Influenza surveillance in animals: what is our capacity to detect emerging influenza viruses with zoonotic potential?

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

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.

FluChip-8G Insight: HA and NA subtyping of potentially pandemic influenza A viruses in a single assay

BACKGROUND

Global influenza surveillance in humans and animals is a critical component of pandemic preparedness. The FluChip-8G Insight assay was developed to subtype both seasonal and potentially pandemic influenza viruses in a single assay with a same day result. FluChip-8G Insight uses whole gene segment RT-PCR-based amplification to provide robustness against genetic drift and subsequent microarray detection with artificial neural network-based data interpretation.

OBJECTIVES

The objective of this study was to verify and validate the performance of the FluChip-8G Insight assay for the detection and positive identification of human and animal origin non-seasonal influenza A specimens.

METHODS

We evaluated the ability of the FluChip-8G Insight technology to type and HA and NA subtype a sample set consisting of 297 results from 180 unique non-seasonal influenza A strains (49 unique subtypes).

RESULTS

FluChip-8G Insight demonstrated a positive percent agreement ≥93% for 5 targeted HA and 5 targeted NA subtypes except for H9 (88%), and negative percent agreement exceeding 95% for all targeted subtypes.

CONCLUSIONS

The FluChip-8G Insight neural network-based algorithm used for virus identification performed well over a data set of 297 naïve sample results, and can be easily updated to improve performance on emerging strains without changing the underlying assay chemistry.

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine

Background

Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

Methods

We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities.

Results

Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively.

Conclusions

Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.

National surveillance and control costs for highly pathogenic avian influenza H5N1 in poultry: A benefit-cost assessment for a developing economy, Nigeria

We conducted benefit-cost analysis of outbreak and surveillance costs for HPAI H5N1in poultry in Nigeria. Poultry's death directly cost US$ 939,734.0 due to outbreaks. The integrated disease surveillance and response originally created for comprehensive surveillance and laboratory investigation of human diseases was adapted for HPAI H5N1 in poultry. Input data were obtained from the field, government documents and repositories and peer-reviewed publications. Actual/forecasted bird numbers lost were integrated into a financial model and estimates of losses were calculated. Costs of surveillance as alternative intervention were determined based on previous outbreak control costs and outputs were generated in SurvCost® with sensitivity analyses for different scenarios. Uncontrolled outbreaks will lead to loss of over US$ 2.2 billion annually in Nigeria with 47.8% of the losses coming from eggs. The annual cost of all animal related health activities was <US$ 99.0 million, only one-third of this amount was linked with H5N1 surveillance and response activities. Recurrent cost was 96.2% of the total surveillance and response costs, and 31.0% of the HPAI surveillance cost was spent on personnel with 3.8% as capital cost. Cost-wisely, routine monitoring and surveillance for HPAI are 68 times more cost effective than to do nothing. Assuming that successful control and eradication of HPAI H5N1 is partially attributable to H5N1 surveillance and response, a quarter or half of the success will result in 17 or 34 times more benefits. Although animal surveillance and response activities for avian influenza appeared expensive, their implementation are economically cost beneficial for developing countries.

Epidemiological features of influenza circulation in swine populations: A systematic review and meta-analysis

Background

The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives of this systematic review and meta-analysis were to describe epidemiological features of swine influenza (SI) across the world and identify factors impacting swine influenza virus surveillance.

Methods

The systematic review followed the PRISMA guidelines. Articles published after 1990 containing data on SI on pig and herd-level seroprevalence, isolation and detection rates, and risk factors were included. Meta-regression analyses using seroprevalence and virological rates were performed.

Results

A total of 217 articles were included. Low avian influenza (AI) seroprevalence (means pig = 4.1%; herd = 15%) was found, showing that AIV do not readily establish themselves in swine while SIV seroprevalence was usually high across continents (influenza A means pig = 32.6–87.8%; herd = 29.3–100%). Higher pig density and number of pigs per farm were shown by the meta-regression analyses and/or the risk factor articles to be associated with higher SI seroprevalence. Lower seroprevalence levels were observed for countries with low-to-medium GDP. These results suggest that larger industrial farms could be more at risk of SIV circulation. Sampling swine with influenza-like illness (ILI) was positively associated with higher isolation rates; most studies in Europe, Latin and North America were targeting swine with ILI.

Conclusions

To improve understanding of SI epidemiology, standardization of the design and reporting of SI epidemiological studies is desirable. Performance of SI surveillance systems in low-to-medium GDP countries should be evaluated to rule out technical issues linked to lower observed SIV prevalence. Targeting certain swine age groups, farming systems and swine with ILI may improve the surveillance cost-effectiveness. However, focusing on pigs with ILI may bias virus detection against strains less virulent for swine but which may be important as pandemic threats.

Using oral fluids samples for indirect influenza A virus surveillance in farmed UK pigs

Influenza A virus (IAV) is economically important in pig production and has broad public health implications. In Europe, active IAV surveillance includes demonstration of antigen in nasal swabs and/or demonstration of antibodies in serum (SER) samples; however, collecting appropriate numbers of individual pig samples can be costly and labour‐intensive. The objective of this study was to compare the probability of detecting IAV antibody positive populations using SER versus oral fluid (OF) samples. Paired pen samples, one OF and 5–14 SER samples, were collected cross‐sectional or longitudinally. A commercial nucleoprotein (NP)‐based blocking ELISA was used to test 244 OF and 1004 SER samples from 123 pens each containing 20–540 pigs located in 27 UK herds. Overall, the IAV antibody detection rate was higher in SER samples compared to OFs under the study conditions. Pig age had a significant effect on the probability of detecting positive pens. For 3–9‐week‐old pigs the probability of detecting IAV antibody positive samples in a pen with 95% confidence intervals was 40% (23–60) for OF and 61% (0.37–0.80) for SER (P = 0.04), for 10–14‐week‐old pigs it was 19% (8–40) for OF and 93% (0.71–0.99) for SER (P < 0.01), and for 18–20‐week‐old pigs it was 67% (41–85) for OF and 81% (0.63–0.91) for SER (P = 0.05). Collecting more than one OF sample in pens with more than 25 less than 18‐week‐old pigs should be further investigated in the future to elucidate the suitability of OF for IAV surveillance in herds with large pen sizes.

Weighing serological evidence of human exposure to animal influenza viruses - a literature review

Assessing influenza A virus strains circulating in animals and their potential to cross the species barrier and cause human infections is important to improve human influenza surveillance and preparedness. We reviewed studies describing serological evidence of human exposure to animal influenza viruses. Comparing serological data is difficult due to a lack of standardisation in study designs and in laboratory methods used in published reports. Therefore, we designed a scoring system to assess and weigh specificity of obtained serology results in the selected articles. Many studies report reliable evidence of antibodies to swine influenza viruses among persons occupationally exposed to pigs. Most avian influenza studies target H5, H7 and H9 subtypes and most serological evidence of human exposure to avian influenza viruses is reported for these subtypes. Avian influenza studies receiving a low grade in this review often reported higher seroprevalences in humans compared with studies with a high grade. Official surveillance systems mainly focus on avian H5 and H7 viruses. Swine influenza viruses and avian subtypes other than H5 and H7 (emphasising H9) should be additionally included in official surveillance systems. Surveillance efforts should also be directed towards understudied geographical areas, such as Africa and South America.

Modelling the species jump: towards assessing the risk of human infection from novel avian influenzas

The scientific understanding of the driving factors behind zoonotic and pandemic influenzas is hampered by complex interactions between viruses, animal hosts and humans. This complexity makes identifying influenza viruses of high zoonotic or pandemic risk, before they emerge from animal populations, extremely difficult and uncertain. As a first step towards assessing zoonotic risk of influenza, we demonstrate a risk assessment framework to assess the relative likelihood of influenza A viruses, circulating in animal populations, making the species jump into humans. The intention is that such a risk assessment framework could assist decision-makers to compare multiple influenza viruses for zoonotic potential and hence to develop appropriate strain-specific control measures. It also provides a first step towards showing proof of principle for an eventual pandemic risk model. We show that the spatial and temporal epidemiology is as important in assessing the risk of an influenza A species jump as understanding the innate molecular capability of the virus. We also demonstrate data deficiencies that need to be addressed in order to consistently combine both epidemiological and molecular virology data into a risk assessment framework.