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.