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Table 1 Origin of the Pakistani avian samples from which viruses were sequenced

From: Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

Farm ID/Flock ID Collection date Location Chicken type Flock size Age of birds (days) Health status Vaccination status Type of farm Type of sample Sample ID H9 AAVV-1 IBV aMPV ILTV
S/6 13/7/14 Kasur Broiler 3000 10 MRS V (ND, IB) open OP 11 + +
S/8 17/7/14 Rawalpindi Broiler 10,000 16 MRS NV control OP 12,15 +
H/9 19/7/14 Kasur Broiler 3000 38 MRS NV open OP 17,18 +
K/10 22/7/14 Multan Broiler 3000 20 MRS NV open OP 20 +
A/11 25/7/14 Kasur Broiler 3000 9 MRS NV open OP 21,22 +
K/12 27/7/14 Kasur Broiler 3000 12 MRS V (ND) open OP 23,24 +
R/13 29/7/14 Kasur Broiler 2500 31 MRS V (ND, IB) open OP 26   +
Y/21 13/8/14 Lahore Layer 3000 80 MRS NV open OP 41,42 + +
A/22 14/7/14 Kasur Layer 3000 120 MRS NV open OP 44 +
R/23 15/7/14 Lahore Broiler 10,000 31 MRS V (ND) control OP 45,46 + +
Z/32 23/7/14 Okara Broiler 3000 10 MRS NV open OP 64,65 +
A/38 18/10/14 Kasur Layer 3000 78 MRS NV open lung swabs 74 + +
H/41 14/1/14 Multan Layer 3000 108 MRS NV open OP 77 + +
H/42 28/11/14 Multan Layer 2500 145 MRS NV open OP 78 + +
K/51 15/10/14 Multan Layer 3000 66 MRS NV open OP 87 +
A/59 14/8/15 Rawalpindi Broiler 3000 14 Open mouth breathing, mucus plug in bronchi V (ND) open OP 98,99 +
W/62 17/8/15 Kasur Broiler 3000 35 Respiratory distress, congested lungs V (ND, IBD) open OP, lung swabs 106,107 + +
I/64 26/8/15 Rawalpindi Broiler 3000 25 MRS V (ND) open OP 110,111 +
U/65 26/8/15 Mansehra Layer 3000 208 sickness, congested lungs, pale carcass V (ND) open OP 112,113 +
T/66 29/8/15 Abbottabad Layer 3000 180 fever, sneezing, gasping, airsacculitis V (ND) open OP, lung swabs 114 + +
F/67 2/9/15 Kasur Broiler 3000 33 MRS V (ND, IBD) open OP 115 + +
S/70 27/9/15 Sheikhupura Broiler 3000 35 MRS V (IB, ND) control OP 122,123 + +
K/80 13/12/15 Faisalabad Broiler 3000 26 MRS V (ND) control OP 142,143 + +
K/84 2/1/16 Lahore Broiler 2500 29 MRS NV control OP 150,151 + +
A/88 9/1/16 Kasur Layer 3000 120 MRS NV open OP 158,159 +
  1. V vaccinated, NV non-vaccinated, OP oropharyngeal swab, ND Newcastle disease, IB infectious bronchitis, IBD infectious bursal disease, aMPV avian metapneumovirus, IBV infectious bronchitis virus, NDV Newcastle disease virus, ILTV infectious laryngotracheitis virus, MRS Mild respiratory signs: slight opening of the beak and chest movements. “Control” versus “open” farms: environmentally controlled (versus not controlled) poultry farms. Sample numbers: each number corresponds to a pool of 10 swabs from a chicken flock. Data in this table include only those samples and flocks which were found positive for selected viruses