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.

Contents

• Introduction: 00:00-01:58
• Introducing environmental surveillance for infectious diseases: 01:58-03:30
• COVID-19 response vs previous environmental sequencing work and how it has prepared people for COVID-19: 03:30-06:18
• The benefits of wastewater screening over clinical testing: 06:18-07:10
• Challenges of wastewater testing: 07:10-09:10
• Monitoring for SARS-CoV-2 variants: 09:10-10:55
• Understanding transmission patterns: 10:55-12:00
• Identifying signs of viral vaccine escape and tracing transmission: 12:00-14:50
• PCR vs NGS techniques for environmental sequencing: 14:50-16:05
• Tips for best practice when conducting environmental sequencing: 16:05-17:50
• Practical results of environmental sequencing data on outbreak suppression: 17:50-20:40
• Investigating mutation rates in the environmental samples: 20:40-23:20
• Emerging techniques in wastewater surveillance: 23:20-25:10
• Developing standard protocols and structure for wastewater surveillance: 25:10-28:20

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