The Malaria virus is transmitted through the Anopheles mosquito whereas Zika virus, Dengue fever, Yellow fever and Chikungunya are transmitted through the Aedes mosquito.
Both mosquitoes reproduce itself in stagnant water.
Most risk of infection is the the early morning or late afternoon hours.
Cases of Malaria, Dengue fever and Chikungunya around Manaus had come down and there had been no cases of Yellow fever reported the recent years.
So far there have been reported less then 100 cases of Zika Virus in Manaus and none in the tourist areas.
On our tour we operate in black water Eco-systems as on the Rio Negro or Rio Juma. The water is acid and therefore very few mosquitoes are found. Further on the lodges are equipped with mosquito nets and repellent is recommended.
Malaria treatment is available in all medical stations in the Amazon.
Yellow fever vaccination is required for entering Brazil.
So far there is no vaccination against Zica virus, Dengue and Chikungunya, but the Brazilian government is working on it.
From my own experience I had 2 times Malaria and 1 time Dengue fever, the sensation is similar to a flu, with fever and body pains.