Lightning Talk about Genomics by Nate Grubaugh

Transcript

• 00:00So I'm just going to give a pretty
• 00:03broad overview of some of the
• 00:05stuff that we study in in my group.
• 00:08Obviously we can't get into too much details,
• 00:11but I'd be happy to chat more about it
• 00:13with any of you that might be interested.
• 00:15The, the central aspect of it is how
• 00:18can we use pathogen genomics and and my
• 00:20group primarily works on viruses here.
• 00:23So how can we use virus genomics
• 00:25to answer questions about disease
• 00:28ecology and epidemiology?
• 00:29And to take this a step further is how
• 00:32can we use virus genomics to actually
• 00:34to implement that within public health
• 00:37systems to help provide more detailed
• 00:40information for surveillance programs.
• 00:43So what do I mean by this?
• 00:45There's several different ways
• 00:47in which genomics can be helpful
• 00:50for outbreak investigations for
• 00:53understanding disease ecology.
• 00:55One of the and I'm going to use
• 00:57SARS COV two as some examples here
• 00:59because I feel like a lot of people
• 01:01can relate to this aspect.
• 01:03But to start with see if
• 01:04this works detection.
• 01:05There's this process called metagenomic
• 01:08sequencing where you can take a clinical
• 01:11sample that has that you don't know
• 01:13what the pathogen that is causing it.
• 01:14You can sequence all the nucleic
• 01:16acid that is in there and you can
• 01:18do some bioinformatics to try
• 01:20to figure out like what pathogen
• 01:22might be causing this infection.
• 01:23And indeed, when the,
• 01:25you know,
• 01:26first cases of pneumonia for
• 01:27Wuhan were coming out,
• 01:28it was many genomic sequencing that
• 01:30identified that this was a novel coronavirus.
• 01:33And this is becoming more and more popular
• 01:35to screen undiagnosed fever illnesses,
• 01:38meningitis,
• 01:39encephalitis,
• 01:40these sorts of things that have
• 01:41a better idea of what pathogens
• 01:43are circulating caustic disease.
• 01:45Once we've kind of identified
• 01:47an outbreak that's happening,
• 01:49we can sequence some of the first
• 01:51cases here and what I like to call
• 01:54the snapshot to get a basic idea of of
• 01:56of what is happening in this scenario.
• 01:59So here's just a sort of a cartoon
• 02:01representation of a phylogenetic tree.
• 02:03But if you sequence some of these
• 02:04first cases, you can get an idea like,
• 02:06is this a zoonosis?
• 02:07Is this something that was not
• 02:09circulating in the human population
• 02:11that recently spilled over?
• 02:12Was this something that happened
• 02:14multiple times or one time based on
• 02:17the other viruses that it's related to,
• 02:19we can get an idea of transmission,
• 02:22develop diagnostics, these sorts of things,
• 02:25some really basic information that
• 02:27could be helpful for an immediate
• 02:29public health response.
• 02:31And taking this another step further,
• 02:33you can also do very dense sequencing
• 02:36of outbreaks this year showing from
• 02:38like a long term care facility where
• 02:40if you sequence a lot of the different
• 02:43cases that were occurring there,
• 02:44you can get information about how
• 02:46are the residents getting infected,
• 02:48Are they getting infected from
• 02:50the skilled nurses or other sort
• 02:52of employees they're bringing it
• 02:53from the community?
• 02:54Is there transmission actually
• 02:56within these facilities?
• 02:58We actually did this for Star School
• 03:00Week 2 with the National Basketball
• 03:01Association and the NFL to help
• 03:03them monitor their protocols.
• 03:05So when they have outbreaks and teams,
• 03:07are these caused by team meetings
• 03:09or is this caused by you know the
• 03:11players and coaches and staff getting
• 03:13infected in their communities
• 03:15and and everybody bringing it in.
• 03:17Then on a bigger level you can use
• 03:20sequencing and and phylogenetics
• 03:21to understand patterns of spread.
• 03:23So on the bacterial side of things
• 03:26you can look for the emergence
• 03:28and spread of drug resistance.
• 03:30For viruses like SARS, COV two,
• 03:32we can look to see patterns of human
• 03:34movement and how they relate to
• 03:35viruses that are are are spreading.
• 03:39And so there is some fundamental aspects
• 03:41of this of of virus evolution that
• 03:43allows us to do these types of work.
• 03:45So we start here at the bottom,
• 03:47this is where we want to get to
• 03:49where these dots here are sequence
• 03:51samples and each of these nodes
• 03:53that connect them are an inferred
• 03:55ancestor at some point in time.
• 03:56And for you know epidemiology we we
• 03:59want to have that time aspect of things.
• 04:01So not only can we estimate like where
• 04:04this ancestor might have occurred,
• 04:06we want to know when did that occur.
• 04:08And to do that we have to know a little
• 04:10bit about the evolution of the pathogen.
• 04:12So here you have a virus that
• 04:14starts with some sort of error prone
• 04:17replication within a host and as
• 04:19it transmits between host,
• 04:21there's these bottlenecks that
• 04:22randomly select for some of the
• 04:24viruses that go on to the next person.
• 04:26And when you track these over time,
• 04:28there's almost like this clock like
• 04:30evolution where there's a semi
• 04:32predictable amount of change that
• 04:34is happening over time and which
• 04:36you can use to then help scale your
• 04:38phylogenetic tree.
• 04:39So in this situation where you have
• 04:41an outbreak at location D,
• 04:43you can estimate when that outbreak
• 04:45happened as well as determined that
• 04:46this was caused by multiple interactions.
• 04:51Here are some of the systems we primarily
• 04:54study tick and mosquito borne viruses.
• 04:56We like to study them across different
• 04:59sort of complexities in their ecology here
• 05:01with with a tick borne virus blossom that
• 05:04is the host is small mammals and then we
• 05:07have mosquito borne viruses like Eastern
• 05:10equine encephalitis virus in West Nile
• 05:13that are where their hosts are birds.
• 05:16In both these cases humans would
• 05:18be dead end hosts so they're not
• 05:20contributing to onward transmission.
• 05:22And then you have things like Dengue virus
• 05:23and Zika virus where the hosts are humans.
• 05:25And if you think about just some basic
• 05:27differences in the ecology here,
• 05:28right here, we have very low potential for
• 05:31it to move between locations very fast.
• 05:35Right Now you add some wings to the
• 05:36system and they can spread a lot further.
• 05:39And here we have, you know,
• 05:39humans and you have planes and things
• 05:41can get around the world quite quickly.
• 05:45So here's just a plug if you
• 05:47are interested in some of this.
• 05:48I do teach a class on genomic
• 05:51epidemiology with a very much a focus
• 05:53on how to apply this for public health.
• 05:56There's there's not necessarily any
• 05:58prereqs needed for it other than
• 06:00a basic understanding of molecular
• 06:02biology and and microbiology that
• 06:03hopefully you're getting from within
• 06:05this program or from previous education.
• 06:07But I do want to know if you
• 06:10are interested in this.
• 06:11I'm probably not going to offer it
• 06:13in spring of 2025 as long as my
• 06:16sabbatical approval or gets approved.
• 06:18So I would suggest taking it this
• 06:22spring and here is my information
• 06:24if you want to get a hold of me.
• 06:26Thank you.