Water treatment during Avian Influenza outbreak

Drinking water is one of the transmission methods of Avian Influenza (AI). Water sources can be contaminated by infected materials and transmitted to poultry farms. The risk of the chicken being exposed to the virus via water is high. When AI hit the poultry industry in the US in 2015, water samples were tested positive for the virus. Taking samples from poultry drinking water lines is an efficient way to conduct avian influenza surveillance. Water treatment is an important control strategy at the farm level.

Taking water samples

As a part of a good water management system, a water sample should be submitted for analysis annually during normal times but more frequently over the course of disease outbreaks. For a general water test, water samples can be sent to a water lab, but if you are looking for some specific microbial test such as Pseudomonas, Pneumovirus take your water sample to a diagnostic lab. Water samples should be taken from the source, barn entry point, and the beginning and end of the waterline through the nipple drinkers. To take a proper water sample follow these steps:

  1. Wipe the nipple drinker with alcohol swabs to remove any possible contaminants from the nipple drinker prior to water sample collection.
  2. Activate the nipple drinker using sterile tweezers to collect the water sample in a sterile container. 
  3. Take approximately 20 mL of water before sealing the bag. 
  4. Immediately upon collection, store the container in ice and transport them to the laboratory for physicochemical and microbial analysis.

Drip samples provide some information about the water quality but not the full picture and additional steps such as swabbing will provide a  better indicator of the microbial integrity of the water system. When taking a swab sample, make sure not to stand in front of a fan or other air movement  to avoid unintentional contamination of the swab.  Use a hydrated sterile swab to take the sample from inside the waterline. Swabs should be collected before and after water treatment. If you are dealing with biofilm in your waterline, you will need to clean out the biofilm. Instructions to clean biofilm can be found by following this link https://poultryinnovationpartnership.ca/cleaning-waterline-biofilm/

Water treatment program

A routine and functioning treatment system is highly recommended to limit the risk of water contamination with microbes no matter what source of water you are using. Even if you are using city water or reverse-osmosis water on your farm there is no guarantee that your water is pathogen-free. The three most common sanitation systems are chlorine dioxide, chlorine with acidification, and hydrogen peroxide which can inactivate the Avian Influenza virus.  There is no perfect, uniform solution and the efficacy of sanitizers depends on the physicochemical properties (especially pH and minerals) of the water.   Focus  should be to create and maintain a cleaning program that works for your water condition which is best informed by routine testing.  

Without knowing the mineral content you are fighting in dark. High levels of iron, manganese, and sulfur in water make it prone to pathogen contamination. Hydrogen peroxide is an oxidizer and can clean up sulfur and iron. The following steps should be done for cleaning the water for minerals:

  1. Oxidation with chlorine dioxide or hydrogen peroxides – follow manufacturer’s instructions (Correct pH=7 to 7.5 and contact time= 20 min help)
  2. Filtration
  3. Acidification: Citric acid is useful for removing scale from lines after removing slime but should not be used as a cleaner.  

Once cleaning is complete, total flush should be conducted to completely remove the cleaning solution, minerals, and microbes from the line. Adding a colored dye makes visualization of the flushing process easier.  Once the colour has run out and the water runs clear you can be confident that the flush is complete and the harmful materials have been purged from the line.

Water pH affects the efficacy of disinfectants. Chlorine-based disinfectants (e.g. bleach) work better if the water pH falls between 4 and 7. Chlorine level needs to reach 4 to 5 ppm at the end of the waterline to inactivate the virus.  With a pH around 8 (due to mineral content), chlorine dioxide is a good disinfectant.  Chlorine dioxide can be made on-site by injecting sodium chlorite into an acid (citric acid).  Special attention should be made to follow all safety precautions.   Once prepared chlorine dioxide can be pushed into the water system. The end of line residual for free chlorine dioxide should be 0.5 to 0.8 ppm. Hydrogen peroxide can also be used  if the water pH is above 7. During early flock life when the water flow rate is low, a stabilized hydrogen peroxide is more effective. The concentration of hydrogen peroxide at the end of the waterline should be 25 to 75 ppm. Last but not the least, before using any product, confirm with the manufacturer or supplier that it is safe to use with your equipment.


P. Maharjan, T. Clark, C. Kuenzel, M. K. Foy, and S. Watkins. 2016. On farm monitoring of the impact of water system sanitation on microbial levels in broiler house water supplies. Journal of Applied Poultry Research. 25:266–271. link

Mini Singh, Jenny-Ann Toribio, Angela Bullanday Scott, Peter Groves, Belinda Barnes, Kathryn Glass, Barbara Moloney, Amanda Black, Marta Hernandez-Jover. 2018. Assessing the probability of introduction and spread of avian influenza (AI) virus in commercial Australian poultry operations using an expert opinion elicitation. PLoS ONE 13(3): e0193730. Link

Y. H. Connie Leung, Li-Juan Zhang, Chun-Kin Chow, Chun-Lok Tsang, Chi-Fung Ng, Chun-Kuen Wong, Yi Guan, J.S. Malik Peiris. 2007. Poultry drinking water used for Avian Influenza surveillance. Emerging Infectious Diseases. 9:1380–1382. link

Eugene W. Rice, Noreen J. Adcock, Mano Sivaganesan, Justin D. Brown, David E. Stallknecht, and David E. Swayne. 2007. Chlorine inactivation of highly pathogenic Avian Influenza virus (H5N1). Emerging Infectious Diseases. 10: 1568–1570. Link

About the author(s)

Research Associate at Poultry Innovation Partnership | + posts

2 Responses

  1. Great stuff and info, WE NEED all the help we can get ,to curb AI, As i think it is here to stay, do you have any reference on peracetic acid for poultry water treatment and or iodine
    would any of the 2 latter kill AI

  2. Peracetic acid is a strong oxidant and disinfectant with a higher oxidation potential than chlorine or chlorine dioxide. Peracetic acid is on the list of Registered Antimicrobial Products with Label Claims for Avian Influenza (https://www.epa.gov/pesticide-registration/list-m-registered-antimicrobial-products-label-claims-avian-influenza).
    Iodine and iodophors are effective but require a long contact time (https://www.biosafety.be/content/contained-use-micro-organisms-viability-and-susceptibility-disinfectants-annexes)