A leading private health company, poised to win much of the new wave of NHS outsourcing contracts, is under investigation for allegedly providing an "unsafe" out-of-hours GP service, and over claims that it manipulated results where it failed to meet targets.

Serco, which runs a large range of outsourced services for the government and local authorities, was subject to an unannounced inspection by NHS watchdogs in Cornwall last month in response to whistleblowers who claim that it:

• allowed queues of up to 90 patients at a time to build up at its telephone helpline;

• met its targets, in part, by adjusting figures to blame delays on patients;

• rang at least one patient who had waited too long to see a doctor to give them a new waiting target instead;

• repeatedly took visiting doctors off roving duties in order to operate clinics and hotlines because it had too few staff on duty to cover the county.

Many of the concerns appear to be supported by evidence gathered in a Guardian investigation that has drawn on data from computer records, drivers' logs, internal correspondence and interviews with several sources connected with different parts of the Serco operation in Cornwall who have asked to remain anonymous.

Serco has also confirmed some of the allegations. But it denies that the service is unsafe and says it is acting within the terms of its contract with the local primary care trust, which allows it to adjust waiting time figures according to who was to blame and make "comfort calls" to patients who have waited a long time. It did not comment on the whistleblower reports of how many patients were left waiting to be assessed at its call centre.

The Guardian has learned that the health regulator, the Care Quality Commission (CQC) made an unannounced inspection of the service in April, shortly after it took on responsibility for registering out-of-hours GP services under new rules. It was unclear until then who, if anyone, was able to monitor Serco's performance independently of the primary care trust (PCT) that commissioned it.

Both Serco and the Cornwall NHS PCT vigorously denied that patient safety was ever at risk. They said that the allegations are not new and that the claim that performance data have been manipulated has already been rejected by an independent audit for the PCT. They added that they have been advised that if the CQC had serious or urgent concerns for patients' safety they would have been raised immediately, and that they have not been raised.

The PCT remains confident that the service is adequately resourced and meeting national standards. Bridget Sampson, director of primary care for Cornwall, said: "We are disappointed that rumours still persist around the quality of service provided by Serco. Patient surveys show a high level of satisfaction with the service and an independent audit did not find any evidence of data being changed. The contract provides a value for money, high quality service for patients with equitable access to GP appointments out of hours."

However, critics of the service said they have been pressured to keep quiet and say Serco has launched an investigation of email traffic to see who has leaked information to the press. Serco said any monitoring of emails was within the law and was to protect patient confidentiality.

Dr Gareth Emrys-Jones, a retired BMA council member and former chair of the GP co-operative that used to run the out-of-hours service for Cornwall as a not-for-profit company, was one of several people who contacted the CQC.

"I have been approached by a significant number of people representing all classes of employees at Serco who felt unable to whistleblow directly but who perceived the service to be unsafe because of a lack of clinicians and inadequate cover for the needs of the patients of Cornwall," he said. "They have cited incidents where it appears that data has been altered in order to achieve compliance with quality standards that they knew had been missed. These related to an extended time period and were not one-off incidents. I was concerned for the staff and for the service because if the allegations are true it would have serious implications."

The CQC investigation comes as the NHS undergoes radical restructuring now that the government's controversial health and social care bill has been passed.

Under coalition policy, all 52 newly formed PCT clusters in England are required this year to identify at least three of their community services to put out to competitive tender in a process that will lead to a rapid increase in private sector involvement in the NHS. Serco, which generated revenue of £4.6bn in 2011, is likely to bid for many of the NHS contracts.

Serco first won the Cornwall contract in 2006 with a bid that valued it at approximately £6.1m a year over five years. It was awarded a further five-year contract last October, valued at £6.4m a year. The out-of-hours service had previously been run by a company set up by a co-operative of local GP practices for a cost of approximately £7.5m a year.

Staff allege that shifts for doctors and nurses have repeatedly been unfilled in the past few months, so that target times for visiting the sickest patients at home have been missed repeatedly.

They claim that staff shortages in the call centre — where patients' calls are first received and their urgency is assessed in a return call by a clinician as part of a "triage" stage – have resulted in long queues building up.

They also allege that clinicians have been pressed to downgrade the priority of calls when assessing them because there are not enough doctors available to make home visits. To deal with the queues, GPs allocated to home visits have repeatedly been pulled in from being out on the road to triage phone calls in the call centre instead.

On 28 January patients queuing for a triage phone call faced waits of up to four hours at some points, they say. Staff have alleged that on the Thursday before Easter more than 50 calls were waiting for triage for part of the evening.

On Good Friday, a long wait built up for out-of-hours clinic appointments and the only slot available for some patients meant a one and a half hour drive across the county, they said. On Easter Saturday they alleged staff shortages led to more than 90 calls building up in the queue for triage during the evening. Serco did not comment on the allegations about queue lengths.

Staff also said that the target times for patients to be seen by a clinician are repeatedly missed.

Once patients have been assessed, they are allocated a priority depending on how urgent their case is. They are then given either a clinic appointment if they are able to travel, or a home visit, in under one hour, two hours or six hours, according to their need.

On 14 February, they say, because shifts were unfilled, a clinician who had been assigned to home visits for the Penzance area had instead to cover for clinics in two areas for part of the night and for the home visits for two other additional areas while another clinician was called off the road to triage calls.

Several calls waiting for urgent home visits in under two hours missed their target that night. A distressed terminally ill cancer patient who had been warned on calling the service that no GP would be available for up to six hours had to wait for nearly seven hours to be seen. The GP who visited the patient's home allegedly said he was the only doctor available for home visits for the whole county west of Bodmin.

Correspondence seen by the Guardian suggested that another GP believed he was in a similar position on a different night last year. Further correspondence reveals that senior clinicians have repeatedly expressed concern to Serco management about staff shortages jeopardising the safety of the service.

Serco rejected any allegations that just one or two GPs were covering the whole of the county on any occasion. It said that the contract does not dictate how many GPs should be on the road.

"Serco employs a range of skills across Cornwall to meet patients' needs and the PCT's requirements. These include nurse practitioners, emergency care practitioners and GPs. It is typical to use a range of roles to provide out-of-hours services and there is no service requirement for Serco to supply all cars, clinics or the call centre solely with GPs."

Serco pointed out that a national benchmarking exercise looking at data from 104 PCTs found Serco's out-of-hours service to be one of the best performing in the country. (The exercise was conducted by the Primary Care Foundation, a business consultancy that counts Serco and the Department of Health among its clients and was based on data for the financial year 2010-2011 supplied by the services themselves.)

Sources also alleged that calls that are in danger of not meeting their targets have been retriaged to "start the clock" again. On 25 February a call logged at 9.34am, and triaged at 9:37am, was given a home visit time of "before" 3.37pm. When it became clear that the target time could not be met the call was retriaged with a call at 3.12pm, completed at 3.16pm. A new target time of 9.16pm was then allocated to the visit, it is alleged.

Sue Matthews, regional officer for the Royal College of Nursing in Cornwall, said: "I have expressed concerns to Serco management on a number of issues. Our members have reported waiting hours being extended by several hours, and that the current reporting system is being manipulated so that it does not reflect accurate activity or the time of visits or callback times."

Serco said it recognised the example the Guardian gave on 25 February and had reported the matter to the PCT after an internal audit, "indicating that the call had failed". The company stated that "calls back to patients are only made when Serco believes it may exceed the timeframes set by the Department of Health, and they are deemed 'comfort calls' rather than retriages and are made to assess if conditions have worsened or improved to ensure patient safety is not compromised."

Among the most serious allegations being investigated by the CQC are that Serco management altered logs tracking response times and targets. The PCT said that its audit found no evidence of this and showed that the systems used by Serco would not allow data to be altered after the fact.

Computer logs, seen by the Guardian, of data-tracking calls to the service and response times measured daily and weekly against targets, show one set of figures at the end of 12 February for the number of calls meeting or failing to meet targets in various priority categories on 11 and 12 February. But different figures for the same dates appear in the log as displayed on 15 February.

The effect of the altered figures is to remove some of the "red" failed targets and make them "green" achieved targets, and to alter the percentage of targets met in other categories.

Explaining the apparent discrepancy in figures, Serco said that it "audits all calls daily to understand areas in which issues are highlighted and where these may have fallen outside its control, including where a patient is deemed to have caused delay. Such cases are then reported to the PCT and changed accordingly on the internal management systems." This enables the company to give the PCT two reports, one with figures that include "cases where patients have caused delays" and one without. This promotes greater transparency and does not constitute the wrongful alteration of data, it said.

Among those who have reported the service to the CQC are Sarah Newton, Conservative MP for Truro and Falmouth and Andrew George, Lib Dem MP for St Ives. "The out-of-hours service provides GP services for two-thirds of the full week," said George. "People don't just fall ill during surgery opening hours. There has been a pattern of complaints and concerns that have come to me particularly over the last year that give rise to question over the safety of the service alongside other information that suggests the service is being run on the very margins of what is clinically safe.

"I have contacted the PCT and Serco but the concerns have continued, which is why I have blown the whistle to the CQC to get the issues properly investigated." Newton said she contacted the CQC after receiving concerning reports from her constituents.

Serco rejected any suggestion that clinicians were under pressure to downgrade calls and said that it met all required standards. "All staff have been trained to prioritise cases individually and as per the clinical judgment of the clinician. In addition, Serco uses decision-support software to ensure consistency of triage and prioritisation.

"Serco has consistently achieved the target times for home visits. For January 2012 Serco reported that 97.5% of patients were seen face to face by a clinician within the Department of Health timeframes. For 11 Febrary, 88.37% of patients were seen face to face by a clinician within the timeframes. On 14 Febrary, there were four GPs covering west Cornwall until midnight.

"The area was also fully staffed after this time until 8am the following day. The contract requirement is for the service to be able to respond to patients' needs within set timeframes and does not dictate car allocations across the county."

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