A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

Abstract

This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.

Avian influenza outbreaks: evaluating the efficacy of cleaning and disinfection of vehicles and transport crates

“…Only virus isolation and titration directly inform on the risk of AI transmission. However, environmental sampling coupled with detection of AIV genome by rRT-PCR is widely used, both for the evaluation of AI control measures ( Kang et al, 2015 ; Chowdhury et al, 2020 ) and for disease surveillance ( Hood et al., 2019 ). This method is easy to apply and remains affordable (around 30 euros/sample), despite its cost being higher than bacteriologic methods (around 5 euros/sample for the plate count method and 13 to 15 euros/sample for enumeration on swabs).…”

“…In addition, the previous study relied on environmental sampling coupled with avian influenza virus ( AIV ) genome detection by real-time reverse-transcription polymerase chain reaction ( rRT-PCR ) to evaluate cleaning and disinfection. This protocol has been found to be useful to monitor the effectiveness of control measures against AI ( Hood et al., 2019 ), but it is not commonly used by abattoirs to evaluate cleaning and disinfection of crates and trucks. According to a survey in France in 2019 ( ANSES, 2019 ), abattoirs use visual inspection of surface cleanliness and microbiologic controls such as counts of coliforms on surfaces after decontamination.…”

Longitudinal Analysis of Influenza A(H5) Sero-Surveillance in Myanmar Ducks, 2006–2019

“…Future surveillance programmes should focus more on the detection of H5 viruses. Given the low rates of detection of H5 viruses at the farm level via swab samples from ducks, a shift to greater use of surveillance in markets or to alternative, environmental samples at the farm level, such as drinking water or feathers, should be considered [26]. Repeated, intensive duck serology is not recommended unless results can be provided in real time to assist in determining sites where H5 viruses are actively circulating and to serve as a tool for disease control and local virus elimination.…”

Avian influenza virus in water: global subtype diversity and spatial distribution patterns

“…Environmental sampling has been effectively used for AIV surveillance since the 1970s. Nevertheless, the methods and protocols are not completely standardized, as well as, an international guideline about data management is absent (Hood et al, 2020). This was one of the most noticeable limitations in our analyses since several AIV no specified the type of environment sampled (i.e., feces, water, air, mud, or surface swabs), and thus, those HA sequences were excluded.…”