A Field Guide to Sars-CoV-2
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A Field Guide to Sars-CoV-2 Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen
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A Field Guide to Sars-CoV-2
- 1. A Field Guide to Sars-CoV-2 Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
- 2. A Field Guide to Sars-CoV-2 Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
- 3. Obsessed with Microbes for a Long Time
- 4. Also a bit obsessed with birds …
- 5. The Story of a Bird
- 6. 2004 Bird Sighting photo by J. Eisen
- 7. photo by J. Eisen 2004 Bird Sighting
- 8. People Got Excited photo by J. Eisen
- 9. What Bird Is This?
- 10. Field Guide to the Birds of North America photo by J. Eisen
- 11. Field Guide to the Birds of North America photo by J. Eisen
- 12. Field Guide to the Birds of North America photo by J. Eisen
- 13. iBird photo by J. Eisen
- 14. Get Some Help With ID - Taken Wednesday in my yard
- 16. AI System Suggests ID Based on Location
- 17. AI System Suggests ID Based on Location
- 19. Help with ID
- 20. Back to the Bird …
- 39. ! 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
- 40. We Need A Field Guide to the Microbes MICROBES
- 41. Components of a Field 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
- 42. Many Challenges
- 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: Diversity of Form
- 45. Challenge III: Diversity of Functions The Bad The Good The Unusual The Consumable The Burnable The Planet
- 46. Challenge IV: Evolutionary Diversity Viruses Bacteria & Archaea Fungi Other Eukaryotes
- 47. Challenge V: Microscale Localization 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 Challenge VI: Collecting Data The Great Plate Count Anomaly Appearance Not A Good Indicator of Type, Function
- 49. MICROBES We Need A Field Guide to the Microbes
- 50. MICROBES CRAZY We Need A Field Guide to the Microbes
- 51. <<<< Culturing Observation Count Count DNA/RNA Analysis is a Solution to Some Challenges DNA
- 52. Science Solution I: DNA Sequencing
- 53. Other Science Solutions: Other Advances
- 54. MICROBES LESS
- 55. Talk for Yolo County Community of Practice February 9, 2022 Jonathan A. Eisen @phylogenomics University of California, Davis
- 58. January 30, 2020 - The Lance https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 59. MICROBES
- 60. Family Tree of Novel Virus NEW https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 61. Family Tree of Novel Virus NEW What Does This Tell Us? https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 62. Family Tree of Novel 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 of Novel 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 of Novel 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
- 72. Family Tree of Novel 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 of Novel 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 an RNA virus https://media.hhmi.org/biointeractive/click/covid/index.html
- 75. SARS-CoV-2 is a Coronavirus https://media.hhmi.org/biointeractive/click/covid/index.html
- 77. Coronaviruses cause colds & respiratory infections https://media.hhmi.org/biointeractive/click/covid/index.html
- 78. Predicting SARS-CoV-2 Virus Biology • 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 of Novel 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 of Novel 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 of Novel 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
- 83. Family Tree of Novel Virus How Was This Made? https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930251-8
- 84. Genome ~30,000 nucleotides long https://media.hhmi.org/biointeractive/click/covid/index.html
- 85. Genome made up of four different bases (AUCG) https://media.hhmi.org/biointeractive/click/covid/index.html
- 86. Genome gets copied inside 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 of mutations https://media.hhmi.org/biointeractive/click/covid/index.html
- 89. Evolution - different forms of virus can have https://media.hhmi.org/biointeractive/click/covid/index.html
- 90. Evolution - different forms of virus can have https://media.hhmi.org/biointeractive/click/covid/index.html
- 91. Evolution - different forms 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 S ACUGCACCUAUCGUUC 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 vertebrates have 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
- 97. NextStrain
- 102. An Hour Ago …
- 103. Attempt at Another Live Demo? https://clades.nextstrain.org
- 104. NextClade Allows Analysis of Your Data
- 105. NextClade Demo
- 106. Epidemiology
- 107. Epidemiology
- 108. NY Times Coronavirus Variant Tracker https://www.nytimes.com/interactive/2021/ health/coronavirus-variant-tracker.html
- 109. NY Times Coronavirus Variant Tracker
- 110. NY Times Coronavirus Variant Tracker
- 111. NY Times Coronavirus Variant Tracker
- 112. NY Times Coronavirus Variant Tracker
- 113. Detection
- 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 Baselineis defined 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 identifies key 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 genotyping during PCR https://www.bioline.com/media/wysiwyg/pdf/ppt/PCR_Based_SNP_Genotyping_Assay.pdf
- 119. Wastewater SARS-CoV-2 Sampling Spreading See also https://microbe.net/tag/wastewater/
- 120. Monitoring wastewater to inform COVID-19 public health Slide from Heather N. Bischel
- 121. Example Data from Wastewater Monitoring https://healthydavistogether.org/wastewater-testing/ Slide from Heather N. Bischel
- 122. Air filter sampling Slide from David Coil
- 123. Air filter pilot for school •-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 A Field Guide to the Microbes
- 125. MICROBES NOT
- 126. • Heather Bischel • UC Davis • Healthy Davis Together • Eisen Lab • CDC Spheres Group • Epitwitter Community • Many others