^6.7 – 10^3.0 vs. 10^6.6 - 10^3.1 EID₅₀ for H5N8 HPAIV and 10^5.5 - 10^1.4 vs. 10^5.1 – 10^1.3 EID₅₀ for H7N1 LPAIV); and fewer passages were required with less filtration for both H5N8 HPAI and H7N1 LPAI strains.

Conclusion

Ostrich tracheal swab pool size could be increased from 5 to 10 in 3mls of VTM with no loss in sensitivity of the RT-rtPCR assay in detecting HPAI or LPAI viruses, and HPAI virus could be isolated from a greater proportion of swabs stored in VTM compared to PBS: glycerol without antibiotics.

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

Aptamers, the bivalent agents as probes and therapies for coronavirus infections: A systematic review

The recently known coronavirus, SARS-CoV-2, has turn into the greatest global health challenge, affecting a large number of societies. The lack of specific treatment and gold-standard diagnostic system has made the situation more complicated. Efforts have led to production of several diagnostic kits that are associated with limitations such as inadequate sensitivity and accuracy. Aptamers as multipotent biological probes could be promising candidates to design sensitive and specific biosensors. Although few studies have introduced specific aptamer types of coronavirus, they may help us select the best approach to obtain specific aptamers for this virus. On the other hand, some of already-introduced aptamers have shown the inhibitory effects on coronavirus that could be applied as therapeutics. The present study has provided a systematic overview on use of aptamer-based biosensors and drugs to diagnose and treat coronavirus.

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.

ASSESSMENT OF A LANCET-AND-SWAB BLOOD SAMPLING TECHNIQUE FOR SURVEILLANCE OF ELEPHANT ENDOTHELIOTROPIC HERPESVIRUS INFECTION

Lancing a finger elicits minimal pain in humans and is applied routinely to obtain small volumes of blood for clinical diagnostics. A modified lancet bleeding method and several blood sampling matrices were evaluated in this study for the purpose of routine elephant endotheliotropic herpesvirus (EEHV) surveillance in Asian elephants (Elephas maximus). The procedure enabled weekly sampling from elephants as young as 9 mo of age. The blood sampling matrices were evaluated for their sensitivity measuring β-actin, tumor necrosis factor α, and/or EEHV-1 by quantitative polymerase chain reaction assays. Foam and flocked swabs produced significantly (P < 0.05) lower quantitation cycles, ie, increased analytical sensitivity, than filter papers, Whatman® FTA cards, or conventional cotton-tipped swabs. The two swab types also demonstrated comparable analytical sensitivity to that of a similar volume of EDTA whole blood for the detection of EEHV-1 DNA. This lancet-and-swab technique proved satisfactory for the detection of EEHV-1 viremia in two Asian elephant calves, and in one instance viremia could be detected 5 days prior to the development of clinical signs. Low blood yield from the lancet application may reduce sensitivity and compromise early detection of viremia. Therefore, standard venipuncture remains the recommended blood sampling method, and training for consistent and regular vein access should continue to be the priority for collections holding elephants. However, if appropriate measures are taken to collect an optimum blood volume, this lancet-and-swab technique offers a suitable alternative for EEHV surveillance in situations where venipuncture may not be practical.

Sample preparation for avian and porcine influenza virus cDNA amplification simplified: Boiling vs. conventional RNA extraction

RNA extraction and purification is a fundamental step that allows for highly sensitive amplification of specific RNA targets in PCR applications. However, commercial extraction kits that are broadly used because of their robustness and high yield of purified RNA are expensive and labor-intensive. In this study, boiling in distilled water or a commercial lysis buffer of different sample matrices containing avian or porcine influenza viruses was tested as an alternative. Real-time PCR (RTqPCR) for nucleoprotein gene fragment was used as read out. Results were compared with freshly extracted RNA by use of a commercial extraction kit. Different batches of virus containing materials, including diluted virus positive allantoic fluid or cell culture supernatant, and avian faecal, cloacal or oropharyngeal swab samples were used in this study. Simple boiling of samples without any additional purification steps can be used as an alternative RNA preparation method to detect influenza A virus nucleoprotein RNA in oropharyngeal swab samples, allantoic fluid or cell-culture supernatant. The boiling method is not applicable for sample matrices containing faecal material.

Equivalence of influenza A virus RNA recovery from nasal swabs when lysing the swab and storage medium versus storage medium alone

Surveillance of healthy individuals at high risk for zoonotic influenza A transmission is important for tracking trends in influenza A epidemiology. Practical measurement methods that maximize viral recovery and produce low variability are essential when low viral loads are expected. For this study, lysing both a nasal swab and its storage medium was compared to lysing the storage medium alone to determine which method results in greater influenza A virus recovery. Independent results from two laboratories suggest that including the swab in the lysis step does not lead to higher influenza A virus recovery, and that recovery is less variable when only the swab storage medium is extracted. These results indicate that simply lysing the swab storage medium is an effective extraction method for nasal swabs collected during studies of influenza A virus exposure among healthy populations.

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.

Failure of productive infection of Mallards (Anas platyrhynchos) with H16 subtype of avian influenza viruses

Background

Mallard ducks and other waterfowl represent the most important reservoirs of low pathogenic avian influenza viruses (LPAIV). In addition, mallards are the most abundant duck species in Eurasia that migrate over long distances. Despite extended wild bird monitoring studies over the past decade in many Eurasian countries and investigating hundreds of thousands of wild bird samples, no mallard duck was found to be positive for avian influenza virus of subtype H16 in faecal, cloacal or oropharyngeal samples. Just three cases of H16 infections in Anseriformes species were described worldwide. In contrast, H16 viruses have been repeatedly isolated from birds of the Laridae family.

Objective

Here, we tested the hypothesis that mallards are less permissive to infection with H16 viruses.

Methods

Groups of mallard ducks of different age were inoculated via the oculo-nasal-oral route with different infectious doses of an H16N3 AIV.

Results

The ducks did not show any clinical symptoms, and no virus shedding was evident from cloacal and respiratory routes after experimental infection as shown by negative RT-qPCR results. In addition, all serum samples taken on days 8, 21 and 24 post-inoculation were negative by competitive NP-ELISA.

Conclusions

This study provided evidence that mallards are resistant to infection with H16N3 LPAIV.

Evaluation of avian influenza serologic and virologic diagnostic methods in wild Anseriformes and Charadriiformes

Evaluation of avian influenza virus (AIV) diagnostic methods, including a nucleoprotein (NP) competitive enzyme-linked immunosorbent assay (c-ELISA), hemagglutination inhibition (HI) test, type A real-time reverse transcription polymerase chain reaction (RRT-PCR), and embryonating chicken egg (ECE) virus isolation (VI), suggested validity of these tests in wild birds comparable to that reported in poultry. This was determined by analyzing the results from experimental inoculation of three species of wild birds with a low-pathogenicity AIV and from field surveillance data. The NP c-ELISA in a high-AIV prevalence setting had 100% diagnostic sensitivity (Se; 95% confidence interval [CI]: 81.5%-100%) and 91% diagnostic specificity (Sp; 95% CI: 70.8%-98.9%) in negative controls compared with the RRT-PCR. In low-AIV prevalence flocks using a > 60% inhibition positivity threshold, relative to the HI test, c-ELISA performed with 90.5% Se (95% CI: 86.2%-93.8%) and 41.2% Sp (95% CI: 38.1%-44.5%). Assessment of HI suggests a titer > or = 8 is a positive test result in wild-bird sera, and using this titer had 83.3% Se (95% CI: 58.6%-96.4%) in experimentally infected birds. The RRT-PCR diagnostic performance compared with VI in cloacal swabs varied over 2-6 days postinoculation, having high Se (83.3%-100%) and Sp (94.1%-100%) with substantial agreement (kappa = 0.8). The cycle thresholds (C(t)) for the RRT-PCR of C(t) < 37 for positivity and C(t) = 37-40 as indeterminate were found to be valid for the species included in this study. In view of the interpretative diagnostic difficulties in heterogeneous populations of wild birds, this evaluation in three species of wild birds and in surveillance data should provide greater confidence in the application of these methods routinely used in poultry.

The use of Nanotrap particles for biodefense and emerging infectious disease diagnostics

Detection of early infectious disease may be challenging due to the low copy number of organisms present. To overcome this limitation and rapidly measure low concentrations of the pathogen, we developed a novel technology: Nanotrap particles, which are designed to capture, concentrate, and protect biomarkers from complex biofluids. Nanotrap particles are thermoresponsive hydrogels that are capable of antigen capture through the coupling of affinity baits to the particles. Here, we describe recent findings demonstrating that Nanotrap particles are able to capture live infectious virus, viral RNA, and viral proteins. Capture is possible even in complex mixtures such as serum and allows the concentration and protection of these analytes, providing increased performance of downstream assays. The Nanotrap particles are a versatile sample preparation technology that has far reaching implications for biomarker discovery and diagnostic assays.