Demonstrations took place in several other cities, including Guayaquil, the epicenter of Ecuador's health crisis, where union leaders said hundreds marched through the city.
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The flower industry has already lost an estimated $8.5 billion due to the coronavirus.
Mortuaries, funeral homes and hospital services are overwhelmed, and Mayor Cynthia Viteri said the actual death toll from the virus is likely much higher than the official national figure of 369.
Ecuador said police have removed almost 800 bodies in recent weeks from homes in Guayaquil, the epicentre of the country's coronavirus outbreak, after the disease overwhelmed emergency services, hospitals and funeral parlours.
Authorities in the Pacific port city say they've received a donation of 1,000 pressed cardboard caskets from local producers, and delivered them for use in two local cemeteries.
Vice President Otto Sonnenholzner seeks forgiveness from people as police collect at least 150 bodies from streets and homes in the most populous city Guayaquil.
A joint military and police task force sent out to gather corpses in the horror-struck port city collected 150 bodies in just three days, government spokesman Jorge Wated said.
The race, known as "Llamingada" takes place every year in Llanganates National Park to raise awareness among indigenous communities about the importance of the park's care.
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