ʻĀina-Informatics Network Spring 2023 Newsletter

Growing the network

 
 

The ʻĀina-Informatics Network expanded over the Spring through mobile lab deployments at 15 schools, welcoming 11 new teachers to the network and 4 new schools. With support from the Hawaiʻi Academy of Science, we also forged new connections with teachers from American Sāmoa, who visited our lab in January with students participating in JSHS. Talofa lava!

Teachers and students from Tutuila, American Sāmoa participated in a mini-training at ʻIolani School while on island for the Junior Science and Humanities Symposium.

AP Biology students from Roosevelt High School - new to our network in 2023 - load an agarose gel.

The ʻĀina-Informatics Network is also honored to have formalized collaborations with the Hawaiʻi Science and Technology Museum on Hawaiʻi Island and STEMworks Hawaiʻi on Maui as new neighbor island community partners this Spring.

Research highlights

A major push this semester for our network was the development of robust protocols optimized for eDNA sequencing of stream water in order to detect rare native species not typically observed in catch surveys. In collaboration with ‘Iolani School's Pa‘ēpa‘ē o Waikolu stream biodiversity monitoring network, AIN began pairing eDNA surveys with catch data in an effort to understand which fish, decapod and arthropod species are most likely to be counted (or not) using each method. A custom bioinformatics pipeline designed to automate clustering and classification of stream eDNA sequences was also developed to produce easy-to-interpret results summaries for each site.

Comparison of fish data generated by University Lab School students using catch vs. eDNA surveys at Ka Papa Lo‘i ‘o Kānewai on May 3. Native fish species in red.

Our Haku Inoa naming campaign for novel lava cave bacterial genomes newly described by ʻĀina-Informatics Network schools is still underway! In addition to three species previously sequenced and named by students, including Paraflavitalea speifideiaquila, we are currently seeking scientific name submissions for five additional novel species. Visit our Lava Cave Microbial Biodiversity Project site to learn more about this collaborative effort between AIN, the University of Hawaiʻi at Mānoa (Drs. Stuart Donachie and Rebecca Prescott), NASA’s Johnson Space Center and the Los Alamos National Laboratory.

Student independent research

AIN also supported several student independent projects this year at various network schools, all of which advanced to the State round. At Kaua‘i High School, two student teams made use of our mobile sequencing lab to analyze eDNA isolated from water sampled from ‘Alekoko Fishpond. The goal of these projects was to characterize phytoplankton and fish populations in the loko i‘a as a baseline survey to support the community's ongoing biocultural restoration efforts.

 

Kauaʻi High School science fair entry utilizing eDNA techniques and bioinformatics pipelines developed by ʻĀina-Informatics this year.

 

At ‘Aiea High School, a student team conducted 16S sequencing of microbial communities in Hālawa Stream at locations above and below the discharge point of treated Red Hill water in search of bacterial bioindicators of environmental impacts. Another student at ʻAiea High School explored genetic methods to classify Wolbachia strain types in local mosquito populations with the support of AIN primers and reagents. Hawaiʻi Preparatory Academy entered multiple student submissions to their district fair for the first time in recent years (also advancing to States!), establishing an in-house MinION sequencing lab supported by the ʻĀina-Informatics Network. Hoʻomaikaʻi to all of our haumāna who participated in science fairs this year!

Teacher professional development

The four teachers from the second cohort of our ʻĀina-Informatics Teacher Fellows program all made significant progress in their classroom implementation of new genome science projects co-developed with AIN instructors.

Johanna Anton (Hawaiʻi Preparatory Academy) - Loading a MinION sequencer as part of multiple soil and plant root microbiome projects

Amber O’Reilly (Kahuku High School) - Characterizing bacterial community composition in sediments at Loko Ea Fishpond using 16S sequencing

Daniella Griffay (Radford High School) - Extracting DNA from water samples to investigate bacterial nutrient cycling in an axolotl tank

Susan Rickards (Parker School) - Genetic barcoding and identification of deep sea cephalopods. Seen here unboxing new lab equipment supported by AIN!!

AIN also hosted teacher workshops this Spring on Maui in March and at the Hawaiʻi STEM Conference in Honolulu in May. Our upcoming second annual Kula Aʻo Kālaiōewe Summer Genomics Intensive will be taking place June 8-10 at ʻIolani School with 18 confirmed participants, and registration is still open for our 3-hour mini-workshop for teachers as part of the STEMS2 Symposium. E hele mai!

 

Participants practice pipetting drills at our Maui teacher workshop hosted at Hawaiʻi STEMworks in Kīhei.

 

Kūlia i ka Nuʻu

This year’s Public Schools of Hawaiʻi Foundation (PSHF) Awards Banquet brought many AIN teachers and students together for an intimate reception with 2020 Nobel Laureate in Chemistry, Dr. Jennifer Doudna. Known for her contributions to the discovery of CRISPR gene editing technology, Dr. Doudna is also a distinguished graduate of Hilo High School, where her foundation joined PSHF in awarding a total of $20,000 in equipment grants and STEM scholarships. It was an honor for the ʻĀina-Informatics Network to be featured as a leading initiative providing the access and expertise needed to inspire the next generation of homegrown luminaries in STEM innovation.

Mary Margaret Peterson, Alyssa Bailey and their students (ʻAiea High School) with Dr. Doudna at the PSHF Awards Banquet.

Dr. Doudna presents a check from the Public Schools of Hawai‘i Foundation to her alma mater and AIN partner school, Hilo High School.

Growing and naming a new bacteria species

by Dr. Stuart Donachie

Professor of Microbiology at the University of Hawaiʻi at Mānoa

We might raise many cultures of microorganisms from a sample. The actual number of separate cultures depends on the number of different microorganisms in the sample, how many different growth (or culture) media we apply the sample to, and to other factors such as the temperature and duration of incubation. In this respect, differences in culture media cater to the needs of different microorganisms, as do different incubation temperatures and durations; some microorganisms take longer to grow, for example. We can also encourage other microorganisms to grow, or even not to grow, by incubating the samples on media in light, or by adding antibiotics to the growth medium to give less competitive microorganisms an advantage. As you can see, we could apply an infinite number of media and growth conditions in our quest to cultivate as many different microorganisms as possible.

Once we have a pure culture of bacteria on a medium, we determine if it belongs to a species that is already known, or is it one that is new and for which we might provide a formal binomial name. The methods we use to do this have changed a lot over the years; through much of the twentieth century they largely comprised a range of metabolic and biochemical tests, such as whether the culture could use a particular carbon source, or produce a particular enzyme. In the last 25 years or so, an alternative approach to provide insight into a culture’s identity has been developed. This was based on sequencing a specific gene in the culture’s DNA becoming easier, and the importance of DNA sequences in distinguishing and classifying all organisms increased greatly. Instead of running a battery of nutritional and enzyme tests, we now routinely sequence part of a gene in the bacterial DNA, the 16S rRNA gene. Knowing the sequence of nucleotides in part of this gene is enough for us to at least identify the genus the culture belongs to. The more nucleotides we have, though, the more confident we become that our culture belongs not only to a genus, but in some cases that it belongs to a certain species. If the nucleotide sequences of two 16S rRNA genes are identical over the length of about 1400 to 1500 nucleotides, meaning the nucleotides in each align perfectly, they are said to share 100% identity. If 99% of the nucleotides in two sequences of this length align, the sequences are not only said to be 99% identical, but we assume the bacteria from which these sequences were likely belong to the same species. This is a general rule of thumb to 98.6% sequence identity, although that value is only an indication of relatedness; we need more information to determine if the two bacteria in question belong to the same species or not. Historically, an in vitro laboratory method called DNA-DNA hybridization allowed DNA extracted from two bacteria to be compared; a value of less than 70% was considered definitive evidence that the bacteria belonged to different species. This could be supported by determining the combined percentage amount of the G and C nucleotides in the genomes. Within a species, the values cannot be more than one percent different, while that in different species in the same genus can vary markedly, such as by several to over 10 percent.

The in vitro methods of the past are no longer necessary. Although bacteria genomes vary considerably in size, with those of free-living bacteria ranging from less than one million nucleotides to over 10 million nucleotides, we now determine their G+C percent content and nucleotide sequence by in silico analyses of high-throughput sequencing data. Having sequenced and assembled a bacterial genome, we compare it nucleotide by nucleotide with others in an online database known as the Type Strain Genome Server (TYGS). Through a Genome-to-Genome Distance Calculator (GGDC) we are provided a measure of the intergenomic distance, and where the outcome indicates, a statement that a potential new species [has been detected]. The GGDC also lists differences in G+C percentage contents between the genomes compared. Although we would now have strong indications through 16S rRNA gene and whole genome sequencing of a new species, we cannot propose that a new species exists without further work.

Examples of bacterial cultures growing in different lab media.

To publish a new species in a peer-reviewed scientific journal we familiarize ourselves with any requirements pertaining to what will be the host genus. These requirements are often referred to as the minimal standards, and include describing which characteristics distinguish the new species from its nearest relatives. These characteristics might include the presence or absence of a certain enzyme, or if the new species is motile while its nearest neighbor or neighbors are not. Here again, the G+C percentage of the genome is a crucial factor, as is the percentage nucleotide identity in the 16S rRNA genes. We also routinely determine temperature, pH, and salinity optima and ranges for growth. An absolute requirement is that a live copy of the new species is deposited in recognized culture collections in at least two countries; we prove that has been done by including with our manuscript certificates of deposit from those culture collections.


Once we’ve completed all laboratory tests and administrative procedures, which in the latter includes uploading gene and genome sequences to public databases, we must finalize the selection of a species name, and in some cases even a genus name. The new name must comprise two parts, as in the system known as binomial nomenclature. Well known examples are Homo sapiens, and Escherichia coli. Whatever name we propose must also conform to the rules of Latin grammar. If the new species will be placed inside an existing genus, then we only must develop the species name, or epithet. We do not name anything after ourselves! However, we have named species after places the new species was originally isolated from, e.g., loihiensis, kilaueensis, and papahanaumokuakeensis: these were assigned to the genera Idiomarina, Gloeobacter, and Terasakiispira, respectively. Coincidentally, the latter was a new genus we proposed to accommodate the sole new species, with the genus being named after a Japanese microbiologist, Yasuke Terasaki, to recognize his contributions to the study of spiral-shaped bacteria. Naming a new bacteria genus and species is quite an adventure. It is certainly one that might demand some patience.

ʻĀina-Informatics Network Fall 2022 Newsletter

Last year, the ʻĀina-Informatics Network underwent extraordinary growth, propelled by a Governor’s Emergency Educational Relief Grant, which in turn allowed students across Hawaiʻi to mobilize a response to the ongoing COVID-19 pandemic through DNA sequencing.

This fall, our network pivoted back towards our commitment to understanding the biodiversity of our islands using real world applications of genome science. Deploying our mobile lab at 12 different schools on three islands, we continued to generate data for existing projects such as our GM Papaya study (134 new trees tested) and our Non-tuberculous Mycobacteria sequencing project (3 new NTM genomes assembled).

Our network also focused on new projects under development, such as a pilot collaboration between Lea-Carol Glennon (KS Hawaiʻi), Liz Steiner and Richard Sypniewski (Kapaʻa HS) and ʻIolani School examining Wolbachia strain types in invasive mosquitoes which carry avian malaria. While we are still refining our protocols to maximize the reliability of our results, student generated data are being shared with our partners at the USGS Pacific Island Ecosystems Research Center, the University of Hawaiʻi at Mānoa and Birds, Not Mosquitoes.

Pipe cleaner mosquitoes designed by Kapaʻa High students as part of Liz and Sy’s mosquito unit for 9th grade general biology.

Prototype for a DIY mosquito larvae rearing chamber made by Liz and Sy’s students.

Photo credits: E. Tong

Network Highlights

ʻAiea High School investigating microbial community changes in Hālawa Stream

Following the contamination of the Kapūkakī well with petroleum products leaked from the Navy’s Red Hill fuel storage facility, regulators approved the treatment and subsequent discharge of the well water into Hālawa Stream. AIN Fellows Cohort 1 teacher Alyssa Bailey and her students at ʻAiea High School leapt into action, conducting water quality surveys on their campus and around the community. With support from Drs. Yinphan Tseng and Andrea Jani at UH Mānoa, students are conducting 16S sequencing on eDNA filtered from various points along Hālawa Stream to profile changes in the microbial community resulting from the discharge. Preliminary results indicate that the bacterial taxa students identified downstream of the discharge site may be bioindicators for specific hydrocarbon contaminants persisting in the water even following treatment.

Hawaiʻi Baptist Academy to name a novel bacterium discovered in a lava cave

In March 2020, students at HBA participated in an ongoing effort by ʻĀina-Informatics (and our partners Drs. Stuart Donachie and Rebecca Prescott at UH Mānoa) to sequence unknown microbes isolated from Hawaiʻi Island lava caves. Known simply as BL16E, one such organism sequenced and assembled by HBA students would later prove to be previously undescribed to science. The scientific name they have proposed for this bacterium is Paraflavitalea speifideiaquila, combining the Latin words for hope (spes), faith (fides) and eagle (aquila - HBA’s mascot). This is the second novel organism our network has had the honor of naming. In 2018, students at St. Andrews sequenced a novel bacterium and proposed the name Bradyrhizobium prioratisuperbia.

Teacher Professional Development

Kona 2022 Teacher Workshop

In November, ʻĀina-Informatics hosted a free, two-day teacher workshop at Kealakehe High School in Kailua-Kona introducing projects from our place-based genome science curriculum to both new and returning teachers. Hosted by Gigi Goochey with support from Justin Brown, we were stoked to spend a couple of days working on basic and advanced techniques with teachers from all over Hawaiʻi Island.

Educators from Kealakehe High, Keaʻau High, Kaʻū Middle, Parker School, Hawaiʻi Preparatory Academy and West Hawaiʻi Explorations Academy were in attendance at our November Kona workshop.

Photo credit: Ethan Hill

For returning participants, the advanced workshop focused on new foundational bioinformatics content designed by ʻĀina-Informatics to make genomic data analysis more accessible to non-coders. Pipelines for environmental DNA (eDNA) analyses written by Ethan Hill - containerized in Docker and publicly available via Github - allow students and teachers to input raw amplicon sequences and produce clear, understandable summaries of what taxa are present within a mixed eDNA sample.

A sample output of an eDNA pipeline surveying a stream for native and invasive fish using just the water itself.

Save the date!

We are collaborating with STEMworks Hawaiʻi to bring you our next teacher workshop in Kīhei, Maui on March 11-12, 2023. Travel to/from Kīhei for two teachers each from Molokaʻi and Lānaʻi will be supported by ʻĀina-Informatics.

ʻĀina-Informatics Teacher Fellows Cohort ʻElua

Our Teacher Fellows program provides selected teachers with tailored professional development and equipment support around a custom genome science project of their design. This year’s cohorts’ projects investigate deep sea cephalopods (Susan Rickards, Parker School), sediments in loko iʻa (Amber O’Reilly, Kahuku High School), microbes in Korean natural farming (Johanna Anton, Hawaiʻi Preparatory Academy) and nutrient cycling in an axolotl tank (Daniella Griffay, Radford High School).

A year of sequencing COVID-19

 
 

In Spring 2021, ʻĀina-Informatics partnered with Dr. Ed Desmond (Hawaiʻi Department of Health) and Dr. Marguerite Butler (University of Hawaiʻi at Mānoa, Pacific Biodiversity Lab) to design the COVID Trackers Project, a lab-based curriculum which enabled students to use MinION sequencing technology to contribute towards variant assignment of SARS-CoV-2 samples. All test samples were isolated from individuals who tested positive at State testing locations between 4/22/2021 and 8/31/2021 (capturing the Delta surge in Hawaiʻi) and only brought into classrooms once processed and deactivated by our DOH and UHM collaborators.

Dr. Marguerite Butler (University of Hawaiʻi at Mānoa - College of Natural Sciences)

Dr. Ed Desmond (Hawaiʻi Department of Health - Public Health and Environmental Laboratories)

The in-classroom activities were enabled by the use of a custom mobile sequencing lab outfitted with all the necessary equipment and reagents to conduct this outreach. Lab curricula were designed around the ARTIC Network workflow for processing and sequencing SARS-CoV-2 using a tiled amplicon approach. Beginning with amplicons generated by the Butler Lab, students first constructed multiplex sequencing libraries pooling 6 genomes at a time with NEB’s ARTIC SARS-CoV-2 Companion Kit for Oxford Nanopore Technologies. During the course of this project, our collaborators in the Butler Lab utilized multiple primer schemes (including VarSkip and VarSkip v2) for amplicon generation as each scheme became available. The majority of the sequencing runs were performed on MinION Flongle flow cells, with a smaller subset completed using standard MinION flow cells. Reads were analyzed in real time in the classroom using RAMPART, with final assembly and variant confirmation conducted in Medaka and Pangolin outside of the classroom. A portion of these consensus sequences were contributed to GISAID in Spring 2022. Finally, students ran a biogeographical analysis of 212 publicly available SARS-CoV-2 genomes relevant to Hawaiʻi using data and R scripts developed by Ethan Hill (Butler Lab) and powered by RStudio Cloud.

Ethan Hill (Butler Lab, UH Mānoa) coaching a ʻIolani School student in COVID sequencing library preparation.

Photo credits: Eric Wehner

Global Health teacher Nan Ketpura-Ching working with students on a COVID-19 genome assembly puzzle.

An excerpt from a biogeographic reconstruction generated by students in RStudio Cloud depicting chains of transmission of COVID into and through our islands.


This project has been generously supported in part by a Governor’s Emergency Educational Relief Grant as well as a sponsorship from Hawaiʻi Dental Service.

Schools and student reach

The COVID Trackers Lab was conducted at 14 participating schools on three islands during SY2021-22, reaching over 640 local students. Of these, 2 were public middle schools, 8 were public high schools, 2 were public charter schools and 2 were private schools.

 
School Island Genomes
Attempted		 Participating
Teachers		 Student
Reach
ʻIolani School Oʻahu 114 2 24
ʻAiea High School Oʻahu 12 1 17
Waipahu High School Oʻahu 12 1 28
King Intermediate School Oʻahu 24 2 83
Kailua Intermediate School Oʻahu 30 1 90
Kahuku High School Oʻahu 60 2 208
Hawaiʻi Baptist Academy Oʻahu 96 2 15
Kailua High School Oʻahu 12 1 22
Hawaiʻi Technology Academy Kona Hawaiʻi 6 1 8
Kapaʻa High School Kauaʻi 18 2 28
Hawaiʻi Technology Academy Kauaʻi Kauaʻi 6 1 19
Kauaʻi High School Kauaʻi 6 1 20
Radford High School Oʻahu 12 1 46
Hilo High School Hawaiʻi 12 1 35
TOTALS 420 19 643
 

A student at King Intermediate School preparing a sequencing library for loading on a MinION Flongle flow cell.

Photo credit: E. Tong

Data

The student generated data include a total of 236 unique samples sequenced in classrooms 6 or 12 at a time plus two additional 96-well plates. A subset of the 236 unique samples (n = 84) were resequenced in classrooms when prior sequencing runs in the Butler Lab yielded insufficient reads, allowing for multiple datasets to be merged for a more robust combined sequencing depth.

A summary of student-generated variant assignments by sampling week (96 well plate samples omitted).

The vast majority of samples sequenced were taken from surge testing efforts on or around 8/12/2021, with results capturing the Delta surge across the islands. Approximately 70% of all samples originated on Oʻahu, 20% in Hawaiʻi County, and 5% each in Kauaʻi and Maui counties.

Reflections

The disruption to school and student learning brought upon by the COVID pandemic may not yet be fully understood, but the pandemic forced all of us to think outside the box and innovate new ways to engage students both in and out of the classroom. At the same time, the DOH was facing a shortage of skilled technicians crucial in developing the sequencing infrastructure required to conduct genomic surveillance of a new virus. This unique confluence of problems was met head on with a bold idea: to train the next generation of genome scientists in the midst of an ongoing genome science crisis.

With huge mahalo for our academic and funding partners, the ʻĀina-Informatics Network rallied around this bold idea, committing countless hours and resources in order to empower students to join the pandemic response. In a year where COVID held control over their everyday lives, students found a way to assert agency over COVID using a pipette, a sequencer and a laptop.

Kailua High School students presenting a completed COVID genome assembly puzzle designed to illustrate the evolution of new variants.

Photo credit: Sara Anglin

The pandemic also opened up new case studies in bioethics, especially surrounding the novel mRNA vaccines developed with unthinkable speed in response to variant after variant. Ripped straight from the headlines, our bioethics unit engaged students in considering the ethics surrounding the initially limited vaccine rollout, subsequent mandating of vaccines in the workplace and inequities in the global distribution of vaccine access.

We are grateful for the opportunity to have brought this project to so many in our community of schools, but we are also relieved that the pandemic is at a place where genomic surveillance at this scale is no longer necessary. And while the pandemic brought with it heartache and suffering, it has also presented a unique opportunity for our program to directly engage students in genome science in the most timely and urgent way possible. It is our hope that among the students we reached with this project is a new generation of homegrown genome science professionals ready to lead us through the next crisis when it arrives.

Genomic sequencing by ʻAiea High School students identifies multiple variants in Hawaiʻi swabs

by Sarah Gallardo, ʻAiea High School Medical Biotechnology student

Teacher: Mrs. Mary Margaret Peterson

What did you do on the four days of the project?

For four days we worked with instructors from ‘Iolani and UH to identify the type of variant of twelve different COVID-19 samples which originated throughout the state of Hawai’i around late June to early July of 2021. Using the given genetic material, we created a mixture to produce a single nucleotide overhang where the barcodes, which identifies each sample, can be attached. In the next step we attached distinct barcodes assigned to each of the twelve samples.

Students preparing a sequence library for barcoding.

Photo credit: Mary Margaret Peterson

Then we combined all of the barcoded libraries into a single mixed library. Before putting the samples through a DNA sequencer, we had to get the DNA in its purest form which we did with a process called DNA purification. We then sequenced the library with nanopore sequencing. This is where “a nanopore, a synthetic membrane channel, allows a strand of DNA through its pore. As the molecule passes, changes in the electrical field are detected.” This is decoded resulting in a DNA sequence. 

Why is it important to track variants in Hawaiʻi and around the world? 

We can identify which variants are more transmissible than others thus becoming more proactive when controlling outbreaks. We can understand how the coronavirus arrives in our community and how it moves around within the state. The data retrieved from genomic surveillance helps track mutations occurring within the SARS-CoV-2 genome as it transfers from infected people. 

What variants did your class find?

In viewing our results, we found

one new case of Gamma,

three cases of Alpha,

seven samples of Delta,

and one of Mu.

This proves that during late June and early July of 2021 the Delta variant started to become the most transmissible and common variant in the population. 

Student preparing sample for loading on the MinION sequencer.

Photo credit: E. Tong

Write about how you felt completing the project. What did you learn?

This experience involved an immense amount of complex thinking and being exposed to new concepts and scientific terminology. I’m grateful that I had this opportunity to partake in a process that most people my age don’t get to experience until college. Through the guidance of Mr. Tong and Mr. Hill, I became more aware of how the coronavirus is traveling within the state of Hawai’i and the importance of genomic surveillance. Knowing that my class and I were contributing data to our current health crisis is extremely rewarding.

Chasing the Variants

by Katelyn Shu, ʻIolani School Global Health student

Teacher: Mrs. Nan Ketpura-Ching

This past week my classmates and I have been fortunate enough to participate in a COVID-19 Variant Trackers Project with ʻĀina-Informatics. Viruses like SARS-CoV-2 are constantly mutating and changing into new variants. When the highly contagious delta variant came to Hawaiʻi, the resulting surge during the summer had COVID case numbers higher than ever before. Part of the job of someone who specializes in bioinformatics is to use computer tools to analyze biological data, which can be used to learn about these variants and how they spread around the world.

We began the project learning a little bit about how SARS-CoV-2 is sequenced to find the order of the nucleotide bases that make up the RNA. Many runs are taken to be more accurate. If when it’s being sequenced, a base doesn’t match up with the reference genome, it could be a possible error or mutation. The method of sequencing we were able to see with ʻĀina-Informatics was called Nanopore sequencing, where DNA goes through nanopores that detect electrical changes with sensor arrays. These signals can be read by a flowcell device. We were provided with different samples of swabs from people who contracted COVID-19 during June-July 2021 on Oʻahu. Some of my classmates got to use micropipettes to put the samples into the flowcells.

Taking a closer look at a MinION flow cell.

Photo credits: Eric Wehner

Priming the flow cell for sequencing.

When we returned later, we were able to learn about the programming tool called RStudio. Biologists use RStudio to do complex statistical analysis. Using this tool, Mr. Tong helped us create a “family tree” of sorts for the spread of COVID-19. It’s really fascinating. By sequencing countless nucleotides and tracking the mutations, biologists can track how variants travel based on the similarities between the COVID genomes of swabbed people. I was so fascinated to look at the family tree that was generated. In the end, our references showed that most of the samples we found were the Delta variant. A few others were Alpha or Gamma, but there were no samples from the original Wuhan strain nor the Mu and Beta variants. This fit our hypothesis that most of the samples would be Delta.

Variant assignment of genomic reads in RAMPART.

Photo credit: Eric Wehner

On top of the contact-tracing we learned about during the epidemiology unit, these programs can truly reveal a whole new side to the broad spectrum that is biology. While others interview people and try to piece together correlations between infected people, people in bioinformatics have extremely important jobs as well in biologically mapping out the path of the pathogen.

UH Mānoa researchers share how genomic data are used in pandemic response

At our September 15 STEMplus virtual launch, UH evolutionary biologists Ethan Hill and Dr. Marguerite Butler (Pacific Biodiversity Lab) presented on how we can detect which SARS-CoV-2 variants are circulating around Hawaiʻi. First, Ethan shares how students can safely contribute towards genomic surveillance of the virus. From the mutations observed between samples, students can then use bioinformatics tools to reconstruct the many chains of transmission across the islands. Dr. Butler then updates us on the state of variants in Hawaiʻi, and breaks down how variant tracking is used in our pandemic response.

ʻĀina-Informatics discusses the new COVID Variant Trackers Project on HPR's Bytemarks Cafe

Mahalo nui to Bytemarks Cafe host Burt Lum for inviting ʻIolani teachers Eric and Joanna on to the radio to talk about the new COVID Variant Trackers Project from ʻĀina-Informatics. Learn how our mobile lab can bring SARS-CoV-2 genome sequencing safely into the hands of students across the pae ʻāina. Our segment begins at the 7:14 time mark.

 

Photo credit: Burt Lum