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Suppressing SARS-CoV-2 will likely require the rapid identification and isolation of infected individuals, on an ongoing basis. RT-PCR (reverse transcription polymerase chain reaction) tests are accurate but costly, making regular testing of every individual expensive. The costs are a challenge for all countries and particularly for developing countries. Cost reductions can be achieved by combining samples and testing them in groups. We propose an algorithm for grouping subsamples, prior to testing, based on the geometry of a hypercube. At low prevalence, this testing procedure uniquely identifies infected individuals in a small number of tests. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, parallel searches are preferred. We report proof of concept experiments in which a positive sample was detected even when diluted a hundred-fold with negative samples. Using these methods, the costs of mass testing could be reduced by a factor of ten to a hundred or more. If infected individuals are quickly and effectively quarantined, the prevalence will fall and so will the costs of regularly testing everyone. Such a strategy provides a possible pathway to the longterm elimination of SARS-CoV-2. Field trials of our approach are now under way in Rwanda and initial data from these are reported here. * nturok@perimeterinstitute.ca † wndifon@nexteinstein.org . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

Introduction This study aimed to assess the prevalence and associated risk factors of intestinal parasite infections among children less than two years of age in Rutsiro, Rwanda. Methods A cross-sectional parasitological survey was conducted in Rutsiro in June 2016. Fresh stool samples were collected from 353 children and examined using microscopy to detect parasite. A questionnaire was administered to collect data on hygiene, sanitation, socio-demographic and economic characteristics. Results Approximately one in two children (44.8%) were found to be infected with at least one intestinal parasite. Ascaris (28.5%) was the most prevalent infection followed by Entamoeba histolytica (25.95%) and Giardia lamblia (19.6%). Infection with more than one pathogen was noted e.g. presence of Ascaris and yeasts (8.9%), and amoeba with Trichocephale (4.4%), respectively. Children from non-farming families were less likely to be at risk of intestinal parasite infections (AOR = 0.41, p = 0.028) compared to children from farming families. Children from households with access to treated drinking water were less likely to contract intestinal parasite infections (AOR = 0.44, p = 0.021) compared with those who used untreated water. Children from families with improved sources of water were twice as likely to be diagnosed with intestinal parasitoses compared to those who did not. We postulate that the majority of families (50.1%) who have access to improved water sources do not treat water before consumption. Conclusion The high prevalence of intestinal parasitoses in children warrants strict control measures for improved sanitation, while treatment of drinking water should be considered.