If there had been in place "even the most rudimentary biosecurity measure" at the Eastern Creek Quarantine Station in August last year, it was most unlikely there would have been any escape of equine influenza from quarantine, he argued.
Such measures would have included, at a minimum, people having contact with the horses in the equine enclosure being required to shower and change their clothes before exiting the area, and to leave contaminated clothing and equipment in the quarantine station.
"That such a measure was not being implemented within the quarantine station in August 2007 is a serious failure by those within the Department of Agriculture, Forestry and Fisheries (DAFF) and the Australian Quarantine and Inspection Sercice (AQIS), who were responsible for the management of quarantine risks and in particular the management of post entry quarantine arrangements."
Those who ultimately must take responsibility for that failure, he said, include the Secretary of DAFF in his role as the director of animal and plant quarantine and the person who, under the Minister, is charged with the execution of the Quarantine Act; the executive director of AQIS; and the executive manager of the quarantine and plant programmes within AQIS.
"That such a measure was not being implemented within the quarantine station in August 2007 was the consequence of a number of acts and omissions on the part of various employees and officers of AQIS occurring at different levels of that organisation and over a period of time from at least 2003."
A veterinarian takes a nasal swab for testing.
His arguments, if accepted by Commissioner Callahan, will add fuel to compensation claims likely from those within the horse industry who have suffered economic loss as a result of the outbreak.
Evidence suggests that equine influenza somehow reached a three-day horse event at Maitland, in New South Wales, which began on August 17. The disease was spread across a geographically large area, as far north as Queensland, when competing horses were taken home. The first signs of flu in horses outside Eastern Creek appeared on August 21 and 22.
Mr Meagher, in discussing how the virus likely escaped, referred to the August 8 arrival of 52 horses into Australia, including 13 from Japan by air. Nine were taken to Victoria's Spotswood Quarantine Station, while four continued by air to Sydney, and were taken to Eastern Creek Quarantine Station.
Subsequent blood tests showed one of the four, Snitzel, had been infected between July 24 and August 13 - before arriving in Australia. Testing showed that seven of the nine in Spotswood became infected between July 24 and August 24.
"Those analyses indicate that some of the horses imported by air from Japan were infected with equine influenza at some stage in pre-export quarantine [in Japan] or during their transportation by air to Australia and at the time they entered post-arrival quarantine.
There is, he said, no evidence of any contamination of horses in the general horse population in Victoria which would support a finding that the virus was carried out of Spotswood to horses in New South Wales.
"It is not possible to draw any conclusion as to the source of the infection of those horses in Japan and when it occurred. The horses could have become infected because they were exposed to the virus during pre-export quarantine or during their transportation by road to Chitose airport or in their carriage to Australia," he said.
Mr Meagher offered the following scenarios as to how the virus escaped into the general horse population in Australia.
Decontamination of horse floats, at Richmond.
"Secondly, the weather conditions at the airport in the afternoon of 8 August included an ambient temperature of 22.5degC, a relative humidity of 22% and a fairly clear sky. Those sunny conditions would not have permitted the survival of the virus for any significant period of time.
"Thirdly, the part of Sydney's Kingsford Smith Airport where the horses were unloaded from the aircraft and then loaded into transport vehicles is inside the perimeter of the airport and some distance from roadways and industrial and residential areas.
"The evidence does not indicate that there were any horses in that area likely to be infected by airborne spread. All of these factors taken together make it most unlikely that airborne spread from the airport was the source of the outbreak."
Contamination from the airport via contaminated persons, equipment or transport vehicles could also be excluded as a likely cause, he argued. "The evidence indicates that none of the persons and equipment which were or was likely to have had contact with the infected horses subsequently had contact with any horses in the general horse population which were infected before 24 August.
"The infection cycle of the virus and the absence of any reports of infected horses before the Maitland event makes it unlikely that a horse could have become infected on 8 or 9 August because that fact is not likely to have remained unnoticed and unreported.
"Contamination via windborne spread from Eastern Creek can also be excluded as a likely source of the escape.
"The first horse in ECQS which exhibited noticeable clinical signs was Encosta De Lago on 17 August. Before that time it is unlikely that any horse was shedding sufficient amounts of the virus to result in airborne spread and infection of horses outside the quarantine stations.
"The fact that only a small number of the 52 horses in the quarantine station eventually became infected is not consistent with a horse outside the quarantine station being infected by windborne spread (when those inside were not)," he said.
"That leaves one possible scenario, which is that a person or equipment or dog contaminated with the virus in ECQS left ECQS and in some way contaminated a horse in the general horse population."
Mr Meagher argued that contamination via quarantined dogs could be excluded. They had been kept separate at the station and the infected horses at the station had only been shedding a small amount of virus when compared to fully susceptible horses, such as the naive Australian equine population.
"In addition, there have been no reported instances of dogs infected with equine influenza excreting sufficient virus to reinfect horses."
He continued: "There then remains as the most likely scenario that the virus escaped from Eastern Creek on the person, clothing or equipment of a groom, vet, farrier or some other person who had contact with the horses and who then left the quarantine station without adequately or at all cleaning or disinfecting themselves, their clothing and equipment.
"The timing of the Maitland event and the emergence of clinical signs within Eastern Creek strongly suggest that escape of the virus is most likely to have occurred in the period after 10 August 2007.
"The evidence does not enable a more specific finding to be made as to the most likely mechanism by which the virus escaped from the quarantine station. However, it is possible by reason of the likely timing of any escape to identify the vets and farriers who may have unintentionally carried the virus out of the station.
"However it is not possible to identify any grooms or other persons who in fact did so. In the period from 10 August various of the horses were attended to by their grooms, two farriers and four vets. Their movements in and out of the quarantine station and their activities whilst in the equine enclosure were not supervised or monitored by anyone from AQIS or by any of the other persons residing in the equine closure during the period of the intake."
The evidence allowed the following findings, he argued.
The evidence of each of these witnesses or groups of witnesses has been tested.
The evidence does not suggest that any of the horses attended to by any of the witnesses outside Eastern Creek was infected before the Maitland event.
"In those circumstances the finding which should be made as to how the outbreak occurred can only be expressed in general terms. That finding is that the virus escaped from horses infected within Eastern Creek and that it did so via contaminated persons or equipment leaving Eastern Creek and coming into contact with a horse in the general horse population.
"The contaminated persons or equipment are most likely to have been associated with caring for the horses whilst in quarantine."
Mr Meagher argued there was a lack of procedures at Eastern Creek. As at August 2007 there were no operating procedures or work instructions that had been prepared within AQIS which were understood by quarantine officers at Eastern Creek.
"In this respect the position in the government-owned quarantine station was in stark contrast with that which obtained at the privately owned quarantine station at Sandown which was required by AQIS to have in place fully documented and regularly audited procedures."
He talked of an organisation that lacked clear lines of effective communication between those responsible for formulating procedures and those responsible for implementing them.
"The quarantine station was under staffed. The quarantine station was not manned 24 hours a day and was closed during the weekends. Grooms, vets, caterers and cleaners had access cards to the main gate and/or keys to the gate to the equine facility.
"Visitors including farriers and others entered and left the quarantine station and horse enclosure without the knowledge of AQIS officers particularly out of hours and on the weekends."
Mr Meagher also argued that the live animal import programme was not properly resourced or funded and he proposed wide-ranging changes to improve the quarantine situation, including better staffing levels and a review of the entire quarantine process by Biosecurity Australia.
The Commission is expected to sit again early in April. Mr Callinan's final report is likely by late April.