Mohammed Abdellatif did not see himself as a political activist. As a dentist in Cairo, his concerns were focused on healthcare and issues such as a lack of medical supplies and low wages for doctors.

Then at 3am one day last September, 50 armed security agents stormed his family home. Abdellatif’s alleged crime was to have launched a social media campaign demanding better pay and conditions for health workers in Egypt. The previous month while working at a public hospital in Giza, he had started the Twitter hashtag “Egyptian doctors are angry”.

His brother, Omar Soliman, described what happened after the state agents entered Abdellatif’s home. “They interrogated him for two hours, then blindfolded him and marched him handcuffed to an undisclosed police building. For nine days he remained blindfolded, handcuffed, not allowed to move or talk, given little food, and remained in the same clothes he was wearing since his arrest.”

Nine years after the mass protests that shook the country and toppled the autocrat Hosni Mubarak, the threat of prison shapes the lives of a generation of Egyptians. An estimated 60,000 political prisoners languish in jail, while the risk of imprisonment looms over even the apolitical, from businesspeople to doctors, lawyers and students.

Activists who forced the end of Mubarak’s almost 30-year reign have been silenced or have fled the country, while the Egyptian authorities have recently begun to target family members of outspoken critics based abroad, raiding homes and detaining at least 28 people.

Since coming to power in a military coup in 2013, President Abdel-Fatah al-Sisi has overseen a broad crackdown on political activity and free speech, detaining journalists, NGO workers and even the mildest critics. Egypt has built at least 19 new prisons since 2011, housing a swath of ordinary citizens such as Mohamed Nassif Mohamed Ghoneim, a tax office employee who was jailed in 2018 for a Facebook comment considered “offensive to the ruling regime, Sisi and the tax authority’s leaders.”

Public dissent on even benign issues is risky: 21 people were arrested for protesting against a rise in ticket prices on the Cairo metro the same year and later imprisoned on terrorism charges.

Facebook Twitter Pinterest Anti-government protests in Cairo in September. Photograph: EPA

Anti-government protests in several cities last September only provoked a further crackdown. At least 4,433 people were arrested, according to the Egyptian commission for rights and freedoms, a Cairo-based NGO. (Egypt’s public prosecutor claimed 1,000 were detained.) Many remain in prison on charges of aiding a terrorist group, protesting illegally, misusing the internet, undermining national security or using social media to spread false news.

Abdellatif, the dentist, was also accused of joining a terrorist group and was added to a mass trial that included many people arrested after the protests in September. “He didn’t see a judge since his arrest. No trial, no judicial process, just pre-trial detention,” said Soliman.

Abdellatif’s lawyer, Mohammed Baqir, was arrested later during a visit to see another imprisoned client, Alaa Abd El Fattah, a prominent activist. Abdellatif has been in prison since September on a pre-trial detention order renewed in 15-day increments.

An activity as simple as shopping for clothes for a job interview was all it took for a 19-year-old student to be arrested in downtown Cairo on 21 September. The student, whose family requested anonymity fearing reprisals, crossed one of the checkpoints that had sprung up around the centre of Cairo after protests the previous day, where security officials searched their phones and social media at random.

“We don’t know where he is being held and no one has told us where he is and what he is accused of,” said his brother. “We filed all kinds of police and reports to the public prosecutor about his disappearance. These were bureaucratic and meaningless. He was just shopping for clothes. Our family is waiting every day for him to return home tomorrow.”

Facebook Twitter Pinterest Security forces block a road leading to Tahrir Square in Cairo in September. Photograph: Khaled Desouki/AFP/Getty Images

The threat of prison has been amplified by increasing reports of deaths in custody. Mustafa Kassem, a US citizen, died in prison last week after a hunger strike in protest at his incarceration. Kassem was detained alongside his brother-in-law while changing money in a shopping centre in a Cairo suburb in 2013 and later given a 15-year sentence as part of a mass trial.

The interior ministry said Kassem received “comprehensive healthcare during his sentence”. The US secretary of state, Mike Pompeo, expressed outrage over Kassem’s “pointless and tragic death” in a meeting with Sisi on the sidelines of a diplomatic summit in Berlin. But some observers accused Washington of failing to push hard enough for his release.

A coalition of Egyptian human rights groups pleaded for the Red Cross to be allowed to inspect the country’s prisons following Kassem’s death, pointing to a toll of 917 prisoner deaths between June 2013 and November last year, “with a drastic increase in 2019”. Egypt’s former president Mohamed Morsi died in prison in June last year after he was repeatedly denied medical care and held in conditions that an independent review by British MPs denounced as torture.

In November, the United Nations voiced fears that thousands more detainees across Egypt may be at risk from gross human rights abuses while in detention. Shortly afterwards, Egypt’s state information service released a video intended to contradict the UN’s statement, showing a visit by government officials to Cairo’s infamous Tora prison, including interviews with detainees.

A select group of journalists were invited to tour the same Cairo prison complex, a site associated with mass incarceration and torture, where they were shown a chef carefully tending to an outdoor barbecue and detainees playing football on a freshly mown pitch in an effort to present a different image of prison conditions.

Facebook Twitter Pinterest Inmates at Tora prison cook for visitors on a guided tour organised by the state information service. Photograph: Mohamed El-Shahed/AFP via Getty Images

“Putting so many people behind bars disrupts social life, it disrupts family life and obviously has an impact on politics – particularly to the extent that the Egyptian state has locked up the very people who were most likely to pursue a peaceful version of politics,” said Andrew Miller, of the Project on Middle East Democracy, a Washington thinktank.

He said mass incarceration on this scale was politically and socially unsustainable. “They are either intentionally or unintentionally empowering the violent actors that remain outside of prison to assume a higher profile within opposition activities,” he said. Egypt’s interior ministry did not respond when contacted for comment.

As Saturday’s anniversary of the protest movement approached, Egyptian security forces made their presence felt once again in downtown Cairo, searching homes at random and demanding to see residents’ details to signal that no protests would be tolerated.

One resident said security officials had marched her from her home to a local police station for a precautionary check in case she was later charged with a crime. “It was traumatising,” she said.