Part 2: Active sampling
As the focus was on active detection of HPAI virus, sampling was
targeted and risk-based, and did not aim to achieve a representative
sample. Nomadic ducks were undersampled during the first round, and
proportionally oversampled during the second round. No village poultry
were actively sampled during the first round; the incentivised passive
surveillance was unsuccessful in locating cases or focal outbreaks and
was discontinued. Modified snowball sampling was used to perform
risk-based sampling in the second round, but the number of samples taken
was comparatively low.
Overall, the number of HPAI virus isolates identified was relatively
small. H5 virus was detected in all production systems. The differences
in detection of AIV and H5 virus between enterprise types and between
the two rounds were found to be statistically significant, with
significantly more AIV detections during the second round. It could not
be determined whether this was a result of differences in the
sensitivities of detection between the two rounds, or the consequence of
an underlying causal trend. As a consequence of the study design, the
scope for model-based analytic approaches was limited and the analysis
was mostly descriptive; statistical testing was restricted to hypothesis
testing to investigate strengths of association and differences between
the enterprise types.
Only the commercial farm sector implemented biosecurity practices and
vaccination; however, the extent of implementation was variable between
farms and there was evidence that H5 virus was present, albeit at an
extremely low level. “Silent spread” and persistence of HPAIV in
sub-optimally vaccinated commercial flocks is a concern. In a
comparative trial, Tarigan et al. (2018) used seven different commercial
vaccines produced in Indonesia mostly based on the H5N1 subtype;
vaccination led to highly variable outcomes, including vaccination
failures, and was largely ineffective in providing long-lasting
protective immunity. Poetri et al. (2014) performed an inoculation trial
and showed that a single vaccination applied under field conditions
induced clinical protection but was insufficient to induce protection
against virus transmission. Given reported movements of birds between
Sectors 3 and 4, there is a potential risk of ongoing introduction of
H5N1 in commercial flocks. Furthermore, in contrast to the essentially
local nature of poultry trade patterns of LBMs and collector yards, the
commercial farm network was characterised by longer range movements,
which had the potential to spread virus furthest geographically.
However, as such movements were mainly to slaughter, this would be
unlikely to result in long-distance spatial spread of HPAI.
Snowball sampling was performed to maximise the likelihood of detection
of H5 in backyard and nomadic ducks flocks. Such approaches have been
successfully used in Cambodia (Poolkhet et al., 2016) and Vietnam
(Delabouglise et al., 2016). Despite this, very few H5 samples were
detected in the backyard sector and in nomadic ducks. It was evident
that underreporting of clinical cases is an issue. Our results indicated
that although present in smallholder production systems, the prevalence
of AIV appears to be low. Consequently, control measures focusing on
this sector may target reporting behaviours, but any direct disease
control measures are not indicated.
It was apparent that the largest numbers as well as the highest
prevalences of AI, H5 as well as H9 viruses were found in the value and
marketing chain – at LBMs and collector yards. This was supported by
the pairwise statistical tests for significance between enterprise
types. These showed that the odds of detecting H5 were similar in LBMs
and collector yards and not statistically different; however, the
likelihood of detection at these locations was 3½ to 4 times higher than
for backyard birds and nomadic ducks (these differences were marginally
to highly significant) and 25 to 30 times higher than for commercial
poultry (these differences were highly significant). This finding is
consistent with results elsewhere in South and South East Asia. It could
not be determined from our results whether the value chain concentrates
or even amplifies virus along its length, or whether the LBMs and
collector yards are locations in which AIV persists and actively
circulates (or, indeed, a combination of both). Our SNA suggested that
LBMs represented high-risk enterprises due to their small world network
properties which would enable disease spread more rapidly. Collector
yards played a role as a bridge between enterprises spreading the virus.
Commercial farms had a possible role in the long-range spread of HPAI
virus.
The pattern for H9 was somewhat different. More samples from commercial
farms tested positive than would be expected; approximately half of all
the AIV detected were H9. Equally surprisingly, relatively few H9 were
identified from nomadic ducks. Overall, H9 were identified in 10/41
collector yards (25%), 10/18 LBMs (55%) and 5/31 commercial farms
(16%) over the duration of the study. A number of collector yards as
well as LBMs repeatedly tested positive. One LBM in particular (M-12)
was positive at every sampling. No commercial farm tested positive more
than once; however, these farms were only sampled half as frequently. As
the sampling no or limited repeat sampling was carried out in backyard
and nomadic duck flocks, we were unable to assess this in these sectors.
Therefore, although there was some variation, the H5 and H9 viruses were
present year-round and were co-circulating, although no inference can be
drawn regarding any interactions between these HPAI and LPAI viruses.
It is likely that this higher rate of detections represents a potential
public health risk. For example, in one study (Shimizu et al., 2016) 85
of 101 sera that were collected from workers at a LBM in East Java
tested positive for AIV antibody; over a two-year period, the average HI
titre nearly trebled, and seroconversion occurred in 11 of 25 sera
(44%). However, a questionnaire indicated that no workers had
experienced an episode of severe acute respiratory illness.