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A Field Guide to Sars-CoV-2
The document presents a field guide to understanding SARS-CoV-2 for the Yolo County community, focusing on microbial diversity, challenges in studying microbes, and the evolutionary relationships among viruses. It discusses the need for a comprehensive approach to identify and analyze microbes, particularly in the context of emerging pathogens and public health. The presentation highlights various methods such as DNA sequencing and wastewater sampling to address challenges in microbial detection and monitoring.
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A Field Guide to Sars-CoV-2
- 1. A Field Guideto Sars-CoV-2 Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
- 2. A Field Guideto Sars-CoV-2 Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
- 3. Obsessed with Microbesfor a Long Time
- 4. Also a bitobsessed with birds …
- 5. The Story ofa Bird
- 6. 2004 Bird Sighting photoby J. Eisen
- 7. photo by J.Eisen 2004 Bird Sighting
- 8. People Got Excited photoby J. Eisen
- 9. What Bird IsThis?
- 10. Field Guide tothe Birds of North America photo by J. Eisen
- 11. Field Guide tothe Birds of North America photo by J. Eisen
- 12. Field Guide tothe Birds of North America photo by J. Eisen
- 13. iBird photo by J.Eisen
- 14. Get Some HelpWith ID - Taken Wednesday in my yard
- 16. AI System SuggestsID Based on Location
- 17. AI System SuggestsID Based on Location
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- 20. Back to theBird …
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- 39. ! Phylogenetic catalogof types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 40. We Need AField Guide to the Microbes MICROBES
- 41. Components of aField Guide • What should be included ! Phylogenetic catalog of types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
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- 43. Challenge I: Small,Hard to Study in Field • Microscope picture • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
- 44. Challenge II: Diversityof Form
- 45. Challenge III: Diversityof Functions The Bad The Good The Unusual The Consumable The Burnable The Planet
- 46. Challenge IV: EvolutionaryDiversity Viruses Bacteria & Archaea Fungi Other Eukaryotes
- 47. Challenge V: MicroscaleLocalization Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https://doi.org/10.1073/pnas.1522149113 Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https:// doi.org/10.1073/pnas.1522149113
- 48. <<<< Culturing Observation Count Count ChallengeVI: Collecting Data The Great Plate Count Anomaly Appearance Not A Good Indicator of Type, Function
- 49. MICROBES We Need AField Guide to the Microbes
- 50. MICROBES CRAZY We Need AField Guide to the Microbes
- 51. <<<< Culturing Observation Count Count DNA/RNAAnalysis is a Solution to Some Challenges DNA
- 52. Science Solution I:DNA Sequencing
- 53. Other Science Solutions:Other Advances
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- 55. Talk for Yolo CountyCommunity of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
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- 58. January 30, 2020- The Lance https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
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- 60. Family Tree ofNovel Virus NEW https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 61. Family Tree ofNovel Virus NEW What Does This Tell Us? https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 62. Family Tree ofNovel Virus SARS MERS NEW What Does This Tell Us? I. Related human pathogens https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 63. Family Tree ofNovel Virus SARS MERS NEW BATS BATS What Does This Tell Us? II. Related animal pathogens https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 64. SARS-CoV-2 Origins /PREDICT Wells et al. 2021
- 65. Family Tree ofNovel Virus SARS MERS NEW BATS BATS What Does This Tell Us? III. Classi fi cation https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
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- 72. Family Tree ofNovel Virus SARS-CoV MERS-CoV SARS-CoV2 BATS BATS What Does This Tell Us? IIIb. Names https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 73. Family Tree ofNovel Virus SARS-CoV MERS-CoV SARS-CoV2 BATS BATS What Does This Tell Us? IV. Predict Biology https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 74. SARS-CoV-2 is anRNA virus https://media.hhmi.org/biointeractive/click/covid/index.html
- 75. SARS-CoV-2 is aCoronavirus https://media.hhmi.org/biointeractive/click/covid/index.html
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- 77. Coronaviruses cause colds& respiratory infections https://media.hhmi.org/biointeractive/click/covid/index.html
- 78. Predicting SARS-CoV-2 VirusBiology • It is useful to know that SARS-CoV-2 is closely related to the viruses that cause MERS and SARS since those have been studied for years • Much known about other coronaviruses but note that SARS- CoV-2 is pre tt y distantly related to those
- 79. Family Tree ofNovel Virus SARS-CoV MERS-CoV SARS-CoV2 BATS BATS What Does This Tell Us? V. Predict Novelty https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 80. Family Tree ofNovel Virus SARS-CoV MERS-CoV SARS-CoV2 BATS BATS What Does This Tell Us? VI. Variation w/in SARS-CoV-2 https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 81. Family Tree ofNovel Virus SARS-CoV2 What Does This Tell Us? VI. Variation w/in SARS-CoV-2 https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
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- 83. Family Tree ofNovel Virus How Was This Made? https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 84. Genome ~30,000 nucleotideslong https://media.hhmi.org/biointeractive/click/covid/index.html
- 85. Genome made upof four different bases (AUCG) https://media.hhmi.org/biointeractive/click/covid/index.html
- 86. Genome gets copiedinside host cell https://media.hhmi.org/biointeractive/click/covid/index.html
- 87. Mistakes in copying= mutations https://media.hhmi.org/biointeractive/click/covid/index.html
- 88. Many kinds ofmutations https://media.hhmi.org/biointeractive/click/covid/index.html
- 89. Evolution - differentforms of virus can have https://media.hhmi.org/biointeractive/click/covid/index.html
- 90. Evolution - differentforms of virus can have https://media.hhmi.org/biointeractive/click/covid/index.html
- 91. Evolution - differentforms of virus can have https://media.hhmi.org/biointeractive/click/covid/index.html
- 92. RNA RNA RNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters SACUGCACCUAUCGUUC G R ACUCCACCUAUCGUUC G E ACUCCAGCUAUCGAUC G F ACUCCAGGUAUCGAUC G C ACCCCAGCUCUCGCUC G W ACCCCAGCUCUGGCUCG SARS-COV2-Phylogeny PCR Seq PCR Seq PCR Seq
- 93. • Skeletons !All vertebrateshave skeletons !The structure of the skeleton differs between species and skeletal comparisons can be used to infer phylogeny • SARS-CoV2 RNA Genome !All SARS-CoV2s have RNA Genome !The sequence of bases in the RNA genomes differ between species and sequence comparisons can be used to infer phylogeny SARS-COV2-Phylogeny vs Skeletons
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- 103. Attempt at AnotherLive Demo? https://clades.nextstrain.org
- 104. NextClade Allows Analysisof Your Data
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- 108. NY Times CoronavirusVariant Tracker https://www.nytimes.com/interactive/2021/ health/coronavirus-variant-tracker.html
- 109. NY Times CoronavirusVariant Tracker
- 110. NY Times CoronavirusVariant Tracker
- 111. NY Times CoronavirusVariant Tracker
- 112. NY Times CoronavirusVariant Tracker
- 113.
- 114. Detection and Quantification •Collect samples • Store samples • Lyse virus • Extract RNA (sometimes skipped) • q RT PCR
- 115. qRT PCR Details •q = quantitative • RT = real time • RT = reverse transcriptase • (sometimes call real time reverse transcriptase PCR) • PCR = polymerase chain reaction
- 116. qRT PCR Details Baselineisdefined as PCR cycles in which a reporter fluorescent signal is accumulating but is beneath the limits of detection of the instrument. ΔRnis an increment of fluorescent signal at each time point. The ΔRn values are plotted versus the cycle number. Threshold is an arbitrary level of fluorescence chosen on the basis of the baseline variability. A signal that is detected above the threshold is considered a real signal that can be used to define the threshold cycle (Ct) for a sample. Threshold can be adjusted for each experiment so that it is in the region of exponential amplification across all plots. Ct is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
- 117. Genotyping • Sequencing identifieskey differences between variants • Develop assay to screen for variants at single positions in the genome (e.g., A vs G) • Can run separately from or simultaneous to qRT-PCR • Advantages: Fast, Cheap • Disadvantages: Limited # of sites. Only screen for known variation.
- 118. Example of genotypingduring PCR https://www.bioline.com/media/wysiwyg/pdf/ppt/PCR_Based_SNP_Genotyping_Assay.pdf
- 119. Wastewater SARS-CoV-2 SamplingSpreading See also https://microbe.net/tag/wastewater/
- 120. Monitoring wastewater toinform COVID-19 public health Slide from Heather N. Bischel
- 121. Example Data fromWastewater Monitoring https://healthydavistogether.org/wastewater-testing/ Slide from Heather N. Bischel
- 122. Air filter sampling Slidefrom David Coil
- 123. Air filter pilot forschool •-2 private schools, 2 public schools as pilot, ~60 Classrooms in total •-2x air filters and 1x floor sample per room Slide from David Coil
- 124. MICROBES We Need AField Guide to the Microbes
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- 126. • Heather Bischel •UC Davis • Healthy Davis Together • Eisen Lab • CDC Spheres Group • Epitwitter Community • Many others