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Merino had been in office for less than a week, after Peru's Congress voted last Monday to remove Martin Vizcarra as president over bribery allegations, which he denies. Lawmakers met late on Sunday afternoon to determine who should be the country's next president, or at least, how he or she might be chosen.
In a televised speech at midday, Merino, the former head of Congress who had led the push to impeach Vizcarra, asked his Cabinet to remain in place to assist in the transition. He said his resignation was "irrevocable" and called for "peace and unity."
Peruvians poured onto the streets on Sunday afternoon to celebrate Merino's departure, waving flags, chanting and banging pots. But the announcement nonetheless plunges Peru deeper into uncertainty and legal disarray as lawmakers now wrestle with who will take his place.
Thousands in Peru had staged some of the country's largest protests in decades - mostly peaceful but increasingly marred by clashes - since Congress voted to remove Vizcarra as president.
Just minutes before Merino announced he would step down, Congress president Luis Valdez said all of the country's political parties had agreed he should resign. If he declined, Valdez said, lawmakers would launch impeachment proceedings.
The latest political shakeup comes as Peru, the world's No. 2 copper producer, battles the coronavirus pandemic and what is expected to be its worst economic contraction in a century.
A tense week collapsed into chaos late on Saturday, after mostly peaceful demonstrations grew more intense by nightfall. Two young protesters were killed in clashes, the public ombudsman said. Peru's state medical program, EsSalud, confirmed in a statement two young men had died from gunshot wounds.
Peru's National Human Rights coordinator said 112 people were injured, some after inhaling tear gas, and 41 were still missing. At least nine had suffered gunshot wounds, health officials said.
"Merino has resigned because his hands are stained with blood, with the blood of our children," said Clarisa Gomez, celebrating Merino's departure on the streets of Lima. She said lawmakers who had put him in power should also pay.
Protesters continued to celebrate as night fell across Lima, where a tense calm prevailed as Peruvians awaited a decision by Congress on who would be the next president.
Vizcarra, whose ouster prompted the crisis, called Merino a "dictator" installed by Congress and warned against allowing lawmakers to once again determine who would become Peru's next leader.
"Should those who took these unconstitutional measures be the ones who bring us a solution?" he said to reporters outside his home following Merino's resignation.
He asked instead that Peru's Constitutional Court weigh in immediately on whether or not his own impeachment had been legal. The court shortly after announced it would move a hearing date to Monday from Wednesday this week to fast track arguments in the case.
"I am here to collaborate," Vizcarra said.
The former president, a politically unaffiliated centrist who is popular with Peruvians, has yet to be found guilty of the corruption charges that led to his removal.
FIREWORKS AND TEAR GAS
On Saturday hundreds of mostly young protesters unveiled a massive Peruvian flag and sang the national anthem in Lima's central Plaza San Martín.
But the sprawling coastal city soon echoed with sirens, shouts and chants of protesters' demanding Merino's removal as rallies and the police response grew increasingly violent.
Peru's Ombudsman warned on Twitter late Saturday that security forces had begun "misusing force and throwing tear gas without justification" against young protesters who had gathered in the city's center. The agency has demanded an investigation.
"The march is not for Vizcarra to return, it is strictly against Merino. We are tired of corruption, of the usual politicians who divide and impose their personal interests," said César Anchante, a University of Lima graduate who marched in a rally Saturday.
Merino's prime minister earlier on Saturday told reporters that Vizcarra's removal on corruption charges by the opposition-dominated Congress had been legal. He defended it as a "constitutional change."
Merino too had urged calm and promised to hold presidential elections already scheduled for April 11.