Optimal specimen collection and transport methods for the detection of avian influenza virus and Newcastle disease virus

Spackman, Erica; Pedersen, Janice C.; McKinley, Enid T.; Gelb, Jack

doi:10.1186/1746-6148-9-35

Cited by 37 publications

(31 citation statements)

References 15 publications

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“…Third, our models assumed perfect sensitivity and specificity of real-time RT-PCR for pooled samples. The assays used in this study are considered highly sensitive and specific (27,28), and previous studies did not report any differences in virus detection for pooled and individual samples (40)(41)(42). Furthermore, virus detection in our study was based on parallel interpretation of cloacal or oropharyngeal sample test results (i.e., positive if >1 was positive).…”

Section: Discussionmentioning

confidence: 85%

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh

Kim¹,

Biswas²,

Giasuddin³

et al. 2018

Emerg. Infect. Dis.

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We conducted a cross-sectional study in live bird markets (LBMs) in Dhaka and Chittagong, Bangladesh, to estimate the prevalence of avian influenza A(H5) and A(H9) viruses in different types of poultry and environmental areas by using Bayesian hierarchical logistic regression models. We detected these viruses in nearly all LBMs. Prevalence of A(H5) virus was higher in waterfowl than in chickens, whereas prevalence of A(H9) virus was higher in chickens than in waterfowl and, among chicken types, in industrial broilers than in cross-breeds and indigenous breeds. LBMs with >1 wholesaler were more frequently contaminated by A(H5) virus than retail-only LBMs. Prevalence of A(H9) virus in poultry and level of environmental contamination were also higher in LBMs with >1 wholesaler. We found a high level of circulation of both avian influenza viruses in surveyed LBMs. Prevalence was influenced by type of poultry, environmental site, and trading.

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Section: Discussionmentioning

confidence: 85%

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh

Kim¹,

Biswas²,

Giasuddin³

et al. 2018

Emerg. Infect. Dis.

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“…The transport medium should be supplemented with antibiotics to avoid bacterial contamination during isolation. The swab material also influences the recovery of IAV, and flocked swabs are better than nonflocked swabs (38). Fixation of samples in ethanol (35) and sampling using FTA cards (22) are other preservation methods suitable for IAV surveillance and show advantages for biosafety and transportation, but analysis is limited to molecular screening and sensitivity between methods may vary.…”

Section: Discussionmentioning

confidence: 99%

“…Samples should ideally be frozen at the field site (using liquid nitrogen tanks or ultra-low-temperature freezers) or, if the necessary facilities are lacking, kept at ϩ4°C for a limited time until they are processed in the laboratory. Virus transport media, such as Hanks' balanced salt solution supplemented with protein or brain heart infusion (BHI) broth, increase the stability of the viruses (7,38) and are a preferred choice over phosphate-buffered saline (PBS) or dry swabs. The transport medium should be supplemented with antibiotics to avoid bacterial contamination during isolation.…”

Section: Discussionmentioning

confidence: 99%

How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

Latorre‐Margalef

Avril

Tolf

et al. 2016

Appl Environ Microbiol

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Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (C t ) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given C t value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data.T he number of studies focusing on the role of wild birds as reservoir species for influenza A virus (IAV) has increased dramatically over the last 10 years (1). This increase was to a large extent caused by the emergence of a highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype in Southeast Asia in 1999 (2). This particular virus causes high mortality in domestic poultry and can be transmitted among wild birds, particularly waterfowl. It rapidly reached a large spatial distribution in Asia, Europe, and Africa in 2006 and has remained endemic in parts of this range. Several surveillance programs were initiated in response to the H5N1 spread (3), but standardized methods were not implemented everywhere. In addition, the emergence in Southeast Asia of other IAV subtypes in poultry and in humans, like H5N1 and H7N9, and the recent spread of H5N8 into Europe and North America (4, 5), point to the need for efficient and reliable screening methods (6). As IAV is an RNA virus and is sensitive to changes in the physical environment, such as temperature, pH, and salinity (7, 8), sampling and screening strategies need to be evaluated in order to provide best practice.Traditionally, IAV surveillance has been based on cloacal swabs or fresh droppings (here c...

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“…With this method of detection, specimen processing requires nucleic acid stability rather than organism viability previously needed for culture. Many studies have compared various types of specimens, swabs, and processing buffers for influenza and other respiratory virus RT‐PCR assays [Abu‐Diab et al, ; Hernes et al, ; Irving et al, ; Spackman et al, ]. Laboratory‐based studies have found that influenza RNA was stable on dry swabs for days prior to processing if kept at room temperature or cooler [Moore et al, ; Druce et al, ].…”

Section: Introductionmentioning

confidence: 99%

Detection of influenza by real time RT-PCR is not affected by delays in respiratory specimen processing

et al. 2016

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Background Sample processing for real-time reverse transcriptase polymerase chain reaction (rRT-PCR) based diagnostic assays requires stabilizing sample ribonucleic acid (RNA) in lysis buffer prior to testing. The stability of viral RNA prior to processing is difficult to assure. It is unknown if clinical sample integrity is compromised by delays in processing, as may occur due to weekends and holidays. We sought to examine the integrity of respiratory specimens with variable processing times. Study Design Upper respiratory specimens were collected during 3 influenza seasons 2009-2012 and tested for influenza virus and internal control human RNase P (RNP) RNA by rRT-PCR. Time to processing was measured in hours from specimen collection to placement in lysis buffer. Results 635 (11.4%) of 5583 samples were influenza positive. Mean and median times to processing were 11.5 hours and 6.0 hours respectively (min 0.1h, max 105.2h). There were no significant associations between time to processing and presence of RNP (OR=1.0, p=0.740), or detection of influenza (OR=1.0, p=0.060). Longer duration of illness was associated with a lower likelihood of influenza detection (OR=0.92, p<0.001) and with increased influenza A cycle threshold (Ct) values (p<0.001), while older age was associated with increased influenza B Ct values (p=0.001), indicating the presence of less amplifiable RNA. Conclusion Delays in time to processing of upper respiratory specimens up to 105 hours were not associated with decreased detection of amplifiable RNA, suggesting specimen integrity is not compromised by such delays.

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Optimal specimen collection and transport methods for the detection of avian influenza virus and Newcastle disease virus

Cited by 37 publications

References 15 publications

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh

How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

Detection of influenza by real time RT-PCR is not affected by delays in respiratory specimen processing

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