In this episode, we explore the often overlooked technique of environmental sequencing for infectious diseases and how it is being applied to the response to COVID-19. Taking the state of California as a case study of this application, I speak to Micheal Lisek, Project Manager Environmental Microbiomics at Zymo Research Corp. Micheal outlines the basis of environmental sequencing, predominantly the screening of wastewater for signs of viral RNA, the key techniques involved in the process and challenges associated with it. Micheal also explains the key pieces of information that can be obtained by environmental sequencing and the benefits of the approach vs exclusively using clinical testing. Micheal highlights the value of environmental sequencing for monitoring variants, understanding transmission patterns and identifying outbreaks, providing examples of the information provided to the public health officials in California that were used to successfully manage rising infections and limit the impact of a surge in cases.ContentsIntroduction: 00:00-01:58Introducing environmental surveillance for infectious diseases: 01:58-03:30COVID-19 response vs previous environmental sequencing work and how it has prepared people for COVID-19: 03:30-06:18The benefits of wastewater screening over clinical testing: 06:18-07:10Challenges of wastewater testing: 07:10-09:10Monitoring for SARS-CoV-2 variants: 09:10-10:55Understanding transmission patterns: 10:55-12:00Identifying signs of viral vaccine escape and tracing transmission: 12:00-14:50PCR vs NGS techniques for environmental sequencing: 14:50-16:05Tips for best practice when conducting environmental sequencing: 16:05-17:50Practical results of environmental sequencing data on outbreak suppression: 17:50-20:40Investigating mutation rates in the environmental samples: 20:40-23:20Emerging techniques in wastewater surveillance: 23:20-25:10Developing standard protocols and structure for wastewater surveillance: 25:10-28:20 Hosted on Acast. See acast.com/privacy for more information.

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