VPK 4620

(Dr Siti Zubaidah)

Exercise 1-Answer Scheme (In class)

Highly Pathogenic Avian Influenza in Poultry in Sudan

(Source: Prof. Hussni, Cornell University)

Introduction
Data were collected in the outbreak of HPAI in Sudan. The data were saved in an Excel file
called AIOUTBREAK.

Major risks sources to a farm

Introduction of contaminated live birds; Introduction of contaminated materials or equipment
(cages, feed), fomites; Entry of vehicles coming from bird markets or other poultry farms,
movement between farms.

Data on the outbreak in Sudan.

The data contain the following variables:

ID Real - Farm identification number

State String - The Province where the outbreak is reported
Locality String - Geographical unit within the State
Date Date - Date of the outbreak in a particular farm
Susceptib Real - Total number of birds on the farm before the outbreak
Mortality Real -Total number of birds that were culled as a result of the outbreak
Source Real - Whether the chicks were imported—Yes=1 or No=0.
MortR Real - The proportion of birds that were culled
H5N1 Real - Whether the virus was isolated from samples collected from birds on the
farm (Yes=1 or No=0.)
Manure Real - Whether the farmer purchased manure from other farms (Yes=1 or No=0.)
Type Integer - Type of production (Layers = 1; Breeders = 2).
Biosec Integer - Presence of biosecurity (Yes = 1; No = 2) (Yes = 1; No = 2)
Vaccine Integer - Vaccinated against AI (Yes = 1; No = 0).
Workers Integer - Number of workers on the farm
Training Integer - If there is any training program for the workers

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QUESTIONS

1) Plot the epidemic curve for this outbreak. (Hint: use the option Histogram under
SUMMARY STATISTICS, which is under STATISTICS).

a. What type of epidemic is this outbreak?

Point-source epidemic

b. Estimate the incubation period for the aetiologic agent?

Estimating IP:
Date with highest frequency of H5N1 cases (Peak) = 04/21/2006
Date with the 1st case = 04/09/2006
Date with last cases=07/05/2006
Avg IP = Peak – 1st case = 04/21/06 – 04/09/06 = 12 days
Max IP = Last case – 1st case date = 05/07/06 – 04/09/06 = 124 days
Assuming 2-5 days previous exposure is needed, date of onset is:
i) Min. IP = Ist case – 2 days earlier = 04/-09/06 – 2 days = 04/07/06
ii) Min IP = 1st case – 5 days earlier = 04/09/06 – 5 days = 04/04/06

Most likely period of exposure:

H5N1 IP: average 2-5 days, up to 17 days (https://www.who.int/news-room/fact-
sheets/detail/influenza-(avian-and-other-zoonotic))
Average incubation period from peak - 04/21/2006 – 5 days = 04/16/2006

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 Minimum incubation period from the first case - 04/09/2006 – 2 days = 04/07/2006
Maximum incubation period from the last case - 07/05/2006 – 17 days = 06/10/2006
Most likely period of exposure: 04/07/2006 - 06/10/2006

c. We know that the outbreak was caused by HPAI, H5N1. Explain the difference in the
incubation period between the published length and the observed one in the
outbreak.
Published length: H5N1 IP: average 2-5 days, up to 17 days
(https://www.who.int/news-room/fact-sheets/detail/influenza-(avian-and-other-
zoonotic)
Observed length: 2-12 days, up to 124 days
Reasons for difference: 1. Variation in host susceptibility; 2. Host availability to be
infected; 3. Disease control measures may not be effective enough to stop the
spread/transmission

2) Describe the spatial distribution of the outbreak by state

a. How many flocks were affected in each state?
Count of
H5N1 H5N1
Grand
State negative Positive Total
Gezira 6 1 7
Khartoum 51 167 218
River Nile 1 1
Grand Total 58 168 226

b. What is the average number of birds per farm? (mean, standard deviation, range).
Average of Susceptib 9104.017699
StdDev of Susceptib 14002.02722

Min of Susceptib 90
Max of Susceptib 100000

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 c. What is the average size of the farm by State?
State Average of Susceptib
Gezira 17177
Khartoum 8879.674312
River Nile 1500

d. What is the average mortality rate by State?

State Average of Mortality Rate
Gezira 0.4
Khartoum 0.578669781
River Nile 0.0666667
Overall 0.575530359

3) Was there any significant association between the source of the chicks and the mortality
rate of the disease?

H5N1
Source Grand
Negative Positive Total
Local 47 139 186
Imported 11 29 40
Grand Total 58 168 226

• Chi-square test to assess association between H5N1 and source of chick:

The chi-square statistic is 0.0859. The p-value is 0.76945. This result is not
significant at p < 0.05.

• When T-Test was used to assess association between mortality rate between imported
and local source of chicken - The t-value is -1.2044. The p-value is .229741. The result
is not significant at p < 0.05.

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4) Was there any significant difference in the mortality rate between Khartoum and Gaziera
province?

Grand
State Negative Positive Total
Gezira 6 1 7
Khartoum 51 167 218

The chi-square statistic is 13.9253. The p-value is .00019. The result is significant at p <
0.05.

Error due to only one data of mortality rate for Gezira when T-Test was used to assess
association between mortality rate between Gezira and Khartoum.

5) Was there any association between the manure purchase and the isolation of the virus?

Grand
Manure Negative Positive Total
Own manure 29 34 63
Purchased
manure from
other farms 29 134 163
Grand Total 58 168 226

The chi-square statistic is 18.995. The p-value is .000013. The result is significant at
p < 0.05

a. What was the odds ratio?

Group 1 Odds = 0.82 ÷ (1 - 0.82) = 4.62

Group 2 Odds = 0.54 ÷ (1 - 0.54) = 1.17
Odds Ratio 1 = 4.62 ÷ 1.17 = 3.94 – statistically significant because OR>1.0
95% CI [3.6831, 4.1969] – statistically significant since the interval doesn’t include
OR=1

b. Interpret the computed odds ratio!

Farm that purchase manure from other farms are 3.94 times more likely to be H5N1
positive than farms that don’t purchase manure from other farms

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6) Was there any significant association between the number of workers and the risk of
H5N1?
H5N1
Workers Grand
Negative Positive Total
0 3 4 7
1 18 61 79
2 7 25 32
3 5 21 26
4 9 25 34
5 6 10 16
6 3 13 16
8 7 9 16
Grand Total 58 168 226

Chi-square Value: 6.563589727706

Degrees of Freedom: 7
P value: 0.475685625486

7) Was there any association between the history of vaccination and the isolation of the
virus?

H5N1
Grand
AI-vaccinated Negative Positive Total
No 43 4 47
Yes 15 164 179
Grand Total 58 168 226

a. What was the odds ratio?

Odds ratio 117.5333

95 % CI: 37.1061 to 372.2858

b. Interpret the computed odds ratio.

The odds of H5N1 are 118 times more than in farms that un-vaccinated against
AI. This result was statistically significant.

8) Did the training program help in reducing the incidence of infection with H5N1?

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 Training for Grand
workers Negative Positive Total
No 22 40 62
Yes 36 128 164
Grand Total 58 168 226

OR=1.956, 95% CI = 0.032,1.309

The odds of H5N1 are 1.96 times more in farms that provide training for workers
than in farms that don’t provide training for workers. This result was not
statistically significant.
Therefore, training program didn’t help in reducing the incidence of infection with
H5N1 in farms.