title: Characterizing microscopic and submicroscopic malaria parasitaemia at three sites with varied transmission intensity in Uganda.
abstract: Parasite prevalence is a key metric used to quantify the burden of malaria and assess the impact of control strategies. Most published estimates of parasite prevalence are based on microscopy and likely underestimate true prevalence.
  
  
  
  Thick smear microscopy was performed in cohorts of children (aged 6 month to 10 years) and adults every 90 days over 2 years, at three sites of varying transmission intensity in Uganda. Microscopy-negative samples were tested for sub-microscopic parasitaemia using loop-mediated isothermal amplification (LAMP). Generalized estimating equation models were used to evaluate associations between age and parasitaemia, factors associated with sub-microscopic infection and associations between parasitaemia and haemoglobin.
  
  
  
  A total of 9260 samples were collected from 1245 participants. Parasite prevalence among children across the three sites was 7.4, 9.4 and 28.8 % by microscopy and 21.3, 31.8 and 69.0 % by microscopy plus LAMP. Parasite prevalence among adults across the three sites was 3.1, 3.0 and 5.2 % by microscopy and 18.8, 24.2 and 53.5 % by microscopy plus LAMP. Among those with parasitaemia, adults and persons recently treated with anti-malarial therapy had the highest prevalence of sub-microscopic infection. Children with sub-microscopic or microscopic parasitaemia had lower mean haemoglobin levels compared to children with no detectable parasites.
  
  
  
  Across a range of transmission intensities in Uganda, microscopy vastly underestimated parasite prevalence, especially among adults.
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.
authors.forename: John
authors.initials: J
authors.lastname: Rek
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA. shereen.katrak@ucsf.edu.
authors.forename: Shereen
authors.identifier: 0000-0002-6013-9886
authors.initials: S
authors.lastname: Katrak
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA.
authors.forename: Hannah
authors.initials: H
authors.lastname: Obasi
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.
authors.forename: Patience
authors.initials: P
authors.lastname: Nayebare
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.
authors.forename: Agaba
authors.initials: A
authors.lastname: Katureebe
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.
authors.forename: Elijah
authors.initials: E
authors.lastname: Kakande
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Arinaitwe
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.|School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda.
authors.forename: Joaniter I
authors.initials: JI
authors.lastname: Nankabirwa
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA.
authors.forename: Prasanna
authors.initials: P
authors.lastname: Jagannathan
authors.affiliation: London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Chris
authors.initials: C
authors.lastname: Drakeley
authors.affiliation: London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Sarah G
authors.initials: SG
authors.lastname: Staedke
authors.affiliation: Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Smith
authors.affiliation: Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Teun
authors.initials: T
authors.lastname: Bousema
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda.|School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda.
authors.forename: Moses
authors.initials: M
authors.lastname: Kamya
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Rosenthal
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA.
authors.forename: Grant
authors.initials: G
authors.lastname: Dorsey
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Greenhouse
mesh_terms: D000328:Adult; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D018562:Disease Transmission, Infectious; D005260:Female; D006801:Humans; D007223:Infant; D008288:Malaria / Q000175:diagnosis* / Q000453:epidemiology* / Q000469:parasitology / Q000635:transmission; D008297:Male; D008853:Microscopy; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques; D018512:Parasitemia / Q000175:diagnosis* / Q000453:epidemiology*; D015995:Prevalence; D014454:Uganda / Q000453:epidemiology
keywords: LAMP; Malaria; Parasitaemia; Sub-microscopic infection