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Development of Low Cost Two-Step Reverse Transcription-Quantitative Polymerase Chain Reaction Assays for Rotavirus Detection in Foul Surface Water Drains

Abstract

Commercial kits to determine RNA concentrations are expensive, and sometimes too expensive for laboratories working with tight budgets, especially those in developing countries. We developed, tested, and evaluated two home-made two-step reverse transcription-quantitative polymerase chain reaction assays aimed to detect rotavirus in surface water samples. A commercial one-step master kit was used for comparison. Our results indicated that the efficiency of the home-made assays was comparable to the commercial kit. Furthermore, the lowest detection limit of all assays corresponded to 10−0.2 TCID50 (50 % tissue Culture Infective Dose) per ml. The home-made assays were able to detect rotavirus concentrations in complex surface waters in a slum area in Kampala (Uganda) and their performance was comparable to the commercial kit. The total costs of the two home-made assays was 11 times less than the selected commercial kit. Although preparing home-made assays is more time consuming, the assays can be useful for cases in which consumable costs are more important than personnel costs.

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Acknowledgments

This research has been carried as part of research that was funded by the Korean Church of Brussels, Mangu Jeja Church, Seoul, Korea, and the Netherlands Ministry of Development Cooperation (DGIS) through the UNESCO-IHE Partnership Research Fund. It was carried out in the framework of the research project “Addressing the Sanitation Crisis in Unsewered Slum Areas of African Mega-cities” (SCUSA).

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Correspondence to J. W. Chung.

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Chung, J.W., Foppen, J.W. & Lens, P.N.L. Development of Low Cost Two-Step Reverse Transcription-Quantitative Polymerase Chain Reaction Assays for Rotavirus Detection in Foul Surface Water Drains. Food Environ Virol 5, 126–133 (2013). https://doi.org/10.1007/s12560-013-9111-7

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  • DOI: https://doi.org/10.1007/s12560-013-9111-7

Keywords

  • Rotavirus
  • RT-qPCR
  • Surface water
  • Slums
  • Kampala
  • Uganda