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H2N2 data for Archive.xlsx (26.1 kB)

Data from: The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl

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posted on 2024-02-14, 20:00 authored by Erica SpackmanErica Spackman

Data are the individual group values for oral and cloacal virus shedding and antibody titers for reach treatment group from: Mo et al., The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl. Vet Mic 260:109180, 2021.

Methods: Six H2N2 low pathogenic avian influenza viruses from US LBMs were selected based on recency and to represent the different genotypes present in the live birds markets during the time period (i.e., the presence or absence of a NA stalk deletion): A/duck/PA/14-030488-5/2014 (Dk/PA/14), A/chicken/NY/16-032621-2/2016 (Ck/NY/16), A/chicken/CT/17-008911-4/2017 (Ck/CT/17), A/chicken/NY/18-002471-4/2018 (CK/NY/02471/18), A/chicken/NY/18-042097-3/2018 (Ck/NY/042097/18) and A/chicken/NY/19-012787-1/2019 (Ck/NY/19). Isolates were evaluated in White Leghorn chickens (Gallus gallus), guinea fowl (Numida meleagris) and Pekin ducks (Anas platyrhynchos). Chickens and guinea fowl were challenged at 4 weeks of age and Pekin ducks were challenged at 2 weeks of age with 6log10 of virus by the intra-choanal route. “Contact” birds, which were hatch-mates of the inoculated birds, were co-housed with the inoculated birds 24hrs post inoculation to evaluate transmission. Viral loads in OP and CL swabs collected at 2, 4, 7, 10, and 14 days post inoculation were determined by quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR). RNA was extracted from swabs using the MagMAX96 Viral RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA) and the KingFisher Flex Magnetic Particle Processing System (Thermo Fisher Scientific), with an additional wash step to remove inhibitors (Das et al., 2009). The qRT‐PCR for AIV detection was conducted based on the standard USDA M gene AIV qRT‐PCR procedure (Spackman et al., 2002) using an Applied Biosystems® 7500 Fast Real‐Time PCR system (Thermo Fisher Scientific). Cycle threshold (Ct) values were determined by the 7500 Fast Software v2.3. For relative quantification, Ct values were converted to titer equivalents based on the standard curve method (Larionov et al., 2005). Values were established from ten-fold dilutions of the same titrated stock of the virus used to challenge the birds. The limit of detection was determined to be 0.8Log10 per reaction. Serological testing for antibodies to the virus utilized the hemagglutination inhibition (HI) assays using homologous antigens were performed to quantify antibody responses with serum collected from chickens, guinea fowl and Pekin ducks at 14 dpi based on the standard protocol (OIE, 2019). HI titers were reported as reciprocal log2 titers, and titers greater than 3 log2 (1:8) were considered positive.

Resources in this dataset:

  • Resource Title: H2N2 influenza pathobiology data for avian species.

    File Name: H2N2 data for Archive.xlsx

    Resource Description: Data by day post exposure for birds exposed to low pathogenic H2N2 avian influenza virus.


USDA-ARS: 6040-32000-066-00D

USDA-APHIS: 60-6040-6-005

National Institutes of Health: AAI-12004001.


Data contact name

Spackman, Erica

Data contact email


Ag Data Commons

Intended use

These data are the full shed and virus infection data from a pathobiology study of low pathogenic avian influenza in 3 avian species. The data may be utilized in further analysis and meta analyses of avian influenza pathobiology studies. Virus excretion quantities and numbers of birds are provided by species, date and route of shed (oral or cloacal).

Use limitations

Comparison with other studies need to assure that the quantification methods are compatible. Assay limits of detection are near 1.0log10 per sample, therefore samples where no virus was detected may be true negative or weak positives below the assay limit of detection.

Temporal Extent Start Date


Temporal Extent End Date



  • Not specified

Geographic Coverage


Geographic location - description

Northeast United States

ISO Topic Category

  • health

National Agricultural Library Thesaurus terms

pathogenesis; markets; Influenza A virus; chickens; Pekin; ducks; guineafowl; cloaca; viral shedding; antibodies; pathogenicity; White Leghorn; Gallus gallus; Anas platyrhynchos; viruses; viral load; detection limit; antigens; antibody formation; avian influenza

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 103

ARIS Log Number


Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Spackman, Erica (2023). Data from: The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl. Ag Data Commons.

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