NATIONAL FLYWAY COUNCIL

Pacific est. 1952 - Central est. 1948 - Mississippi est. 1952 - Atlantic est. 1952

Version 3.0 August 2023

Implementation Plan for Avian Influenza 

Surveillance in Waterfowl in the United States

Summer 2023 – Spring 2024
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Contents

INTRODUCTION................................................................................................................................................3

HPAI SURVEILLANCE GOALS.............................................................................................................................3

IMPLEMENTATION PLAN .................................................................................................................................3

1. SAMPLE NUMBERS AND SPECIES ................................................................................................... 3

2. WHAT TO COLLECT ........................................................................................................................ 3

3. WHEN TO COLLECT ........................................................................................................................ 4

4. WHERE TO COLLECT....................................................................................................................... 5

5. SAMPLE SUBMISSION.................................................................................................................... 5

6. PERMITS........................................................................................................................................ 5

7. COORDINATION WITH OTHER AGENCIES........................................................................................ 6

8. REPORTING FIELD DATA................................................................................................................. 6

MORBIDITY AND MORTALITY SURVEILLANCE..................................................................................................6

OTHER SURVEILLANCE STRATEGIES .................................................................................................................7

APPENDIX 1. Number of Wild Bird Samples to be Collected by State, 2023-2024 Surveillance Year.............8

APPENDIX 2. Participating NAHLN Laboratories............................................................................................13
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INTRODUCTION

This document describes the plan to implement national level surveillance for avian influenza viruses 

(AIVs) in wild waterfowl. Collaborating entities include the U.S. Department of Agriculture (USDA) 

Animal and Plant Health Inspection Service (APHIS) Wildlife Services (WS) National Wildlife Disease 

Program (NWDP) and Veterinary Services (VS); the U.S. Department of the Interior (DOI) U.S. 

Geological Survey (USGS) and U.S. Fish and Wildlife Service (USFWS); and the National Flyway 

Council. The Implementation Plan supports the collection of biological samples, diagnostic testing, 

data management, and analysis of data obtained by USDA-APHIS-Wildlife Services (WS), other 

Federal agencies, State wildlife agencies, Universities, and Tribal cooperators.

HPAI SURVEILLANCE GOALS

The goals of this surveillance effort are to maximize our ability to detect and identify the distribution of 

AIVs in wild waterfowl in the U.S., detect spread of AIVs to new areas of concern, and monitor wild 

duck populations for introductions of novel viruses (e.g., Eurasian lineage H5 and H7).

The plan focuses on sample collection at the watershed level (HUC4 sub-regional watersheds), and 

specific watersheds have been selected for sample collection. Watersheds were selected based on 

areas that have a high mixing of wild bird populations (sometimes from multiple flyways) and 

previous evidence of influenza infections in wild birds. Sample numbers were based on dabbling and 

diving duck data from eBird and on populations data from the U.S. Fish and Wildlife Service. If 

targeted sample numbers are reached within each specified watershed, we can determine with 95% 

confidence whether the AIVs of interest are present at the time of the surveillance.

IMPLEMENTATION PLAN

1. SAMPLE NUMBERS AND SPECIES

a. The sample target numbers are listed in Appendix 1 and apply only to apparently healthy 

dabbling and diving ducks. This plan does not address any other bird groups or 

morbidity/mortality samples.

b. The models used to generate 2023-2024 target sample numbers include updated bird 

population estimates and more recent avian influenza detection data compared to 

previous models. As a result, the target sample numbers across many States/watersheds 

are different than the 2022-2023 and earlier surveillance plans.

c. A list of target species can be found in Table 1. The Fulvous Whistling duck is not taxonomically 

a dabbling duck, but because of its foraging habits it is included in the same functional group for 

purposes of this surveillance plan.

d. Captive-reared and released ducks that are subsequently live-captured or hunter-harvested may 

be swabbed like any other dabbling duck and will be counted in the watershed target numbers.

2. WHAT TO COLLECT

a. The target sample numbers in this manual represent samples collected from agency harvested 

birds, hunter harvested birds, and live wild birds.

b. One cloacal and one oropharyngeal swab will be collected from each wild bird sampled. Cloacal 

and oropharyngeal swabs will be combined in the same tube of media.
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Table 1. Target Species for Wild Bird AIV Surveillance

Dabbling Ducks

American Green-winged Teal Mallard

American Black Duck Mottled Duck

American Wigeon Muscovy Duck

Blue-winged Teal Northern Pintail

Cinnamon Teal Northern Shoveler

Fulvous Whistling Duck Wood Duck

Gadwall

Diving Ducks

Bufflehead Lesser Scaup

Barrow’s Goldeneye Long-tailed Duck

Black Scoter Red-breasted Merganser

Canvasback Redhead

Common Eider Ring-necked Duck

Common Goldeneye Ruddy Duck

Common Merganser Spectacled Eider

Common Pochards Steller’s Eider

Greater Scaup Surf Scoter

Harlequin Duck Tufted Duck

Hooded Merganser White-winged Scoter

King Eider

3. WHEN TO COLLECT

a. Sample collection will occur from May 2023 through April 2024.

b. There are three seasons in a sampling year: Summer (May – August), Fall (September –

November), and a combined Winter/Spring* season (December – April). Appendix 1 lists the 

target sample numbers for each season. Generally, these seasons are intended to correspond 

with different stages of a bird’s annual cycle: Summer = end of breeding season, Fall = fall 

migration, Winter/Spring = birds on their wintering grounds and spring migration. Because birds 

may experience these stages at different times depending on the collection site, bird migratory 

patterns, and climate, there is some flexibility in season cutoff dates if needed. Contact the 

NWDP if you have questions about season cutoff dates for your area.

*Note: In previous years, the third sampling season was restricted to Winter months

(December – February) due to the limited availability of Spring sampling in some 

States. For the 2023-2024 surveillance year, a hybrid Winter/Spring season was 

adopted to allow for sampling in States where Spring sampling was of interest and 

permitted, while at the same time accommodating for other States where sampling 

would be primarily limited to Winter months.

c. It is best to collect a smaller number of samples during repeated sampling efforts than to collect 

all of a season’s target numbers in 1-2 visits. Spacing out sampling collections over time 

provides a more accurate estimate of AIV activity on the landscape.
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4. WHERE TO COLLECT

A U.S. map of Hydrologic Unit Code 4 (HUC4) watersheds is shown in Figure 1. Full page maps of 

watersheds in each state are available upon request. There is flexibility in watersheds and seasonal 

targets when on-the-ground conditions deviate from what was anticipated (e.g., no capture 

opportunities in a watershed due to drought). Please contact the NWDP if you know that changes 

need to be made to watershed or seasonal targets.

Figure 1. Sub-region watershed (hydrologic unit code 4) map of the continental 

United States. Watershed boundaries are in gray, state boundaries are in white.

5. SAMPLE SUBMISSION

All samples will be submitted to one of the pre-approved National Animal Health Laboratory 

Network (NAHLN) laboratories. Appendix 2 lists the names and contact phone numbers of 

participating laboratories. The NWDP has established Blanket Purchase Agreements (BPA’s) with 

each lab. Each state is assigned to a specific laboratory to use for diagnostics. Samples shipped to 

non-contracted labs will not be covered by the NWDP and will be the responsibility of submitting 

states. The NAHLN lab will screen samples to determine if type A influenza virus is present; if the 

test is positive, the NAHLN lab will further analyze the sample using H5 and H7 specific assays. The 

NAHLN lab will send all samples testing positive for any AIV (including samples testing positive for 

H5 or H7) to NVSL for sequencing/subtyping.

6. PERMITS

The NWDP has a “blanket” scientific collecting permit from USFWS that includes all States except 

Hawaii. The permit covers the swabbing of most species collected as live birds or hunter harvest by 

Wildlife Services personnel. Agency harvest for the sole purpose of disease sampling is not 

permitted. Wildlife Services personnel must have a copy of this permit in the field when sampling. 

State agency cooperators and banders will need their own permits from USFWS and the USGS Bird 
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Banding Laboratory for live-capture activities, as usual. If HPAI swabbing of live birds is to be 

conducted as a ‘piggyback’ activity, the banding permit must be amended to allow this activity.

The NWDP will complete and submit the annual reporting requirements outlined in the permit for 

all states collecting wild bird samples. To avoid submitting duplicate copies of reports, State WS 

offices should not submit their own copies of the annual report to USFWS. For a copy of the 

USFWS permit, see the document “Wild Bird Avian Influenza Surveillance – Field Procedures 

Manual” or contact the NWDP.

7. COORDINATION WITH OTHER AGENCIES

Sample collection can include efforts by federal, state, Tribal, local, university, and nongovernmental participants as needed. Samples intended to count toward watershed target 

numbers must be entered into the APHIS Veterinary Services Laboratory Submission System 

(VSLS—see below), regardless of which agency collects the samples.

8. REPORTING FIELD DATA

Each biologist is responsible for entering field data directly into the APHIS Veterinary Services 

Laboratory Submission System application (VSLS) (http://vsapps.aphis.usda.gov/vslabsub/login.do) 

within 24 hours of submitting samples to the laboratory. Each biologist is also responsible for 

emailing electronic copies of data forms to NWDPData@usda.gov within 24 hours of submitting 

samples to the laboratory. Results may be requested only after field data is entered into the 

system and results have been received from the diagnostic lab. For new user accounts, please refer 

to the directions in the document “Wild Bird Avian Influenza Surveillance – Field Procedures 

Manual.”

MORBIDITY AND MORTALITY SURVEILLANCE

Agencies should investigate wild bird morbidity/mortality events regardless of the time of year, 

species involved, or the number of samples already collected in the state. Morbidity/mortality 

samples do not count towards meeting the watershed targets, as morbidity/mortality events have 

a different disease risk associated with them, and the data are analyzed differently than those of 

apparently healthy birds (live-capture and hunter harvest).

The USGS National Wildlife Health Center (NWHC) in Madison, WI, is our primary partner for 

performing diagnostics related to morbidity/mortality events and can provide guidance on the 

investigation, sampling, and diagnostics for observed avian mortality. Briefly, the NWHC guidance 

for specimen collection from mortality is to collect and submit whole carcasses. Do not collect 

swabs from carcasses submitted to the NWHC. Always contact the NWHC for guidance prior to 

submitting samples. Sample types submitted will be determined on a case-by-case basis. The 

NWHC should be contacted by phone (608-270-2480) or email (NWHC-epi@usgs. gov) prior to 

shipping any carcass. If NWHC declines to test samples from a morbidity/mortality event and you 

are still interested in getting results, contact the NWDP.

State or regional veterinary diagnostic laboratories may also be used in morbidity/mortality 

investigations. Contact your local lab for sample submission instructions. PLEASE NOTIFY YOUR

STATE WILDLIFE SERVICES OFFICE AND THE NWDP IF YOU ARE SENDING MORTALITY SAMPLES 

TO A STATE OR REGIONAL LABORATORY. If a lab requests multiple sample types (e.g., 3

carcasses and swabs from all other birds involved in the morbidity/mortality event), please 
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keep all samples from the same event together and submit to only one lab.

Do not swab carcasses you are submitting, as the NWHC or other lab of choice will swab the 

carcass at the lab as part of the necropsy procedure.

OTHER SURVEILLANCE STRATEGIES

Other strategies such as environmental (fecal) sampling and sentinels are useful in specific situations 

but are not part of this surveillance plan.
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APPENDIX 1. Number of Wild Bird Samples to be Collected by State, 

2023-2024 Surveillance Year

Watershed by State

Summer 

(May - Aug) 

Sample 

Numbers

Fall 

(Sep - Nov)

Sample 

Numbers

Winter/ 

Spring 

(Dec - Apr) 

Sample

Numbers

Grand Total

Alabama

Middle Tennessee-Elk 308 0 320 628

Alaska

Lower Yukon River 334 0 0 334

Middle Yukon River 334 334 0 668

South Central Alaska 334 334 334 1002

Southeast Alaska 0 333 0 333

Arizona

Lower Colorado 0 333 0 333

Arkansas

Lower Arkansas 0 0 150 150

Lower Mississippi-St. Francis 0 244 244 488

California

Klamath-Northern California Coastal 317 0 0 317

Sacramento 0 334 334 668

San Francisco Bay 0 0 334 334

Tulare-Buena Vista Lakes 0 334 334 668

Colorado

North Platte 0 100 0 100

Rio Grande Headwaters 333 333 0 666

South Platte 0 0 334 334

Connecticut

Connecticut Coastal 0 0 330 330

Delaware

Delaware-Mid Atlantic Coastal 0 119 119 238

Florida

Southern Florida 0 0 330 330

St. Johns 0 333 333 666

Georgia

Apalachicola 0 332 0 332

Hawaii

Oahu N/A* N/A* N/A* N/A*

Idaho

Middle Snake 301 0 0 301

Upper Snake 334 334 0 668
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Watershed by State

Summer 

(May - Aug) 

Sample 

Numbers

Fall 

(Sep - Nov)

Sample 

Numbers

Winter/ 

Spring 

(Dec - Apr) 

Sample

Numbers

Grand Total

Illinois

Lower Illinois 0 334 334 668

Upper Mississippi-Kaskaskia-Meramec 0 333 334 667

Wabash 0 87 0 87

Indiana

Upper Illinois 0 301 301 602

Wabash 0 243 0 243

Iowa

Des Moines 0 334 0 334

Upper Mississippi-Iowa-Skunk-Waps 0 334 0 334

Upper Mississippi-Maquoketa-Plum 0 333 0 333

Kansas

Middle Arkansas 0 334 334 668

Neosho-Verdigris 0 171 0 171

Kentucky

Lower Ohio 0 0 270 270

Louisiana

Boeuf-Tensas 0 0 334 334

Louisiana Coastal 0 334 334 668

Maine

Kennebec 325 323 0 648

Maine Coastal 322 0 0 322

Penobscot 322 0 0 322

Saco 165 0 0 165

Maryland

Lower Chesapeake 0 200 200 400

Massachusetts

Connecticut 136 136 135 407

Massachusetts-Rhode Island Coastal 330 0 332 662

Merrimack 0 79 76 155

Michigan

Southeastern Lake Michigan 333 0 333 666

Southwestern Lake Huron-Lake Huron 0 333 0 333

St. Clair-Detroit 332 333 0 665

Minnesota

Minnesota 334 334 334 1002

Mississippi Headwaters 0 333 0 333

Red 125 125 0 250

St. Croix 0 151 0 151

Upper Mississippi-Black-Root 0 183 0 183
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Watershed by State

Summer 

(May - Aug) 

Sample 

Numbers

Fall 

(Sep - Nov)

Sample 

Numbers

Winter/ 

Spring 

(Dec - Apr) 

Sample

Numbers

Grand Total

Mississippi

Lower Mississippi-Big Black 0 0 329 329

Lower Mississippi-Yazoo 0 334 334 668

Missouri

Lower Mississippi-St. Francis 0 83 83 166

Lower Missouri 0 0 334 334

Montana

Big Horn 0 334 0 334

Kootenai-Pend Oreille-Spokane 0 334 0 334

Missouri-Marias 334 334 0 668

Nebraska

North Platte 0 75 75 150

Nevada

Central Lahontan 0 334 0 334

New Hampshire

Connecticut 145 145 145 435

Merrimack 0 328 319 647

Saco 113 0 0 113

New Jersey

Delaware-Mid Atlantic Coastal 90 91 91 272

New Mexico

Rio Grande-Elephant Butte 0 0 333 333

New York

Southeastern Lake Ontario 0 0 332 332

Southwestern Lake Ontario 0 322 0 322

North Carolina

Chowan-Roanoke 285 0 0 285

Neuse-Pamlico 0 333 333 666

North Dakota

James 0 103 0 103

Missouri-Oahe 0 186 186 372

Red 149 149 0 298

Ohio

Muskingum 0 327 0 327

Upper Ohio 137 139 0 276

Western Lake Erie 0 332 333 665

Oklahoma

Lower Arkansas 0 0 183 183

Neosho-Verdigris 0 110 0 110
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Watershed by State

Summer 

(May - Aug) 

Sample 

Numbers

Fall 

(Sep - Nov)

Sample 

Numbers

Winter/ 

Spring 

(Dec - Apr) 

Sample

Numbers

Grand Total

Oregon

Middle Columbia 0 334 0 334

Oregon Closed Basins 334 334 0 668

Willamette 333 0 334 667

Pennsylvania

Delaware-Mid Atlantic Coastal 119 0 0 119

Susquehanna 0 0 408 408

Upper Ohio 131 133 0 264

Puerto Rico

Puerto Rico N/A* N/A* N/A* N/A*

South Carolina

Edisto-Santee 0 0 401 401

South Dakota

James 0 231 0 231

Missouri-Oahe 0 148 148 296

Tennessee

Lower Mississippi-Hatchie 0 0 334 334

Texas

Brazos Headwaters 0 334 0 334

Neches 0 0 331 331

Trinity 0 334 0 334

U.S. Virgin Islands

Virgin Islands N/A* N/A* N/A* N/A*

Utah

Bear 0 334 0 334

Great Salt Lake 334 334 0 668

Vermont

NE Lake Ontario-LakeOntarioSt. Lawrence 0 333 0 333

Virginia

Lower Chesapeake 0 132 133 265

Potomac 204 205 206 615

Washington

Lower Columbia 0 333 0 333

Puget Sound 0 334 0 334

Upper Columbia 334 334 0 668

West Virginia

Potomac 79 79 79 237

Upper Ohio 57 57 0 114
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Watershed by State

Summer 

(May - Aug) 

Sample 

Numbers

Fall 

(Sep - Nov)

Sample 

Numbers

Winter/ 

Spring 

(Dec - Apr) 

Sample

Numbers

Grand Total

Wisconsin

Northwestern Lake Michigan 0 331 0 331

Rock 0 333 0 333

St. Croix 0 177 0 177

Upper Mississippi-Black-Root 0 150 0 150

Wisconsin 331 330 0 661

Wyoming

North Platte 0 137 237 374

Grand Total 8,828 19,716 13,168 41,712

*Opportunistic sampling will occur in Hawaii, Puerto Rico, and U.S. Virgin Islands. No target numbers 

have been assigned to these States/Territories. Samples from these regions may also include wild 

bird species other than dabbling and diving ducks.
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APPENDIX 2. Participating NAHLN Laboratories

STATES NAHLN LAB SHIPPING ADDRESS TELEPHONE

AK, AZ Arizona Veterinary Diagnostic 

Lab

PO# Contact NWDP

Arizona Veterinary Diagnostic Laboratory 

2831 North Freeway

Tucson, AZ 85705-5021

Phone: 520-621-2356

CA, NV California Animal Health & 

Food Safety Laboratory

PO# Contact NWDP

California Animal Health & Food Safety Laboratory 

University of California, School of Vet Med

620 West Health Science Drive 

Davis, California 95616

Phone: 530-752-8709

ID, OR, 

UT, WA

Oregon State University Veterinary 

Diagnostic Lab

PO# Contact NWDP

Oregon State University Veterinary Diagnostic 

Laboratory

Magruder Hall 134 700 SW 30th St 

Corvallis, Oregon 97331-8628

Phone: 541-737-3261

FL, ME,

NH, NC, 

VT, 

PR/USVI

Bronson Animal Disease Diagnostic 

Laboratory

PO# Contact NWDP

Bronson Animal Disease Diagnostic Laboratory 

2700 North John Young Parkway

Kissimmee, Florida 34741

Phone: 321-697-1400

GA, NJ,

NY, SC, 

VA, WV

Animal Health Diagnostic 

Center College of Vet Med, 

Cornell University

PO# Contact NWDP

Animal Health Diagnostic Center College of 

Veterinary Medicine

Cornell University 

240 Farrier Road

Ithaca, New York 14853-8002

Phone: 607-253-3900

CT, DE,

MD, MA, 

PA

Pennsylvania Veterinary Laboratory

PO# Contact NWDP

PA Veterinary Laboratory, Pennsylvania Department 

of Agriculture

2305 North Cameron Street, 

Harrisburg, PA 17110

Phone: 717-787-8808

IL,IN, MI, 

OH

Michigan State University Veterinary 

Diagnostic Laboratory

PO# Contact NWDP

Michigan State University Veterinary Diagnostic 

Laboratory

College of Veterinary Medicine 

4125 Beaumont Road

Lansing, MI 48910

Phone: 517-353-0635

AR, IA, 

MN, MO

University of Missouri Veterinary 

Medical Diagnostic Laboratory

PO# Contact NWDP

University of Missouri Veterinary Medical Diagnostic 

Laboratory

901 E. Campus Loop 

Columbia, MO 65211

Phone: 573-882-6811

AL, KY,

LA, MS, 

TN

Mississippi State University 

Veterinary Research and Diagnostic 

Lab

PO# Contact NWDP

Mississippi Veterinary Research & Diagnostic 

Laboratory

3137 Highway 468 West

Pearl, MS 39208

Phone: 601-420-4768

CO, MT,

NM, ND, 

SD, WY

Colorado State University 

College of Veterinary Medicine

PO# Contact NWDP

Colorado State University Veterinary Diagnostic 

Laboratory

2450 Gillette Drive 

Fort Collins, CO 80526

Phone: 970-297-1281

KS, NE,

OK, TX, 

WI

Kansas State University, Diagnostic 

Laboratory

PO# Contact NWDP

Kansas State Veterinary Diagnostic Laboratory 

2005 Research Park

Manhattan, KS 66502

Phone: 785-532-5651
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HI State of Hawaii, Department of 

Health

State Laboratories Division

PO# Contact NWDP

State Laboratories Division 

2725 Waimano Home Road 

Pearl City, HI 96782

808-453-6650