1

Please note: These procedures may be revised as the situation develops.

EXECUTIVE SUMMARY OF THE METHOD

Composting is a biological heating process that results in the natural degradation of 

organic resources (such as poultry carcasses) by microorganisms. Composting has 

been successfully used throughout the United States for nearly two decades to control 

outbreaks of low pathogenicity avian influenza (LPAI) and highly pathogenic avian 

influenza (HPAI). Composting can be effective with most bird types and poultry house 

designs. 

Microbial activity within a well-constructed compost pile can generate and maintain 

temperatures sufficient to inactivate the avian influenza virus. The effectiveness of this 

virus inactivation process can be assessed by evaluating compost temperatures and the 

shape of the time and temperature curve, visual observation of carcass decomposition,

and the homogeneity of the compost mix. 

Successful mortality composting requires the following:

1. A qualified composting expert to guide windrow construction.

2. Trained equipment operators.

3. Sufficient carbon, water, and space.

If any of these components is lacking, composting is NOT recommended.

Prepared by members of the USDA Composting Technical Committee: Lori P. Miller, Gary A. 

Flory, Robert W. Peer, Eric S. Bendfeldt, Mark L. Hutchinson, Mark A. King, Bill Seekins, 

George W. Malone, Joshua B. Payne, Jerry Floren, Edward Malek, Mary Schwarz, and Jean 

Bonhotal

FY2016 HPAI Response

Mortality Composting Protocol for 

Avian Influenza Infected Flocks

February 5, 2016

Completed windrow (photo by Gary Flory)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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CONTENTS

Key Elements for Successful Composting....................................................................... 3

Labor, Equipment, and Supplies ..................................................................................... 3

Protocol........................................................................................................................... 3

Prior to Windrow Construction ..................................................................................... 3

Typical Windrow Construction Protocol ....................................................................... 4

Layering Method.......................................................................................................... 7

Approval of Windrow Design ....................................................................................... 7

Temperature Monitoring .............................................................................................. 7

Turning the Windrows.................................................................................................. 8

Release of the Compost .............................................................................................. 8

Composting Layer Manure and Waste Feed ............................................................... 8

Troubleshooting .............................................................................................................. 9

Appendix A Siting a Compost Location for Disposal of Poultry Carcasses ................... 10

Appendix B Methods of Estimating Carbon (Bulking Agent) Needs .............................. 12

Appendix C Variations on Typical Windrow Construction Protocol ............................... 14

Appendix D Temperature Monitoring Procedure ........................................................... 17

Appendix E Temperature Monitoring Log Sheet ........................................................... 19

Appendix F In-House Composting Ammonia Safety ..................................................... 20

Appendix G Compost Approval Checklist...................................................................... 21

Appendix H Windrow Turning Equipment and Methods................................................ 26

Appendix I Characteristics of Raw Material................................................................... 28
Mortality Composting Protocol for Avian Influenza Infected Flocks

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KEY ELEMENTS FOR SUCCESSFUL COMPOSTING

The role of the Subject Matter Expert (SME) is to ensure that these key elements are 

followed in the construction of compost windrows:

1. Windrows (typically 6 to 8 feet high and 12 to 15 feet wide) are constructed on an 

adequate and uniform base layer (10 to 15 inches thick) of a sufficiently porous 

and absorbent carbon material. 

2. The base layer and windrow are not compacted with equipment.

3. Good carcass to carbon contact is ensured by creating a core with a minimum 1:1 

mix, by volume, of carcasses, carbon, and other infected material (manure, egg 

shells, feed, etc.). DO NOT GRIND/CRUSH/MACERATE THE CARCASSES 

DURING CONSTRUCTION!

4. Windrows should be constructed to ensure adequate distribution of moisture 

throughout; the windrows are capped with carbon material (8 to 12 inches thick) to 

ensure that no carcasses are exposed and to minimize odor. 

5. Windrow dimensions, including the 

base and cap, may be reduced for 

smaller carcasses.

LABOR, EQUIPMENT,

AND SUPPLIES 

 Skilled equipment operators and 

general laborers;

 skid loader(s), pay loaders, dump 

trucks, rakes, and scoops;

 sawdust, litter, wood shavings, corn stover, active compost, seed and nut hulls, 

woodchips, or other carbon material; and

 compost thermometers (36” or 48” stem length).

PROTOCOL

Prior to Windrow Construction

 Evaluate barn configuration to determine if space is adequate for windrow(s) 

construction within the poultry barns. If not, assess other on-site structures or 

outside compost sites. 

‒ To assess outside sites, see Appendix A.

 Evaluate type and quantity of infected materials to be composted:

‒ Carcass: type, size, number and condition 

‒ In-barn manure/litter: volume, moisture content, density

Pay loader used for clearing the base (photo by Josh Payne)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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‒ Stored manure/litter: volume, moisture content, density

‒ Feed: quantity, location

 Empty feed from feed bins and pans, distribute evenly into the mix.

‒ Eggs: quantity and condition

‒ Clean bedding

‒ Paper products

‒ Non-infected manure compost.

 Calculate the amount of carbon needed for composting:

‒ See Appendix B for calculations.

‒ The characteristics of various materials are listed in Appendix I.

 Evaluate premise for supplemental water:

‒ Source

‒ Application method.

 Evaluate on-farm equipment and determine supplemental equipment needs.

 Ensure all overhead lines and poultry house equipment are removed or out of the 

way. Secure any loose cords, cables or hoses so that they will not become 

entangled by equipment.

 Minimize ventilation to reduce the risk of disease transmission while balancing air 

quality for worker safety.

 Transfer all infected on-site materials into compost windrows.

Typical Windrow Construction Protocol

Three critical elements of windrow construction are: 1) a porous base layer, 2) a 

uniformly mixed windrow core, and 3) an adequate cap (see Figure 1). These steps may 

be done concurrently or as separate steps.

Figure 1. Cross Section of Compost Windrow
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Windrow Base Construction

 Before in-house composting, clear carcasses 

and litter from the windrow location(s) of the 

poultry house to create a 12–15 foot wide work 

area for construction of the windrow base(s).

Distribute the material from on either side of the 

pathway. (See Appendix C for in-house 

variations.)

 Before outside composting, an adequate site 

must be identified (see Appendix A). Site 

modifications and approval from State and local 

agencies may be required. 

 Using the largest loader possible, begin building 

the windrow base. 

 The windrow base should be 12–15 feet wide 

with a depth of 10 to 15 inches. (Note: base will 

compress over time.)

‒ Carbon material for the base should be porous and bulky enough to allow 

adequate air flow into and through the windrow. Ideal materials for the base 

include bark mulch or coarse wood chips. Other acceptable materials include:

straw, wood shavings, active compost, small grain hulls, and corn stover. Also,

coarse woody material in excess of 2 inches in size should be avoided to ensure 

that the resulting compost can be land applied as a soil amendment. 

‒ If these materials are not available, poultry litter may be used for the windrow 

base if it is sufficiently dry, porous, and bulky.

‒ To maintain the base’s porosity and to avoid compaction, do not drive 

equipment on the base.

Construction of the Core

 The windrow core should consist of a 

uniform mix of carcasses and litter. The 

easiest way to get a uniform mix 

throughout the windrow is to scoop litter 

and birds together in each bucket load 

and add it to the windrow in a manner 

that thoroughly mixes the contents of the 

bucket. If additional carbon material is 

needed, the material should support heat 

generation (i.e., composting). Suitable 

materials include fresh wood shavings, 

active compost, poultry litter, straw, corn stover, and small grain hulls. In many 

instances this material may need to be blended with the existing litter and 

carcasses to be suitable.

Constructing the core (photo by Bob Peer)

Clearing the base (photo by Gary Flory)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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‒ Any remaining feed should be blended and mixed with the carcasses and litter 

before windrow construction. Be sure to move infected material as little as 

possible. 

‒ The mix of carcasses and litter should be added from both sides of the windrow.

This allows the operators to reach the center of the windrow and avoid 

compacting the base with the tires or tracks of the loader.

‒ The windrow core should be constructed such that 1 foot of base material is 

exposed on both sides of the windrow. 

‒ Add water as needed.

‒ The core should be dome-shaped and of sufficient height to include the litter and 

carcass mix from the area adjacent to the windrow. At this stage, the windrow 

height should not exceed 6 feet.

 Continue building the core until all of the litter and carcasses have been placed on 

the base.

 An alternate method of using pre-compost 

windrows is described in Appendix C.

Capping the Windrow

 Prior to capping the windrow, remove any 

carcasses that are near the edge of the 

windrow base and include them in the core of 

the windrow.

 Cap the windrow with 8 to 12 inches of a 

suitable carbon material. Carbon material for 

the cap should prevent flies from contacting 

carcasses, serve as an insulating blanket, and 

allow air to flow out of the piles. This material may be finer in texture than the base.

Suitable material includes small grain hulls, sawdust, new bedding, and wood 

chips. Straw, corn fodder, or similar material may also be suitable; however,

experience has shown that these products can blow off the windrow and may need 

to be thicker to serve this purpose than other materials. 

 Ensure that the entire core is uniformly covered with cap material with no 

carcasses exposed. 

 Avoid compacting the windrow. Do not operate the loader’s tires or tracks onto the 

sides of the windrow while capping.

 The completed windrow should be approximately 6 to 8 feet high.

 Windrows should be numbered and flagged by the SME at a minimum of 10

temperature monitoring locations spaced equidistantly the length of each windrow.

Smoothing the cap on an outside windrow 

(photo by Gary Flory)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Layering Method

As an alternative to the core construction 

method described previously, the 

windrow core can be constructed by 

layering carcasses and carbon material.

Base and cap construction is the same 

as in the standard protocol. Following 

base construction, proceed in the 

following manner:

 Add a 12–15 inch layer of litter and 

birds, then cover with a 12–15 inch 

layer of wood chips or other carbon source. 

 Add another layer of litter and 

birds until the windrow is two or 

three layers high and as long 

as needed. 

 Cover the windrow with an 8–

12 inch layer of wood chips or 

other carbon sources. The 

finished pile should be 6 to 8 

feet high.

The SME may choose to use 

either or both of these construction 

techniques depending on site conditions.

Approval of Windrow Design

SMEs should evaluate the windrows to ensure that they have been constructed 

consistently with this protocol. Approval will be documented on the Compost Approval 

Checklist in Appendix G. 

Temperature Monitoring

Once the windrow construction has been approved by the SME, daily temperature 

monitoring can begin following the standard temperature monitoring SOP found in 

Appendix D. Temperature data should be collected on the temperature log included in 

Appendix E or in a comparable electronic document. The health and safety of the 

individual conducting the temperature monitoring should be protected by following the 

ammonia safety procedures outlined in Appendix F. 

Layering method (photo by Mary Schwarz)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Turning the Windrows

After the State Animal Health Official (SAHO), APHIS Official, Incident Management 

Team (IMT) Official, or SME has provided their approval based on windrow design and 

an evaluation of the temperature data collected during the initial 14-day compost cycle

(Phase 1), the windrow is eligible for turning. Approval will be documented on the 

Compost Approval Checklist in Appendix G. No turning is allowed before the end of the 

14-day period. Turning needs to provide for the homogenization of the core, base, and 

cap materials. Windrows need to maintain adequate porosity and structure after turning.

If soft tissue is observed on the windrow surface, a 2 to 4 inch carbonaceous cap should

be applied. See Appendix H for turning equipment and methods.

Release of the Compost

After the SAHO, APHIS Official, IMT Official, or SME has provided their approval 

based on windrow design and an evaluation of the temperature data collected during 

the second 14-day compost cycle (Phase 2), the compost may be moved without 

restriction on the premises or may leave the premises with appropriate permits. 

Approval will be documented on the Compost Approval Checklist in Appendix G. 

Composting Egg-Layer Manure and Waste Feed

During an HPAI outbreak, there may be a need to compost layer manure and waste 

feed. This may be because the producer has chosen to dispose of their poultry 

mortalities by a method other than composting—such as on site burial, incineration, or 

landfilling—or because there was more manure on the farm than could be practically 

composted with the poultry carcasses. In general, the compost process used for these 

materials is identical to the windrow construction process described above. However, 

because of the density of the manure and feed, it is imperative that the material be 

thoroughly blended with carbonaceous materials to help ensure proper porosity within 

the windrows. Generally, manure can be composted with a 1:1 mix of manure and 

carbonaceous material. Often, layer manure has a high moisture content or is extremely 

dry depending on manure management, and the moisture content of the windrows may 

need to be adjusted. 
Mortality Composting Protocol for Avian Influenza Infected Flocks

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TROUBLESHOOTING

The table below describes some of the most common composting problems and 

possible solutions.

Problem Issue Solution

Excessive flies or odor Exposed carcasses Add additional cap material

Leachate from windrow Mixture too wet Add additional carbon material, 

mix and cap

Temperature does not reach 131 oF Mixture too dry (< 40% 

moisture)

Add water to pile, mix if 

necessary

Temperature does not reach 131 oF Mixture too wet (> 60 

% moisture)

Add additional carbon material, 

mix if necessary

Temperature drops early Not enough oxygen Aerate or mix pile
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX A

SITING A COMPOST LOCATION FOR DISPOSAL OF POULTRY 

CARCASSES

Selection and siting of environmentally suitable and appropriate locations for 

composting of poultry carcasses infected with avian influenza is an important 

consideration in the disease management process. Because of the virulent nature of 

this disease, it is important to locate such sites within or in close proximity to the 

infected premises. The site access should be able to handle heavy truck traffic and 

allow for biosecurity around the site’s perimeter, securing access to and from the site.

Additionally, due to the relative putrescibility of the carcasses and associated litter, it is 

critical to choose sites that will not be adversely impacted by potential releases of 

nutrient-laden leachate nor will result in nuisance complaints in the event that odors, 

flies, or scavengers begin to appear on-site. 

HPAI compost site (photo by Mark King)

In general, emergency poultry mortality compost sites should be large enough to 

accommodate all of the generated carcasses, litter, waste feed, and other contaminated 

materials, as well as have the ability to store any additional amendment materials that 

may be needed for successful composting. Along with the criteria noted above, ideal 

HPAI compost sites should

 be located such that the prevailing wind directions do not travel to nearby residences 

(whenever possible),

 be located at the top of the slope of the field, on moderately-well to well drained soils 

(usually land that is used for crop production),

 have a gentle 2%–4% slope to encourage on-site drainage,

 contain on-site soil depths in excess of 24 inches to seasonal high water tables,

 contain on-site soil depths in excess of 36 inches to bedrock,
Mortality Composting Protocol for Avian Influenza Infected Flocks

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 not be located on a flood plain,

 be constructed or designated for the current emergency,

 have (or construct) diversion ditches, terraces, or berms to direct surface water flows 

and storm water away from active compost piles. (Note that if piles are located 

between production houses, then roof and surface drainage should be directed away 

from the compost area), and

 the edges of the identified site should have these following minimum setbacks, 

including:

‒ 200 feet from a water supply well used for drinking;

‒ 200 feet from water bodies, including: ponds, lakes, streams, rivers;

‒ 200 feet from a nearby residence (not owned by the premises);

‒ 50 feet from a drainage swale that leads to a water body (see above); and

‒ 25 feet from a drainage swale that does not lead to a water body.

Reprinted with permission from Cornell Waste Management Institute
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX B

METHODS OF ESTIMATING CARBON (BULKING AGENT) NEEDS

Methodology

Described below are three approaches to estimating the amount of additional 

carbonaceous materials needed to compost poultry carcasses. All three require 

estimating the volume of litter in a building. To do this:

1. Obtain the length and width of the building.

2. Estimate the average depth of existing litter.

3. Calculate cubic feet of existing litter = length (in feet) × width (in feet) × depth (in 

inches) /12.

4. Convert to cubic yards: volume of litter in cubic feet/27 = cubic yards of litter.

5. Modify the estimate based on the condition of litter (volume should be reduced if 

there is a large volume of ‘cake’ or of very wet litter).

Once an estimate of the existing litter has been made, an estimate of the total amount 

of carbonaceous material is needed. Below are three approaches for estimating the 

total.

Method 1. Weight Based Estimate

a. Effective in-house composting must have a minimum of 1.5 pounds of carbon 

material (based on bulk density of 30 pounds/cubic foot material) per pound of bird,

(1 pound of carbon per pound of bird for the base and cover and the remaining 

carbon for the mix).

b. Determine total pounds of birds

i. Pounds of birds = number of birds × average weight in pounds.

c. Determine total pounds carbon needed 

i. Total carbon = pounds of birds (from above) × 1.5.

d. Determine pounds of litter in house

i. Cubic feet of litter in house (see above)

ii. Pounds of litter = cubic feet of litter × weight of a cubic foot of litter (Average bulk 

density = 30 pounds; Range = 25 to 35 pounds).

e. Determine amount of additional carbon needed 

i. Cubic yards of additional carbon needed = ((total pounds of carbon neededpounds of litter in house)/(weight per cubic feet of carbon material))/(27)

1. wood chips, litter or wet sawdust = 30 pounds/cubic foot

2. dry sawdust = 15 pounds/cubic foot.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Method 2. Volume Based Estimate

a. Assume bulk density of litter is 30 pounds/cubic foot or approximately 800 

pounds/cubic yard. This means the following:

i. Each 20 pound bird requires 30 pounds or 1 cubic foot of carbon material

ii. Each 40 pound bird requires 60 pound or 2 cubic feet of carbon material.

b. To calculate total carbon material needs, perform the following calculations:

i. Multiply number of 20 pound birds by 1 to get cubic feet then divide by 27 for 

cubic yards.

ii. Multiply number of 40 pound birds by 2 to get cubic feet then divide by 27 for 

cubic yards.

c. To estimate additional volume needed, subtract the total volume of litter in the 

building (see above) from the total volume of carbon material required.

Method 3. Computerized Estimator

a. First, use the Spartan Emergency Animal Tissue Composting Planner v1.03 to 

estimate the total amount of amendment needed.

b. Then use the Spartan Compost Recipe Optimizer v1.04 to estimate the 

amounts/proportions of amendments needed; given the availability of amendments 

(poultry manure, poultry litter, sawdust, bark, etc.).

c. Go to this site: http://msue.anr.msu.edu/program/info/managing_animal_mortalities

and then select “Composting Tools.”
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APPENDIX C

VARIATIONS ON TYPICAL WINDROW 

CONSTRUCTION PROTOCOL

Variations Based on House Design

The three critical elements of a porous base 

layer, a uniformly mixed windrow core, and 

an adequate cap, must be maintained for 

successful virus inactivation regardless of 

variations in house design, bird size, or 

available carbon material. 

Pole Supported Houses

 Although the support poles may limit the maneuverability of the loaders, the 

windrow construction protocol remains the same. 

 Avoid constructing windrows against wooden support poles.

 Additional time will be required to construct windrows in this type of house due to 

space and structural constraints. 

 Depending on the width of the house and the pole configuration, two windrows 

may need to be constructed instead of a single windrow in the center of the house.

 Due to structural constraints and limited maneuverability, experienced and skilled 

loader operators are required to minimize damage to the building and equipment.

Pole house with 2 windrows (photo by Josh Payne)

Typical pole house design (photo by Bob Peer)
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Turkey Breeder Houses

 Although designs of turkey breeder houses may vary, generally the nests and 

other equipment can be moved to the center and sides of the house to make 

space for the construction of two windrows.

 Because of limited operating space, 

windrows may need to be shorter (5 feet 

tall) and narrower (10 feet wide). This will 

allow the loader operator to construct the 

windrow core and place the cap from one

side of the windrow.

 Eggs and feed should be evenly distributed 

onto the core of the windrow. 

 Eggs should be broken with the loader 

bucket to facilitate decomposition and 

inactivation of virus.

Breeder Turkey Toms

 Breeder toms can weigh between 60 and 80 pounds.

 Due to their size, more carbon material may be required to maintain good carcass to 

carbon contact. 

 Handling and placing the carcasses in the windrow may be difficult due to their size 

and the tendency of the carcasses to roll to the edge of the windrow. Additional labor 

may be necessary to appropriately position the carcasses on the windrow. 

 Additional capping material may be needed to ensure that all carcasses are 

adequately covered.

Broiler-Breeder Houses with a

Center Scratch Area

 Slats and nests need to be moved 

outside the house after depopulation.

 Carcasses and litter in scratch area 

should be scooped up with a loader(s)

and dumped onto the middle of the 

manure which was under the slats. 

Place equal amount of carcasses on 

both manure piles.

 Dump any feed onto the manure.

 Bring in carbon material to build a base 

10 inches deep and 12 foot wide in the scratch area. Ensure that the base does not 

touch the wooden slat supports.

Windrow in a turkey breeder house 

(photo by Gary Flory)

Typical broiler-breeder house with center 

scratch area (photo by Bob Peer)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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 Using the loader(s), mix the carcasses, manure and feed, and place this core mix on 

the base, maintaining 8 to 10 inches around the edge of the base. Work from both 

sides as you progress down the house making sure there is enough core mix placed 

on the base to evenly distribute the material the length of the house.

 Using the loader(s), place 8 to10 inches of woodchips or bark mulch on top of the 

core mix, making sure that this cap does not touch the wooden slat support and that 

all carcasses are covered.

Broiler-Breeder Houses with Scratch Areas on the Sides

 The manure from under the center slats will be placed on the carcasses in the side 

scratch areas.

 Follow same procedure as above for building the windrow in the area under the 

center slats.

Variation of the Standard Core Construction Technique

Pre-Compost Windrows

An alternative construction method, which increases the amount of carbon material 

mixed within the windrow core, is to form 2 pre-compost windrows, cap, and then form 1 

final windrow. This is especially useful when dealing with large amounts of carcass 

material relative to litter, creating a significant C:N imbalance, or when additional carbon 

material will increase porosity. Forming pre-compost windrows also stabilizes the tissue 

and begins a heating process until a 

single windrow can be constructed.

 Remove litter and carcasses 

along sidewalls and the center of 

the house, forming 2 precompost windrows extending the 

length of the house. 

 Cap each windrow with 8–12 

inches of suitable carbon 

material. 

Pre-compost windrows (photo by Josh Payne)
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 In the center of the house, construct a 12–15 feet wide base that is 10–15 inches 

deep. 

 Combine both capped windrows 

onto the base, mixing litter, 

carcasses, and added carbon 

material.

 Cap the final windrow with 8–12 

inches of suitable carbon 

material.

APPENDIX D

TEMPERATURE MONITORING 

PROCEDURE

Monitor temperatures of the windrow daily at a minimum 

of 10 locations flagged by the SME. The temperature 

monitoring locations should be spaced equidistantly the 

length of each windrow. Take two temperature readings 

at each flagged location within a foot of the flag; one 

reading at a depth of 18 inches and another reading at a 

depth of 36 inches. To ensure consistent temperature 

monitoring to the same depth, mark the thermometer 

probe at 18 inches and 36 inches. Place the 

temperature probe 3⁄4 of the way up the windrow at a 45 

degree angle. Ideally, temperatures should be monitored 

by a single individual for consistency. Temperature probes should be calibrated before 

use. 

Instructions

 Turn on fans or open the doors and curtains 

to all the houses containing compost piles to 

allow them to air out and to maximize 

ventilation.

 USE THE BUDDY SYSTEM. Entering a barn 

with active compost or dead birds requires a 

two person team. 

 Place the stem of the thermometer 

approximately 18 inches and then 36 inches 

into the compost pile half way up the pile at a 

45 degree angle.

 Leave the thermometer at each depth and point for at least 60 seconds.

Example temperature 

monitoring locations

Final windrow (photo by Josh Payne)
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 Log the reading from the thermometer from each 

flag and at both depths.

 Compare readings to previous day’s readings.

 After completing the house readings, close the 

doors and curtains.

 Calculate the average temperature for each pile by 

averaging both depths and note it on the 

Composting Temperature Log.

 Windrows should reach an average temperature of 

131 °F for a minimum of 72 hours at both the 18 

inch and 36 inch depths or be assessed by a SME 

for possible corrective measures.

 Disinfect the thermometer and return it to its protective case.

 Each thermometer will be kept at the respective premises being monitored. Do not 

take a thermometer from one premise to another.

 If 3 days after initial windrow construction, compost temperature averages are 

consistently (more than 3 days) below 100 °F or greater than 160 °F, a SME should 

be consulted immediately.

 During Phase 2, a SME should be consulted immediately if any monitoring location 

is consistently (more than 3 days) below 100 °F or greater than 160 °F.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX E TEMPERATURE MONITORING LOG SHEET

COMPOSTING TEMPERATURE LOG

 County: Site Number:

Street address, city, state:

 Farm Name:

 House/Windrow Number: Date Started: Date Finished: Date Turned:

Use the cells below to record the temperatures each day at 18 inches and at 36 inches.

Date Depth Flag #1 Flag #2 Flag #3 Flag #4 Flag #5 Flag #6 Flag #7 Flag #8 Flag #9 Flag#10 Avg

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”

18”

36”
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX F

IN-HOUSE COMPOSTING AMMONIA SAFETY

Background 

Ammonia is produced naturally from decomposition of organic matter, including plants, 

animals and animal wastes and can become concentrated in enclosed structures. This 

guidance is for ammonia produced from these natural sources, NOT from compressed 

gas cylinders or other sources which may produce very high air concentrations. 

Signs of Exposure to Ammonia 

Strong odor provides adequate early warning of its presence, but prolonged exposure 

can be hard to detect due to olfactory fatigue and adaptation. High concentrations can 

cause airway destruction resulting in respiratory distress or failure. Signs of exposure 

include the following:

 burning of the nose, throat and respiratory tract;

 coughing; and

 skin and eye irritation.

How to Reduce Ammonia Exposure 

 Increase ventilation when possible.

 Reduce the amount of time spent in areas where levels of ammonia are high.

 Wear proper PPE (personal protective equipment)

‒ gloves,

‒ half face with goggles or a full face respirator with at least a particulate/ammonia 

cartridge (green) or a multigas cartridge, and

‒ cloth coveralls or disposable coveralls (Tyvek).

 If possible, measure levels of ammonia in work area with an air gas meter before 

entering, or know recommended exposure times based on the ammonia levels in 

work area.

Exposure Guidelines (NIOSH)

Long term exposure (8 hours) 25 ppm

Short term exposure (15 minutes) 35 ppm

Short term exposure (5 minutes) 50 ppm

If exposed: 

 Seek fresh air.

 Flush irritated skin or eyes with water.

 If needed, seek immediate medical attention.

 Contact your supervisor or the Safety Officer if irritation of skin, nose, throat, or 

respiratory tract is persistent.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX G COMPOST APPROVAL CHECKLISTS 

INITIAL COMPOST WINDROW CONSTRUCTION CHECKLIST

Farm Name: County: 

Farm Address:

Farm Contact: Contact Phone:

Date Windrows 

Started:

Date Windrows 

Completed:

Windrow #: Premises 

County & #:

Who constructed 

windrow? Contact Info:

Yes No N/A Comments/Description

WINDROW DESIGN

1 Height between 6 and 8 feet.

2 Width between 10 and 15 feet

3 Base between 8 and 12 inches

3 Dome shaped without significant irregularities 

4 No soft tissue visible on the surface of the windrow

5 A minimum of 6 inches of carbon cover material

6 Photos taken

7 Sketch of flag locations with dimensions attached

Recommendations:

I have observed the windrows at this site and in my professional judgment they have been 

constructed consistent with the criteria outlined in the Mortality Composting Protocol for Avian 

Influenza Infected Flocks.

I have observed the windrows at this site and in my professional judgment they have NOT 

been constructed consistent with the criteria outlined in the Mortality Composting Protocol for 

Avian Influenza Infected Flocks. The following corrective actions are recommended:

Signature of Composting SME: ________________________________ Date: ______________

Print name of Composting SME: __________________________________________________

The corrective actions recommended above were completed on: ________________________
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Signature of Composting SME: ________________________________ Date: ______________

PHASE 1 WINDROW APPROVAL CHECKLIST

Applicability: This checklist is to be used 14 days after windrow construction to verify that they

have been constructed in accordance with the protocol and have reached temperatures necessary 

for virus inactivation. 

Farm Name: County: 

Farm Address:

Farm Contact: Contact Phone:

Date Windrows 

Started:

Date Windrows 

Completed:

Windrow #: Premises 

County & #:

Who constructed 

windrow? Contact Info:

Yes No N/A Comments/Description

PHASE 1 WINDROW EVALUATION—Days 1–14

1 Height between 4 and 8 feet

2 Width between 10 and 15 feet

3 Dome shaped without significant irregularities 

4 No soft tissue visible on the surface of the windrow

5 A minimum of 6 inches of carbon cover material

6 Moisture adequate

7 Leachate present

8 Excessive flies

9 Vector activity observed

10 Odor observed: VOA, putrid

11 Temperature measured at 18 inches and 36 inches

12 Temperatures reached 131 °F for 3 consecutive days

13 Photos taken

Phase 1 Recommendations of State Animal Health, APHIS or IMT Official: 

I have observed the windrows at this site and in my professional judgment they have been 

constructed consistent with the criteria outlined in the Mortality Composting Protocol for Avian 

Influenza Infected Flocks. Additionally, windrow temperatures have reached the average 

temperature of 131 °F for a minimum of 72 hours. The 14-day initial composting cycle is 

complete.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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I have observed the windrows at this site and in my professional judgment they have NOT

been constructed consistent with the criteria outlined in the Mortality Composting Protocol for 

Avian Influenza Infected Flocks. The windrows should be evaluated by a composting Subject 

Matter Expert to recommend corrective actions if necessary. 

Windrow temperatures have NOT reached the average temperature of 131 °F for a 

minimum of 72 hours. The windrows should be evaluated by a composting Subject Matter 

Expert to recommend corrective actions if necessary.

Signature of State Animal Health

Official, APHIS Official or IMT Official: __________________________ Date: _____________

Print name of signing official: ____________________________________________________

Phase 1 Recommendations of Subject Matter Expert: 

I have observed the windrows at this site and based on their construction and my review of 

the temperature logs, the windrows have performed in a manner demonstrated to inactive the 

avian influenza virus. The 14-day initial composting cycle is complete.

I have observed the windrows at this site and based on their construction and my review of 

the temperature logs, the windrows have NOT performed in a manner demonstrated to inactive 

the avian influenza virus. The following corrective actions are recommended:

Date of windrow evaluation: _____________________________________________________

Signature of Composting SME: ________________________________ Date: ______________

Print name of Composting SME: __________________________________________________

The corrective actions recommended above were completed on: ________________________

Phase 1 was complete on: ______________________________________________________

Signature of Composting SME: ________________________________ Date: _____________
Mortality Composting Protocol for Avian Influenza Infected Flocks

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PHASE 2 WINDROW APPROVAL CHECKLIST

Applicability: This checklist is to be used 14 days after Phase 1 was completed to verify that the

compost windrows may be moved without restriction on the premises or may leave the premises 

with appropriate permits. 

Farm Name: County: 

Farm Address:

Farm Contact: Contact Phone:

Date Windrows 

Started:

Date Windrows 

Completed:

Windrow #: Premises 

County & #:

Who constructed 

windrow? Contact Info:

Yes No N/A Comments/Description

PHASE 2 WINDROW EVALUATION—Days 14–28

1 Height between 4 and 8 feet

2 Width between 10 and 15 feet

3 Dome shaped without significant irregularities 

4 No soft tissue visible on the surface of the windrow

5 A minimum of 6 inches of carbon cover material

6 Moisture adequate

7 Leachate present

8 Excessive flies

9 Vector activity observed

10 Odor observed: VOA, putrid

11 Temperature measured at 18 inches and 36 inches

12 Temperatures reached 131 °F for 3 consecutive days

13 Photos taken

Phase 2 Recommendations of State Animal Health, APHIS or IMT Official: 

I have observed the windrows at this site and in my professional judgment they have been 

constructed consistent with the criteria outlined in the Mortality Composting Protocol for Avian 

Influenza Infected Flocks. Additionally, windrow temperatures have reached the average 

temperature of 131 °F for a minimum of 72 hours during the second composting phase. The 

windrows may be moved without restriction on the premises or may leave the premises with 

appropriate permits.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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I have observed the windrows at this site and in my professional judgment they have NOT

been constructed consistent with the criteria outlined in the Mortality Composting Protocol for 

Avian Influenza Infected Flocks. The windrows should be evaluated by a composting Subject 

Matter Expert to recommend corrective actions if necessary. 

Windrow temperatures have NOT reached the average temperature of 131 °F for a 

minimum of 72 hours during the second composting phase. The windrows should be evaluated 

by a composting Subject Matter Expert to recommend corrective actions if necessary.

Signature of State Animal Health

Official, APHIS Official or IMT Official: _______________________ Date: _________________

Print name of signing official: ____________________________________________________

Phase 2 Recommendations of Subject Matter Expert: 

I have observed the windrows at this site and based on their construction and my review of 

the temperature logs, the windrows have performed in a manner demonstrated to inactive the 

avian influenza virus. The windrows may be moved without restriction on the premises or may 

leave the premises with appropriate permits.

I have observed the windrows at this site and based on their construction and my review of 

the temperature logs, the windrows have NOT performed in a manner demonstrated to inactive 

the avian influenza virus. The following corrective actions are recommended:

Date of windrow evaluation: _____________________________________________________

Signature of Composting SME: ________________________________ Date: ______________

Print name of Composting SME: __________________________________________________

The corrective actions recommended above were completed on: ________________________

Phase 2 was complete on: ______________________________________________________

Signature of Composting SME: ________________________________ Date: _____________
Mortality Composting Protocol for Avian Influenza Infected Flocks

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APPENDIX H

WINDROW TURNING EQUIPMENT AND METHODS

Windrow turning should occur at 14 days after the windrow construction is completed.

There are several methods for turning windrows, both for in-house and outside 

windrows. The windrows constructed in-house may be turned inside the house or 

moved outside and reformed.

Methods for Turning Windrows In-House

1. Use skid loaders or telehandlers with high-capacity buckets to turn windrows.

Starting at the end of the windrow, scoop up all compost, turn machine around and 

drop the mixture forming a new windrow. It needs to be dumped in a manner that 

provides maximum aeration. 

2. Use small dozer to roll over windrows.

a. Requires a skilled operator to avoid damaging equipment and building.

b. Requires building the original windrow off center to allow space to turn the pile.

c. Only feasible in larger houses.

Methods for Turning Windrows Outside

1. Use large articulated loader(s).

a. Skid loaders have too small a bucket for this method (too slow and they don’t mix 

the material as well).

2. Use dozer to roll over windrow.

a. Does not mix material as well as other methods.

3. Use tractor attached mechanical compost turner.

a. Thoroughly mixes and shreds material but may be slower than using large 

loaders or straddle type windrow turners.

Turning in-house with a skid loader (photo by Josh Payne)
Mortality Composting Protocol for Avian Influenza Infected Flocks

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b. Requires 2 passes for larger windrows.

4. Straddle-type windrow turner (tractor pulled).

a. Windrows should be constructed far enough apart to allow the tractor and turner 

to operate (width of tractor approximately 10 to 12 feet).

b. Mixes material well.

c. Need a large unit to turn 12–15 foot windrows (at least 14 foot wide)—the “toe” of 

the windrows can be removed by a loader to reduce the width of larger windrows.

Brown Bear compost turner (photo by Gary Flory) Brown Bear compost turner (photo by Bob Peer)

Tractor-pulled compost turner 

(photo by Mark King)

Self-propelled compost turner 

(photo by Gary Flory)
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APPENDIX I

CHARACTERISTICS OF RAW MATERIAL1

Material Type of 

value

% N 

(dry 

weight)

C:N ratio 

(weight 

to weight)

Moisture 

content % 

(wet 

weight)

Bulk 

density 

(pounds per 

cubic yard)

Crop residues and fruit/vegetable-processing waste

Apple filter cake Typical 1.2 13 60 1,197

Apple pomace Typical 1.1 48 88 1,559

Apple-processing sludge Typical 2.8 7 59 1,411

Cocoa shells Typical 2.3 22 8 798

Coffee grounds Typical — 20 — —

Corn cobs Range 0.4–0.8 56–123 9–18 —

Average 0.6 98 15 557

Corn stalks Typical 0.6–0.8 60–73a 12 32

Cottonseed meal Typical 7.7 7 — —

Cranberry filter cake Typical 2.8 31 50 1,021

(with rice hulls) Typical 1.2 42 71 1,298

Cranberry plant (stems, 

leaves)

Typical 0.9 61 61 —

Cull potatoes Typical — 18 78 1,540

Fruit wastes Range 0.9–2.6 20–49 62–88 —

Average 1.4 40 80 —

Olive husks Typical 1.2–1.5 30–35 8–10 —

Potato-processing sludge Typical — 28 75 1,570

Potato tops Typical 1.5 25 — —

Rice hulls Range 0–0.4 113–1120 7–12 185–219

Average 0.3 121 14 202

Soybean meal Typical 7.2–7.6 4–6 — —

Tomato-processing waste Typical 4.5 11a 62 —

Vegetable produce Typical 2.7 19 87 1,585

Vegetable wastes Typical 2.5–4 11–13 — —

Fish and meat processing

Blood wastes 

(slaughterhouse waste 

and dried blood)

Typical 13–14 3–3.5 10–78 —

Crab and lobster wastes Range 4.6–8.2 4.0–5.4 35–61 —

Average 6.1 4.9 47 240

Fish-breading crumbs Typical 2.0 28 10 —

Fish-processing sludge Typical 6.8 5.2 94 —

 

1 Reprinted with permission from the Cornell Waste Management Institute.
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Material Type of 

value

% N 

(dry 

weight)

C:N ratio 

(weight 

to weight)

Moisture 

content % 

(wet 

weight)

Bulk 

density 

(pounds per 

cubic yard)

Fish wastes (gurry, racks, 

and so on)

Range 6.5–14.2 2.6–5.0 50–81 —

Average 10.6 3.6 76 —

Mixed slaughterhouse 

waste

Typical 7–10 2–4 — —

Mussel wastes Typical 3.6 2.2 63 —

Poultry carcasses Typical 2.4b 5 65 —

Paunch manure Typical 1.8 20–30 80–85 1,460

Shrimp wastes Typical 9.5 3.4 78 —

Manures

Broiler litter Range 1.6–3.9 12–15a 22–46 756–1,026

Average 2.7 14 a 37 864

Cattle Range 1.5–4.2 11–30 67–87 1,323–1,674

Average 2.4 19 81 1,458

Dairy tie stall Typical 2.7 18 79 —

Dairy free stall Typical 3.7 13 83 —

Horse-general Range 1.4–2.3 22–50 59–79 1,215–1,620

Average 1.6 30 72 1,379

Horse-race track Range 0.8–1.7 29–56 52–67 —

Average 1.2 41 63 —

Laying hens Range 4–10 3–10 62–75 1,377–1,620

Average 8.0 6 69 1,479

Sheep Range 1.3–3.9 13–20 60–75 —

Average 2.7 16 69 —

Swine Range 1.9–4.3 9–19 65–91 —

Average 3.1 14 80 —

Turkey litter Average 2.6 16 a 26 783

Municipal wastes

Garbage (food waste) Typical 1.9–2.9 14–16 69 —

Night soil Typical 5.5–6.5 6–10 — —
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Material Type of 

value

% N 

(dry 

weight)

C:N ratio 

(weight 

to weight)

Moisture 

content % 

(wet 

weight)

Bulk 

density 

(pounds per 

cubic yard)

Paper from domestic 

refuse

Typical 0.2–0.25 127–178 18–20 —

Pharmaceutical wastes Typical 2.6 19 — —

Refuse (mixed food, 

paper,

Typical 0.6–1.3 34–80 — —

and so on)

Sewage sludge Range 2–6.9 5–16 72–84 1,075–1,750

Activated sludge Typical 5.6 6 — —

Digested sludge Typical 1.9 16 — —

Straw, hay, silage

Corn silage Typical 1.2–1.4 38–43a 65–68 —

Hay-general Range 0.7–3.6 15–32 8–10 —

Average 2.10 — — —

Hay-legume Range 1.8–3.6 15–19 — —

Average 2.5 16 — —

Hay-non-legume Range 0.7–2.5 — — —

Average 1.3 32 — —

Straw-general Range 0.3–1.1 48–150 4–27 58–378

Average 0.7 80 12 227

Straw-oat Range 0.6–1.1 48–98 — —

Average 0.9 60 — —

Straw-wheat Range 0.3–0.5 100–150 — —

Average 0.4 127 — —

Wood and paper

Bark-hardwoods Range 0.10–0.41 116–436 — —

Average 0.241 223 — —

Bark-softwoods Range 0.04–0.39 131–1,285 — —

Average 0.14 496 — —

Corrugated cardboard Typical 0.10 563 8 259

Lumbermill waste Typical 0.13 170 — —

Newsprint Typical 0.06–0.14 398–852 3–8 195–242
Mortality Composting Protocol for Avian Influenza Infected Flocks

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Material Type of 

value

% N 

(dry 

weight)

C:N ratio 

(weight 

to weight)

Moisture 

content % 

(wet 

weight)

Bulk 

density 

(pounds per 

cubic yard)

Paper fiber sludge Typical — 250 66 1140

Paper mill sludge Typical 0.56 54 81 —

Paper pulp Typical 0.59 90 82 1403

Sawdust Range 0.06–0.8 200–750 19–65 350–450

Average 0.24 442 39 410

Telephone books Typical 0.7 772 6 250

Wood chips Typical — — — 445–620

Wood-hardwoods Range 0.06–0.11 451–819 — —

(chips, shavings, and so 

on)

Average 0.09 560 — —

Wood-softwoods Range 0.04–0.23 212–1,313 — —

(chips, shavings, and so 

on)

Average 0.09 641 — —

Yard wastes and other vegetation

Grass clippings Range 2.0–6.0 9–25 — —

Average 3.4 17 82 —

Loose Typical — — — 300–400

Compacted Typical — — — 500–800

Leaves Range 0.5–1.3 40–80 — —

Average 0.9 54 38 —

Loose and dry Typical — — — 100–300

Compacted and moist Typical — — — 400–500

Seaweed Range 1.2–3.0 5–27 — —

Average 1.9 17 53 —

Shrub trimmings Typical 1.0 53 15 429

Tree trimmings Typical 3.1 16 70 1,296

Water hyacinth-fresh Typical — 20–30 93 405

a Estimated from ash or volatile solids data.

b Mostly organic nitrogen.