Acanthamoeba spp., is a common and widely spread free-living amoeba (FLA) found in various ecological environments (Carnt, Minassian et al. 2023, Megha, Sharma et al. 2023), such as air, dust, soil, water, plant surfaces, and sewage samples (Landell, Salton et al. 2013, Rayamajhee, Willcox et al. 2022). It has two life cycle stages: the cyst stage (resistant form) and the trophozoite stage (active form) (Khan 2006). The morphology of this parasite varies depending on the group classification based on characteristics of stellate endocysts, separated ectocysts, polymorphic endocysts with arms, wrinkled ectocysts, round endocysts without arms, and smooth ectocysts (Schönborn 1989, Saberi, Nakhaei et al. 2022).

There are 23 different genotypes of Acanthamoeba spp. identified to date (Putaporntip, Kuamsab et al. 2021), with T4 being the most abundant genotype among patients and environments (Lanocha, Kosik-Bogacka et al. 2009, Niyyati, Lorenzo-Morales et al. 2009, Siddiqui and Khan 2012) .This amoeba is known to cause granulomatous amebic encephalitis (GAE), amoebic keratitis (AK), skin infection, and occasionally respiratory infection (Sütçü, Aktürk et al. 2018, Kofman and Guarner 2022, Rayamajhee, Willcox et al. 2022). It is also considered a nosocomial infection and can act as a reservoir or Trojan horse for some pathogenic bacteria, viruses, and fungi (Henriquez 2009, Hajialilo, Rezaeian et al. 2019). Bacterial endosymbionts may increase the pathogenicity of Acanthamoeba, which can remain in the cyst form and resist harsh environmental conditions (Iovieno, Ledee et al. 2010).

Acanthamoeba spp., may colonize asymptomatically in the respiratory tract and play a role as a transporter for pathogens (Henriquez 2009, Bradbury, French et al. 2014). With the emergence of SARS-COV-2, there is a need to investigate parasitic infections in addition to other chronic respiratory disorders (CRD). The respiratory tract and oral cavity are the passage and accumulation place for various microorganisms, making Acanthamoeba spp., a potential source of spread to other parts of the body (Niyyati and Rezaeian, 2015, Niyyati et al., 2015, Saberi, Nakhaei et al. 2022). There have been different opinions and assumptions about the transmission of COVID-19 by Acanthamoeba spp., (Baig 2020, Siddiqui and Khan 2020, Muhammad, Siddiqui et al. 2021, Mirabedini, Ahmed Khan et al. 2022),but further investigation is needed.

It is important to study Acanthamoeba spp., in COVID-19 patients due to the presence of endosymbionts, its potential as a nosocomial infection, and the existence of different species in hospital environments. We attempt to compare Acanthamoeba spp., in CRD and COVID-19 hospitalized patients and determine the genotype, bacterial and fungal endosymbionts, and pathogenicity assessment.