The interviews with affected farm owners revealed that the owner of Case farm 1 bought 650 live birds (layers) from a farm in a neighboring region in three consignments of 200, 250 and 200, and transported these birds without any inspection. The birds bought were kept in a separate pen from the farmer’s existing flock. After the owner of the first affected farm (Case farm 1) observed thirty (30) dead and ninety (90) sick birds in his farm 24 hours after taking delivery of the last consignment of birds bought, he returned these birds back to the originating farm for replacement, also without any inspections. Although the birds were replaced, more deaths of birds were reported among the birds that were bought. The farmer sold some of the birds that looked healthy in the live bird market in the district. Subsequently, more deaths of birds were reported among his existing flock and, on a nearby farm. The farmers eventually reported the bird deaths to the Municipal Veterinary Office six (6) days later after they tried self-treating without success. Figure 2 illustrates the key events in the outbreak.

The graph (Figure 3 ) below illustrates an incremental growth in the number of dead birds recorded on the affected farms, after the initial multiple deaths (30 birds) reported on Case farm 1, until the depopulation exercise conducted on June 26.

We found an intersection in the two case-farms within a 200m buffer area plotted around the case and non-case farms (Figure 4 ). S2 Figure illustrates an 6 kilometer radius about the Case farm 1 and all other bird farms within the radius.

In all, 23 human contacts were identified including 20 primary contacts (87%) and 3 secondary (13%) contacts. About 53% (12/23) of the contacts were males. The median age of the contacts was 25 years (range = 5 to 64 years), with majority 65% (15/23) being resident at Amanfrom, an area close to the affected farms. All contacts were exposed between June 15 and 26, 2018 inclusive. None of the 23 contacts identified were symptomatic for influenza during the outbreak period and after follow up.

Reverse transcription polymerase chain reaction (RT-PCR) results confirmed highly pathogenic avian influenza (HPAI-H5N1) for all the six whole bird carcasses tested using universal primers for avian influenza viruses H5 and H7.

Both case farms were sited in a peri-urban area, but none of them was fenced. The two affected farms are about 100 meters apart. Case farm 1 had three pens used for poultry with sizes; 40 by 40 feet, 30 by 40 feet, and 25 by 20 feet. The farm also housed goats, sheep, and rabbits. The structure of the pen comprised concrete foundation with metallic mesh for walls and roofed with aluminum sheets. Each pen had feeding and water troughs. The water troughs were improvised from cooking oil gallons that were cut. Two of the pens lie directly on the side of a pathway that residents living behind the farm, use. There was a well dug on the compound from which water is drawn for domestic use and watering the animals. There was a small pen in-between the three pens where sick birds were kept for observation. There was a stream with a wooden bridge approximately 20 meters northwards from the Case farm 1. Wild birds were seen perching on the pens. The pens housing goats, sheep and rabbits were directly adjacent the pens with birds. The litter produced were stored in sacks by the side of the pens. The beddings were also not regularly changed.

Case farm 2 had two pens used for raising only poultry birds. The pens measure about 25 by 30 feet and 30 by 40 feet respectively. The pens had concrete floors and foundation. Metallic mesh was used to cover the open area from the foundation up to the roofing. The pens were roofed with aluminum sheets. Behind one of the pens was a manhole. No wild birds were seen on Case farm 2. The maintenance of the pens was similar to what was observed on Case farm 1. Human movements were reported between the two case farms.