Rivers in the Brazilian Amazon region have risen to near record levels after heavy rains, flooding small towns and threatening areas hit hard by Covid-19 with another disaster.

In Amazonas state, 52 of the 62 towns and cities have areas under water, and 25 have declared a state of emergency including the capital, Manaus. About 410,000 people have been affected, according to the civil defence service.

In Manaus, the Negro river is at its third-highest level since records began in 1920, at 29.72m (97ft). Brazil’s geological service expects the waters to reach 30.35m, exceeding the record flooding seen in 2012.

Raised wooden walkways for pedestrians have been erected in parts of the city centre, and local officials say they will set up barricades with sand bags to try to contain the waters. The houses of 4,200 people have been flooded across the capital.

The increased precipitation in the region is linked to La Niña, a phenomenon where cooler-than-normal surface temperatures in the Pacific Ocean lead to significant weather changes in different parts of the world.

The town of Anamã, with a population of 12,700, has been totally flooded by the Solimões river. Boats and canoes have become the only way to get around the so-called “Venice of Amazonas”.

Like most residents, Manoel de Oliveira Cardoso and his wife, Eliana dos Santos Madi, have built wooden structures so they can walk around the flooded rooms of their house.

“Look at the state of my house, half flooded, I’ve got nowhere to keep my things,” he told Reuters news agency. “I’m struggling to see if I can salvage at least half of my things.”

As Anamã experiences inundations almost every year, some of the houses have a second level where people move their belongings in case of severe flooding. Others are built on wooden poles to keep them above the river level, known locally as palafitas.

The Solimões and Negro rivers are the main branches of the Amazon river, which has flooded the towns of Parintins and Itacoatiara. In Manacapuru, crops were destroyed.

Meanwhile, cases and deaths related to Covid-19 were rising again in the state amid a slow rollout of vaccines and lack of co-ordinated measures to curb the spread of the virus, according to the Fiocruz Amazonas institute.

By boat, Neuda Sousa, a local health worker, carried a box of Oxford-AstraZeneca jabs to vaccinate residents in flooded areas.

Manaus and nearby areas reported the first cases of a highly contagious variant of Covid-19 that has spread throughout Brazil, one of the countries hardest hit by the pandemic. Earlier this year, the city’s health system collapsed, with hospitals running out of oxygen amid a steep rise in infections.

There are now fears Amazonas state could face a devastating third wave.