What Can Genetics Reveal About Coronavirus Pandemics?

Why do some people get sick with SARS-CoV-2 when people who have the virus show no symptoms?

Why some people develop neurological, cardiovascular or gastrointestinal symptoms when the infection is attached to the respiratory system of another person?

Why do young, healthy people barely survive the disease because the elderly and the underlying illness increase the risk of COVID-19-induced morbidity or mortality?

In addition to individual behavior, pre-existing conditions, and good luck, the answer may be in people’s genes.

“We have the opportunity to see if there are genetic mutations that distinguish those who are susceptible to the virus from those who are resistant,” said Ting Wu, a professor of genetics at Harvard Medical School.

Geneticists, including many at HMS’s Bravatonik Institute, will investigate such important issues as the COVID-19 pandemic invades the world, infecting millions and killing hundreds of thousands. For this reason, I joined a scientist across disciplines.

They hope that their insights will help other researchers identify or design effective treatments, develop vaccines, track infections, and prevent future illness and death. I work day and night to understand the coronavirus.

Most HMS on-campus research declined in March to protect the health of the community, but some laboratories in the Department of Genetics have limited the number of projects that could have an immediate impact on the COVID-19 pandemic. We have obtained permission to continue face-to-face operations. Others have found ways to contribute from home.

“We are all trying to put our expertise into this,” said Jenny Yang, PhD in Biology and Biomedical Sciences. HMS students specializing in genetics and genomics.

Some HMS geneticists Human genomeOthers analyze the viral genome to help track the spread of various strains around the world and help determine if a mutation affects the potency of the virus.

Some people are studying gene dynamics Cell culture Reveals clues about how the body responds to the virus at the molecular level, whether it allows entry into SARS-CoV-2 or causes a cascade that leads to tissue or organ damage or runaway inflammation. Animal model to do.

In addition, some are applying their knowledge of DNA and RNA-based technologies to improve existing tests and develop new tests that can diagnose COVID-19 and detect evidence of past infections. ..

It is not clear which of these experiments will provide useful information or how fast. In science, failure ultimately outweighs success, and discovery takes time.

Keeping researchers moving is identifying discoveries or tools to identify weaknesses in the virus or strength of the human body, inform public policy, protect human health today, or prevent future pandemics. Is possible.

Harald Ringbauer, HMS Postdoctoral Researcher in Genetics, said: “It’s important to learn more about viruses and their behavior now, and genetics has great potential to teach us these things.”

Seeking for genetic outliers

If there are genes that affect human susceptibility to the new coronavirus, it will take a long time to get a complete picture and the analysis of the genomes of thousands of people. Meanwhile, Wu and colleagues are existing resources Personal Genome Project (PGP), and looking at the extreme case,

“We are looking for people who have been pushed to the edge of the COVID-19 bell curve, a genetic outlier,” said Professor Robert Winthrop, Professor of Genetics at HMS, and founding core faculty member of the Wyss Institute for Biologically. Says George Church. Inspired Engineering, where the lab is undertaking several initiatives related to the COVID-19 pandemic.

“We don’t necessarily have to dig deep into 7 billion people to predict who is likely to get sick or asymptomatic, but they are still shedding the virus and should be exposed to others. Not,” he said.

It was launched in 2005 at a church institute and is now spanning multiple countries. PGP invites volunteers to share health and genetic information for scientific research. The program currently includes more than 6,000 participants, of which about 500 have uploaded the complete genome sequence. The church is one of them.

The team provided clues from self-reported data collected from participants for details such as ZIP code, gender, race, ethnicity, health status, smoking and vaping behavior, COVID-19 symptoms, test results, and potential exposure. I am looking for. To the virus. The team can analyze the submitted DNA if the individual participants are noticeable.

Wu also envisions to recruit additional participants in the COVID-19 hotspot and use the findings to prioritize gene sequencing for participants to reveal relevant gene mutations. I will.

If the PGP team or other researchers find variants that increase or decrease the risk of serious illness or death from COVID-19, people may be tested for those variants. This will make it easier for you to determine who can work the safest at the forefront of a particular industry, who should be better protected, and who should take special precautions in their community, such as those found to be high. You risk carrying and spreading the virus without experiencing the symptoms.

PGP provides only one of many ways to investigate the genetics of SARS-CoV-2 infection. There is a weakness. For example, the repository is smaller than other international genetic databases, but it is already IRB-approved and boasts an avid patient base.

“PGP is unique in that it’s ready,” said Wyss associate teacher Wu. “This round may or may not produce useful results, but it shows how well existing programs can prepare for new needs and how proactive planning can help. There is.”

“With sufficient care and financial support, such programs can be poised for the next pandemic,” she added.

The members of the project team are Sarah Wait Zaranek, Alexander Wait Zaranek, Ranjan Ahuja, Michael Chou, Jason Bobe, Preston Estep and Jeantine Lunshof.

Insights from ancient DNA research

What is the link between the 2020 epidemic of SARS-CoV-2 and the movement of early human groups from Africa? Similar genomic analysis techniques reveal both.

When SARS-CoV-2 infects and replicates in humans, individual viruses evolve and acquire genetic mutations. Different sets of mutations begin to distinguish different strains of the virus, which can be linked to different parts of the world. By tracking these mutations, researchers can look at how the virus is moving.

For example, a virus sampled from a cluster of Baton Rouge patients may share a unique genetic fingerprint that indicates a localized spread of SARS-CoV-2, whereas New York City patients circulate. You may have about the same version of the virus that you have in Italy, suggesting that human travel contributed to the infection.

The gene sequencing and computational techniques used to track the movements of the SARS-CoV-2 lineage and tie them to specific locations depend on how groups of people tens of thousands of years old interact with each other and Is similar to the one used to reconstruct how it moved the Earth based on DNA recovered from ancient human bones. It’s no coincidence. Many of the tools used in the study of ancient DNA were first developed for virology.

HMS geneticists, who are used to scrutinizing prehistory, are now transforming their talents into COVID-19.

“We want to reinject the expertise gained from the study of ancient DNA into virology,” said Postdoclingbauer, a member of the lab at David Reich, an ancient DNA expert who is a professor of genetics at HMS. ” Reich also has commitments at Harvard University and MIT and the Broad Institute at Harvard.

“Of course there are already great scientists working on the new coronavirus,” said Ringbauer. “I wish I could contribute a little”

Ancient DNA researchers have several skills, including being familiar with analyzing big data sets. When scientists studied Zika and Ebola virus strains over the past decade, they worked with hundreds of sequences, Ringbauer said. As of June 10, more than 42,000 genomic sequences have been collected for SARS-CoV-2.

The virus replicates by cloning its RNA, making an identical copy of itself (excluding new mutations). In contrast, most human DNA replicates by recombining a mixture of genetic material from two parents.

However, ancient DNA researchers are also specialized in the study of the two exceptions to this rule. It is the Y chromosome passed from the parent to the male without recombination, and the mitochondrial DNA inherited from the mother.

Tracking the similarities and differences between mitochondrial DNA and the Y-chromosome that evolves like viral RNA narrows the timing of non-African migration and tracks viruses for thousands of years, similar to tracking viruses. And now it is possible to reconstruct the paternal family tree, patient-to-patient RNA can reconstruct the SARS-CoV-2 family tree in real time.

Once the data has been collected and cleaned up, Ringbauer and Reich aim to analyze the SARS-CoV-2 genome to help researchers answer many questions about pandemics, including: How much flame occurs between a locally generated spark and a distant spark? Is it mostly due to a few super spreaders, or do most people have an average of a few interactions with the infected person?

And one of the mutations alters the behavior of the virus, making the infection easier or more difficult, more likely to cause a disease, less likely-essentially a new strain. Create?

Fly fishing

A virus cannot infect a person unless some of the cells invade it. Certain cell surface proteins allow entry into SARS-CoV-2, while other proteins in the cell are selected to help the virus replicate.

By revealing each protein that is working, scientists offer a new opportunity to find drugs that work on the protein and make it difficult for the virus to harden its scaffold.

Researchers have identified major offenders deploying the new coronavirus welcome mat, including the ACE2 receptor and the molecular scissors known as TMPRSS2. Three researchers at HMS Natural medicine In April, we detail the activity of the genes that make these proteins in the cells that line the airways, blood vessels, heart, cornea, and intestine.

The contributor was Deborah Hung, HMS Professor of Genetics at Massachusetts General Hospital. Christine Sidman, Thomas W Smith Medicine Professor at HMS, Brigham and Women’s Hospital. Jonathan Sidman, Henrietta B., Frederick H. Buger HMS Professor of Genetics.

However, the list of genes and proteins may not yet be complete. Norbert Perimon, a professor of developmental biology for James Stillman at HMS, wants to join us using a genetic screen for Drosophila cells.

Why do you fly cells? For one thing, the genomes of humans and other mammals are complex. A single gene can make multiple proteins, and a single protein can be made by multiple genes. The fly’s genome is simple, making it easy to flag the true actors involved in the viral invasion.

“We might identify a human-equivalent protein in flies, which would have been overlooked in mammalian studies,” Perimon said.

Many, but not all, of the basic biological mechanisms found in flies apply to other organisms, including people. If Perrimon’s team was able to generate a list of genes and proteins that seemed to be associated with SARS-CoV-2 entries in fly cells, researchers would compare it to the list generated from human and mammalian studies, Using duplication is likely to be important as you can think based on the most factors.

However, the team must first clear some hurdles. For example, wild flies do not get COVID-19, so Perimon and genetic researcher Raghuvir (Ram) Viswanatha need to find out if fly cells naturally uptake SARS-CoV-2 particles. If not, researchers can engineer the cells to express human ACE2 and TMPRSS2, and if that works, observe which additional genes act when the virus internalizes.

The idea is not too far away. Flies don’t get the flu, but the same technique allowed scientists to see how the flu virus invades cells using insects.

“If it works, it should give interesting results,” Perimon said. “If not, then the project is done.”

If Friesel somehow allows entry into SARS-CoV-2, Viswanatha uses a platform developed by him based on the gene editing tool CRISPR to expedite all the genes that appear to be involved. Identify

Viswanatha will use the platform this year to use flying cells to introduce insect pathogens when scientists announce that some of the same proteins may be involved in SARS-CoV-2 infections. I found a protein.

Researchers are not sure if their experiments will work, but they are confident enough to believe it is worth trying.

“It would be a good achievement if we could find new elements involved in virus invasion that would lead to a complete “parts list”,” Perimon said. “We are happy.”

When Jenny Yan and colleagues started studying RNA (a molecule that translates DNA instructions into proteins) in the Caenorhabditis elegans worm, they didn’t anticipate that their findings would become relevant to the global pandemic. did.

“We are a very basic science lab,” said Yang, a research assistant at HMS’s Philip and Aya Leader’s genetics professor Scott Kennedy. “We are interested in gene expression and worm biology.”

Many RNAs end with a series of repeating adenine bases. The so-called poly (A) tail. Journal in May NatureKennedy’s group is C. We reported that we discovered a previously unknown type of RNA with repeated uracil and guanine tails in elegans. Researchers dubbed them with poly (UG) or pUG RNA.

Both the pUG and poly(A) tails allow RNA to mobilize other proteins that perform important tasks such as RNA polymerase, which makes copies of RNA molecules.

The week the researchers posted their manuscript to the preprint server in December 2019, the first case, now known as COVID-19, was reported in China. It was quickly revealed that SARS-CoV-2 belongs to a family of viruses whose genome is made of RNA rather than DNA.

Countless groups jumped and applied their knowledge of RNA to counter new threats. Kennedy wondered if his team could contribute.

Currently, several researchers in the lab are trying to find out. Does coronavirus contain pUG RNA? If so, what does it use them for? And can they then become targets for treatment?

The team has detected some promising signs so far, but work is still in its infancy and it is not yet clear if the early signs are genuine.

“It’s enough to motivate us, but I’m not sure yet,” said Yang. “It’s still very preliminary. Here are some tips that need to be validated.”

When SARS-CoV-2 uses pUG RNA to recruit RNA polymerase, scientists may interfere with signals that attach to the tail or recruit enzymes to prevent the virus from replicating.

If the virus contains pUG RNA but doesn’t behave the same as the worm, Kennedy and coworkers can tell about what the molecule is doing and how they suggest antiviral strategies. I also have some guesses.

Also, if researchers do not detect pUG RNA, the lab will pay full attention to what they were doing before the pandemic, unless a new inspiration strikes.

“That’s the great part of research. I don’t know where the project will go,” says Yan.

Test, test

Testing for current or past SARS-CoV-2 infections is the basis for understanding and controlling the spread of COVID-19, but testing capabilities and reliability in the United States still do not meet national needs. Researchers are trying to change that.

HMS and Brigham and Women’s Greven Mendel Genetics and Medicine Professor Steven Eledge’s lab includes: Updated VirScan, a comprehensive antibody detection toolFlags Past Exposure to SARS-CoV-2 in Blood Samples to Better Measure Immunological and Epidemiologic Virus Mortality, Population Exposure Rates, and Short- and Long-Term Effects on the Immune System To be able to. Elledge has received MassCPR funding for these efforts.

Church Labs is participating in a national effort to build faster, cheaper, more accessible tests for diagnosing COVID-19. The same is true of Connie Sepco’s lab, Ballad Professor of Genetics and Neuroscience at HMS, and Steven McCarroll’s laboratory, Dorothy and Milton Flyer Professor of Biomedical and Genetics at HMS.

Brian Rabe’s Cepko Institute bioscience and biomedical candidates adapt existing assays to detect SARS-CoV-2 in patient samples in 30 minutes. No special equipment or training required. This work is based on Cepko’s expertise in using viruses as research tools.

Rabe et al. are working on improvements such as stabilization and inactivation of viral particles in patient samples. If they can make the necessary changes, the researchers hope the test will eventually be deployed in the doctor’s office or other medical facility.

Meanwhile, other members of the team at Curtis Melo and McCarroll, research assistants in genetics, combine nanotechnology droplets and digital PCR to more accurately measure and characterize viral RNA in patient samples. Focuses on different technologies and offers more reliable COVID-19 diagnostics.

This method is designed to distinguish large viral RNA molecules produced by live replicating virus from fragmented viral RNA, which can be released over long periods of time after active infection.

In contrast, current tests usually give positive results, whether the viral RNA is completely detected or broken. This could explain at least some of the cases that tested positive for COVID-19 despite at least weakening the symptoms, the researchers said.

With McCarroll’s technology, individual patient samples are encapsulated in microscopic droplets along with the chemicals needed to amplify and detect genetic material from coronaviruses. Tens of thousands of these drops can be analyzed simultaneously.

The droplet is designed to glow when it contains SARS-CoV-2 RNA. Those that contain long, intact RNA will glow in multiple colors. The glowing fluid is digitally counted as it flows through the microfluidic device. According to researchers, digital counting should provide more accurate results than traditional PCR (polymerase chain reaction), which is the standard method for amplifying genetic material.

The goal is to assist epidemiologists, measure infectivity at various points throughout the disease, and quickly detect surface active viral particles to help people maintain a safe space for life and work. Is to

Additional research members involved in this project are Nolan Kamitaki, a research assistant in genetics, and Heather de Rivera, a researcher in natural sciences. The study is supported by the HMS Department of Genetics.