* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download 1. Background on HPAI H5N1 control policies in
Survey
Document related concepts
West Nile fever wikipedia , lookup
Hepatitis C wikipedia , lookup
Hospital-acquired infection wikipedia , lookup
Eradication of infectious diseases wikipedia , lookup
Swine influenza wikipedia , lookup
Ebola virus disease wikipedia , lookup
Middle East respiratory syndrome wikipedia , lookup
Marburg virus disease wikipedia , lookup
Antiviral drug wikipedia , lookup
Hepatitis B wikipedia , lookup
Bioterrorism wikipedia , lookup
Henipavirus wikipedia , lookup
Yellow fever in Buenos Aires wikipedia , lookup
Transcript
1 Evaluating the control of HPAI H5N1 in Vietnam: virus transmission 2 within infected flocks reported before and after vaccination. 3 4 5 Technical Appendix 1. Background on HPAI H5N1 control policies in Vietnam 6 The two initial epidemic waves occurred during the period of December 2003 to May 7 2005 during which vaccination was not included as part of the national disease control 8 program. Vaccination-based control policy interventions are officially put in place in 9 September 2005 until this date. The infected premises (IPs) of the third HPAI H5N1 10 epidemic wave are reported in October 2005 until December 2005. The fourth and 11 fifth epidemic waves occurred during November 2006 to November 2007 when 12 countrywide vaccination-based disease containment policies were in place. During the 13 first epidemic wave, depopulation dominated the portfolio of disease control measures 14 and the extent of its application was not systematically documented [1]. Overall, the 15 implementation of depopulation during this period is expected to have varied in 16 nature, quality, time and space across the country in contrast to later epidemic waves 17 and this would have contributed to a higher heterogeneity of within-flock 18 transmission estimates compared with those for the second wave. In addition, at that 19 time, the laboratory diagnostic capacity of the country was insufficient, which 20 increased the confirmation time of suspected IPs. This in turn vindicated the 21 application of rapid depopulation of the flocks. Finally, the technical guidelines for 22 prevention and control of avian influenza were released 6 months after the first 23 outbreaks of the first wave were reported. During the third outbreak wave, 24 depopulation upon identification of an IP was applied and flocks within different 1 25 provinces were already being vaccinated. Surveillance data available for this period 26 did not allow unbiased ascertainment as to whether the IPs recorded in the dataset 27 were in an area where vaccination was being put in place. 28 During the second epidemic wave (2004-2005), depopulation was implemented at the 29 village level and poultry had not been vaccinated. IPs and pre-emptively culled farms 30 were allowed to repopulate their flocks after a period of 60 days but data on the 31 proportion of farms which repopulated are unreliable. 32 During the 2006-2007 epidemic (fourth epidemic wave) a protection zone (PZ) was 33 established which equals the area of the village where the IP was located. Within the 34 PZ the IP was depopulated and movement restricted. For this period, pre-emptive 35 depopulation of flocks in the PZ was no longer compulsory as was the case during the 36 first to third waves; poultry farms within the PZ were offered the option of 37 compensated depopulation. By the time the first outbreak of the fourth epidemic 38 wave was reported, three vaccination campaigns had taken place and the fourth 39 campaign was ongoing. This campaign focused on poultry flocks located in 33 40 provinces, which had a history of being high-risk areas for HPAI H5N1 outbreaks in 41 poultry. A H5N2 vaccine (Nobilis, Intervet) was made available at cost for 42 commercial breeders of great grandparent (GGP) and grandparent (GP) stocks. This 43 vaccine required primo-vaccination followed by a booster after a 4 week interval and 44 a second booster another 4 months later. An inactivated Re-1 strain, reassortant 45 H5N1 vaccine (Homologous Habin-Weike Reassortant Avian Influenza vaccine) was 46 used for vaccination of broiler ducks, the cost of which was fully borne by the 47 government. With this vaccine, ducks required a booster one month after primo- 48 vaccination and a second booster 6 months thereafter. The Homologous Habin-Weike 2 49 Reassortant Avian Influenza vaccine was also being used in chicken broiler flocks as 50 a single booster vaccine (i.e. two injections). In addition a H5N1 recombinant 51 vaccine (Trovac) had been introduced for use in chicken breeder hatcheries and 52 applied to day-old-chicks. 53 2. Data quality and data handling issues 54 Outbreak surveillance data generated during the period from December 2003 to 55 September 2008 is publically available at the World Organization for Animal Health 56 (OIE) which is officially notified by the Department of Animal Health of the Ministry 57 of Agriculture and Rural Development of Vietnam (DAH-Vietnam) [2]. The HPAI 58 H5N1 outbreak surveillance data considered for this study was kindly facilitated by 59 the Epidemiology Division of DAH-Vietnam. Data concerning flock type (i.e. species 60 reared), total poultry population initially at risk (i.e. flock size) and the number of 61 observed bird deaths were available. 62 Upon discussion with senior animal health officials and epidemiologists at DAH- 63 Vietnam we made the decision of excluding the data from the first (i.e. December 64 2003 to March 2004) and third (i.e. October 2005 to December 2005) epidemic waves 65 from the analysis. The criteria for exclusion were based on evidence about the lack of 66 consistency across the country in data recording for the first epidemic wave and in 67 disease control policies for the first and third epidemic waves[1]. Furthermore, data 68 aggregation was a caveat of the outbreak surveillance data generated during the first 69 epidemic wave while uncertainty with respect to regional vaccination status of IPs 70 recorded during the third epidemic wave were issues that supported the exclusion of 71 these data. 3 72 For the comparative investigation between periods of vaccine-based control versus 73 depopulation-based control we considered a dataset which included outbreak 74 surveillance data from the second (i.e. depopulation-based control; Period I) and 75 fourth (i.e. vaccination-based control; Period II) epidemic waves. 76 The dataset for Period I included infected premises (IPs) which were pre-emptively 77 depopulated as part of the control policy; however, these records were excluded from 78 the final dataset for analysis. None of the IPs of Period I had been vaccinated. 79 The official reporting data contained a total of 1005 IPs for the period 1st January 80 2005 to 1st May 2005 (second epidemic wave; Period I) and a total of 114 IPs for the 81 period from 16th November 2006 to 7th March 2007 (fourth epidemic wave; Period II) 82 with observed bird mortality due to H5N1 infection. During these epidemic periods a 83 total of 545 communes from 32 (50%) provinces of Vietnam were affected and in 84 90% (491/545) of affected communes the number of IPs with reported mortality 85 ranged from one to four. The majority of IPs during Period I (81%; n=818) and 86 Period II (96%; n=110) epidemic waves were located in provinces within the Mekong 87 River delta (in South Vietnam). For the Period II the dataset did not contain any IPs 88 located in provinces other than the Red River (North Vietnam) and Mekong River 89 deltas. 90 We were interested in obtaining unbiased estimates of the within-flock R0 therefore 91 the final dataset for analysis needed to contain unbiased records of estimates of 92 mortality and respective denominators for each IP. Therefore, and based on 93 discussions with the DAH-Vietnam officials, we anticipated recording biases of the 94 total mortality observed in some of the flocks particularly in those with flock sizes 4 95 greater than 1,500 heads. This lead to the inclusion in the final dataset for analysis of 96 924 flocks for Period I (i.e. 8% (81/1005) were excluded) and 106 flocks for Period II 97 (i.e. 7% (8/114) were excluded). 98 We could have introduced biases in our analysis for Period II (vaccination-based 99 control) if vaccinated flocks had been included; in this scenario, mortality in 100 vaccinated flocks would not be a good indicator of infection. According to 101 information provided by the DAH-Vietnam and information available at OIE (at the 102 World Animal Health Information Database (WAHID) Interface) none of the flocks 103 considered in the analysis for this period was listed as being vaccinated at the moment 104 when the outbreak was reported. 105 For the comparative investigation of the reproductive number of infection between 106 flocks of different type/sizes compositions we have classified infected premises of the 107 final dataset for analysis into discrete categories pertaining to their expected scale of 108 production. The Vietnam’s poultry sector has been historically sub-divided according 109 to different criteria [3-5] and the IP categorization used assumes 6 cut-offs based on 110 the frequency distribution of IPs by flock type and size composition (see Table 1). 111 This was also performed in order to take into account possible non-linearity of effects 112 of size during statistical analysis. 113 Finally, we argued whether mortality in duck flocks due to H5N1 might not be a good 114 indicator of virus transmission. Indeed, available evidence suggests that the initial 115 1997-2004 highly HPAI H5N1 viruses in domestic and wild waterfowl tended to 116 behave like low-pathogenic avian influenza viruses in other avian species. In addition, 117 experimental evidence specific to viruses isolated from Vietnam during outbreak in 118 2003 and 2004 show that those tended to replicate and transmit efficiently in ducks 5 119 but exhibited variable pathogenic potentials in ducks, ranging from the complete 120 absence of clinical disease (intravenous pathogenicity index [IVPI] 0.0 in ducks) to 121 severe neurological dysfunction and death (IVPI of 3.0 in ducks) [6]. However, recent 122 experimental evidence for viruses lineages circulating in Viet Nam from 2005 onward 123 – which corresponds to the epidemic periods analysed in the manuscript – suggests 124 that these were highly virulent in ducks , causing 100% mortality in 2-week old Pekin 125 ducks within four days of virus challenge [7, 8]. In addition, mortality figures caused 126 by these viruses are suggested to correlate well with mortality figures observed in 127 chicken and these viruses were much more virulent to ducks compared with viruses 128 circulating before 2005 [7]. Based on this recent evidence the decision was made to 129 include the outbreak data from duck flocks. 130 131 3. Estimation of the within-flock reproductive number of infection, R0 based on the method of moments 132 The basic reproductive number R0 allows the quantification of the infection potential 133 of a population and is an averaged epidemiological property that summarises the 134 relationship between the effective contact rate (β) and the mean duration of 135 infectiousness (1/α) adjusted for the size of the initial population at risk. It is difficult 136 to estimate β when complete follow-up data for animals are not available [9]. In order 137 to do estimate the within-flock reproductive number, R0 we have assumed that the 138 same category of flock size/type would have the same degree of mixing as their 139 homologous flocks. In this scenario we estimated the within-flock R0 which will be 140 the average number of secondary cases created by a typical infectious bird from the 141 point it became infectious until the moment of flock depopulation. 6 142 The theory of moments of martingales applied to the general epidemic model allows 143 the estimation of the parameters for β and 1/α simultaneously [10]. This quantitative 144 approach takes into account the final size of an outbreak, the initial population at risk 145 and time. We have used the expression below to calculate the infection potential of a 146 flock up to the time point when it was culled, considering the following relationships, 147 ˆ f 1 s0f 0.5 ln f f f cT N 0 cT 1 0.5 148 where f is the infected flock.The parameter (θ) to be estimated is conceptually equal 149 to β/α which, as mentioned above, are the primary ingredients for the estimation of R0. 150 The necessary parameters for the estimation of θ were the total number of birds at risk 151 in the flock at the start of the outbreak ( s 0f N 0f 1 ), the number of birds in the flock 152 at the start of the outbreak ( N 0f ) and the cumulative number of observed deaths (new 153 cases) when the infection chain was stopped by culling ( cTf ). Assuming there was a 154 single case introduced to the flock, the actual initial population at risk at the start of 155 the outbreak for a given flock was estimated as N 0f -1, with N 0f being the recorded 156 total population of the flock at the moment when infection was reported. Previous 157 studies have shown that mortality observed on a given day had a positive linear 158 association with time after initial infection and that without any intervention, entire 159 flocks would die within 12 days of introduction of the HPAI virus to the infected farm 160 [11]. However, the aim of our analysis was to estimate the efficacy of the control 161 policy and not to examine the biological properties of transmission. 162 The R0 of an IP was calculated by multiplying θ by the total number of birds initially 163 at risk in the flock. An estimator of the standard error of θ has also been previously 7 164 described [10] and was used for the estimation of confidence intervals around the 165 estimated R0 values. 166 4. References 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. Pfeiffer DU, Minh PQ, Martin V, Epprecht M, Otte MJ: An analysis of the spatial and temporal patterns of highly pathogenic avian influenza occurrence in Vietnam using national surveillance data. Vet J 2007, 174(2):302-309. Office International des Epizooties. Update of Highly Pathogenic Avian Influenza in Animals (Type H5 and H7) [http://www.oie.int/downld/avian%20influenza/A_AI-Asia.htm] Delquigny T, Edan M, Nguyen DH, Pham TK, Gautier P: Impact of Avian Influenza Epidemic and Description of the Avian Production in Vietnam. In. Rome, Italy: Food and Agriculture Organization of the United Nations; 2004: 119. Rushton J, Viscarra R, Bleiche EG, McLeod A: Impact of influenza outbreaks in the poultry sectors of five South east Asian countries (Cambodjia, Indonesia, Lao PDR, Thailand, Viet Nam) outbreak costs, responses and potential long term control. In.: FAO, Rome, Italy; 2004: 25. ACI: The Economic Impact of Highly Pathogenic Avian Influenza Related Biosecurity Policies on the Vietnamese Poultry Sector In. Bethesda, Maryland: Prepared for the Food and Agriculture Organization of the United Nations and the World Health Organization, Agrifood Consulting International; 2007: 1013. Sturm-Ramirez KM, Hulse-Post DJ, Govorkova EA, Humberd J, Seiler P, Puthavathana P, Buranathai C, Nguyen TD, Chaisingh A, Long HT et al: Are ducks contributing to the endemicity of highly pathogenic H5N1 influenza virus in Asia? J Virol 2005, 79(17):11269-11279. Pantin Jackwood MJ, Suarez DL, Swayne DE: Increased pathogenicity of H5N1 Vietnam viruses in ducks. . In: Proceedings of the 110th United States Animal Health Association Meeting: October 2006 2006; Minneapolis, Minnesota.; 2006. Pantin Jackwood MJ, Suarez DL: Pathogenicity of H5N1 HPAI viruses from Vietnam in chickens and ducks [abstract]. In: Workshop on Avian Influenza: Research to Policy, June 16-18, 2008. Hanoi, Vietnam; 2008. Diekmann O, Heesterbeek JAP: Mathematical Epidemiology of Infectious Diseases: Model Building, Analysis and Interpretation. Chicester, West Sussex: John Wiley & Sons Ltd; 2000. Becker N: Martingale methods. In: Analysis of Infectious Disease Data. London: Chapman and Hall Ltd; 1989: 224. Yoon H, Park CK, Nam HM, Wee SH: Virus spread pattern within infected chicken farms using regression model: the 2003-2004 HPAI epidemic in the Republic of Korea. Journal of veterinary medicine 2005, 52(10):428-431. 8