Donald Trump's partial government shutdown is over, but the haunting effects are not.

Perhaps nowhere is that demonstrated more than in the Internal Revenue Service (IRS), one agency that affects all Americans.

Listen to the words of advocate Nina Olson, an independent official within the IRS. Her latest report describes an agency with a "shocking" level of service, suffering a "cycle of frustration," and one beset with long-standing problems made worse by the 35-day partial shutdown.

She described an agency so damaged that taxpayer trust and confidence in our tax system have been crippled.

"It is irresponsible for an agency that touches all aspects of people's lives to be underfunded, understaffed, and at the mercy of shutdowns," she wrote. "It is making strategic decisions that ultimately burden taxpayers, increase its own rework, and create distance and distrust between taxpayers and the tax agency, thereby undermining voluntary compliance."

Trump shuts down US government over Mexico border wall – in pictures Show all 15 1 /15 Trump shuts down US government over Mexico border wall – in pictures Trump shuts down US government over Mexico border wall – in pictures Federal workers and contractors rally against the partial federal government shutdown Getty Images Trump shuts down US government over Mexico border wall – in pictures The US Capitol on the first morning of a partial government shutdown in Washington EPA Trump shuts down US government over Mexico border wall – in pictures Federal workers and contractors rally against the partial federal government shutdown Getty Trump shuts down US government over Mexico border wall – in pictures President Trump speaks with children who called the North American Aerospace Defense Command Santa tracker in the State Dining Room of the White House. He earlier in the day, tweeted that he was 'all alone in the White House' waiting for Democrats to make a deal on border security EPA Trump shuts down US government over Mexico border wall – in pictures Furloughed federal workers pick up free food at a pop-up store of Kraft Heinz Getty Images Trump shuts down US government over Mexico border wall – in pictures Hundreds of federal workers and contractors rally against the partial federal government shutdown Getty Trump shuts down US government over Mexico border wall – in pictures A pedestrian walk past the U.S. Capitol ahead of a possible partial government shut down in Washington, U.S., December 20, 2018. REUTERS/Joshua Roberts JOSHUA ROBERTS Reuters Trump shuts down US government over Mexico border wall – in pictures From left, House Majority Leader Steny Hoyer, Senate Minority Leader Chuck Schumer, Sen. Dick Durbin and Speaker of the House Nancy Pelosi walk to speak to reporters after meeting with President Donald Trump about border security in the Situation Room of the White House. Trump declared he could keep parts of the government shut down for "months or even years" as he and Democratic leaders failed in a second closed-door meeting to resolve his demand for billions of dollars for a border wall with Mexico Evan Vucci AP Trump shuts down US government over Mexico border wall – in pictures Federal workers and contractors rally against the partial federal government shutdown Getty Images Trump shuts down US government over Mexico border wall – in pictures A sign alerts visitors to the closure of the National Archives on the fifth day of a partial government shutdown EPA Trump shuts down US government over Mexico border wall – in pictures Hundreds of federal workers and contractors rally against the partial federal government shutdown Getty Images Trump shuts down US government over Mexico border wall – in pictures Visitors read signs announcing the closure of the White House Visitor Center EPA Trump shuts down US government over Mexico border wall – in pictures President Donald Trump speaks during a round-table discussion on border security and safe communities with State, local, and community leaders in the Cabinet Room of the White House Getty Images Trump shuts down US government over Mexico border wall – in pictures A sign alerts visitors to the closure of the White House Visitor Center on the first day of a partial government shutdown EPA Trump shuts down US government over Mexico border wall – in pictures Furloughed federal workers show their IDs for entering a pop-up store of Kraft Heinz Getty Images

The report provided a slew of statistics demonstrating the depth of the problem. For the last week of the shutdown, ending 26 January, 12.8 per cent of taxpayer calls on instalment agreements and balance-due questions were answered. Those that were answered waited 93 minutes. The day before the shutdown stopped, the IRS had:

"Over 5 million pieces of mail that had not been batched for processing."

"80,000 responses to FY 2018 Earned Income Tax Credit audits that had not been addressed."

"87,000 amended returns waiting to be processed."

Metrics like these "translate into real harm to real taxpayers," Ms Olson said. "And they represent increased rework for the IRS downstream, at a time when the IRS is already resource challenged."

IRS officials responded with a statement that said the agency "successfully reopened operations following the shutdown, and the agency is seeing a good start to the 2019 filing season.

It added: "We are continuing to assess the impact of the shutdown on our various operations across the agency and remain proud of the many IRS employees who have risen to the resulting challenges."

The full impact of the shutdown will not be known for "months, and even years, down the road," Ms Olson predicted.

She praised IRS employees who "returned to work with energy."

National Treasury Employees Union (NTEU) president Tony Reardon said "in some cases, employees are being asked to work overtime specifically to get the agency caught up. Orientation for new hires and refresher training for employees is also behind schedule in some areas. These are all signs of an agency still grappling with a record five-week shutdown on the eve of a tax filing season that was already going to be challenging because of the new tax law."

Despite its many difficulties, the IRS remains the lifeblood of the federal government. Tax collectors raise about 93 per cent of the national budget.

They do so on a relative shoestring. The $3.5 trillion (£2.7 trillion) collected in fiscal 2018 was on an $11.43 billion IRS budget, a return on investment of about 300 to 1.

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"I don't know how anyone can read this report," Mr Reardon said, "and not be alarmed at the massive amount of damage that has been done to the agency's workforce and the taxpayers they want to serve."

The damage did not begin with the shutdown. Years of taxpayer-advocate reports, congressional testimony, taxpayer protests and employee complaints have chronicled an agency that suffered at the hands of Republican appropriators who wanted to punish the tax collectors. Republicans charged the IRS with unfairly scrutinising conservative nonprofit organisations under the Obama administration, despite evidence that progressive groups were also scrutinised.

The IRS still has not recovered. The title of the report's list of "Most Serious Problems" is illustrative - "The Taxpayer's Journey."

The problems, which cause "extreme frustration" for taxpayers and employees, include "antiquated technology systems" that if not replaced will "increasingly harm taxpayers and impair revenue collection," according to the report.

Ms Olson also cited agreements between private tax collectors (PCA) and low-income taxpayers "to make payments they cannot afford." Of "taxpayers who made commissionable payments while their debts were assigned to PCAs," she added, "24 per cent had incomes at or below the federal poverty level."

Because of the shutdown, employees estimate "it may take them almost a year to catch up, but many taxpayers cannot wait that long because they need their responses" by 15 April, when 2018 taxes are due, said David Carron, a revenue agent speaking as president of NTEU Chapter 6 covering Louisiana and Arkansas.

"We would relate this to an assembly line that has been stopped for over a month, but the same amount of products have to be produced" by then.