Tag: Human coronaviruses

LJI scientists identify potential targets for immune responses to novel coronavirus

LA JOLLA, CA—Within two months, SARS-CoV-2, a previously unknown coronavirus, has raced around globe, infecting over a 100,000 people with numbers continuing to rise quickly. Effective countermeasures require helpful tools to monitor viral spread and understand how the immune system responds to the virus.

Publishing in the March 16, 2020, online issue of Host, Cell and Microbe, a team of researchers at La Jolla Institute for Immunology, in collaboration with researchers at the J. Craig Venter Institute, provides the first analysis of potential targets for effective immune responses against the novel coronavirus. The researchers used existing data from known coronaviruses to predict which parts of SARS-CoV-2 are capable of activating the human immune system.

When the immune system encounters a bacterium or a virus, it zeroes in on tiny molecular features, so called epitopes, which allow cells of the immune system to distinguish between closely related foreign invaders and focus their attack. Having a complete map of viral epitopes and their immunogenicity is critical to researchers attempting to design new or improved vaccines to protect against COVID-19, the disease caused by SARS-CoV-2.  

“Right now, we have limited information about which pieces of the virus elicit a solid human response,” says the study’s lead author Alessandro Sette, Dr. Biol.Sci, a professor in the Center for Infectious Disease and Vaccine Research at LJI. “Knowing the immunogenicity of certain viral regions, or in other words, which parts of the virus the immune system reacts to and how strongly, is of immediate relevance for the design of promising vaccine candidates and their evaluation.”

While scientists currently know very little about how the human immune system responds to SARS-CoV-2, the immune response to other coronaviruses has been studied and a significant amount of epitope data is available.

Four other coronaviruses are currently circulating in the human population. They cause generally mild symptoms and together they are responsible for an estimated one quarter of all seasonal colds. But every few years, a new coronavirus emerges that causes severe disease as was the case with SARS-CoV in 2003 and MERS-CoV in 2008, and now SARS-CoV-2.

“SARS-CoV-2 is most closely related to SARS-CoV, which also happens to be the best characterized coronavirus in terms of epitopes,” explains first author Alba Grifoni, Ph.D, a postdoctoral researcher in the Sette lab

For their study, the authors used available data from the LJI-based Immune Epitope Database (IEDB), which contains over 600,000 known epitopes from some 3,600 different species, and the Virus Pathogen Resource (ViPR), a complementary repository of information about pathogenic viruses. The team compiled known epitopes from SARS-CoV and mapped the corresponding regions to SARS-CoV-2.

“We were able to map back 10 B cell epitopes to the new coronavirus and because of the overall high sequence similarity between SARS-CoV and SARS-CoV-2, there is a high likelihood that the same regions that are immunodominant in SARS-CoV are also dominant in SARS-CoV-2 is,” says Grifoni. 

Five of these regions were found in the spike glycoprotein, which forms the “crown” on the surface of the virus that gave coronaviruses their name; two in the membrane protein, which is embedded in the membrane that envelopes the protective protein shell around the viral genome and three in the nucleoprotein, which forms the shell. 

In a similar analysis, T cell epitopes were also mostly associated with the spike glycoprotein and nucleoprotein.

In a completely different approach, Grifoni used the epitope prediction algorithm hosted by the IEDB to predict linear B cell epitopes. A recent study by scientists at the University of Texas Austin determined the three-dimensional structure of the spike proteins, which allowed the LJI team to take the protein’s spatial architecture into account when predicting epitopes. This approach confirmed two of the likely epitope regions they had predicted earlier.

To substantiate the SARS-CoV-2 T cell epitopes identified based on their homology to SARS-CoV, Grifoni compared them with epitopes pinpointed by the Tepitool resource in the IEDB. Using this approach, she was able verify 12 out of 17 SARS-CoV-2 T cell epitopes identified based on sequence similarities to SARS-CoV. 

“The fact that we found that many B and T cell epitopes are highly conserved between SARS-CoV and SARS-CoV-2 provides a great starting point for vaccine development,” says Sette. “Vaccine strategies that specifically target these regions could generate immunity that’s not only cross-protective but also relatively resistant to ongoing virus evolution.”

The work was funded in part by the National Institute of Allergy and Infectious Diseases, a component of the National Institutes of Health through contracts 75N9301900065, 75N93019C00001 and 75N93019C00076.

Full citation: Alba Grifoni, John Sidney, Yun Zhang, Richard H Scheuermann, Bjoern Peters and Alessandro Sette. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell, Host and Microbe, 2020.

A pre-proof is available here.

About La Jolla Institute for Immunology

The La Jolla Institute for Immunology is dedicated to understanding the intricacies and power of the immune system so that we may apply that knowledge to promote human health and prevent a wide range of diseases. Since its founding in 1988 as an independent, nonprofit research organization, the Institute has made numerous advances leading toward its goal: life without disease.

What does self-quarantine mean?

As people wrestle with spring travel, many may choose – or be asked – to self-quarantine for a period of time to help deter the spread of COVID-19.

Isolation requires sick people to be separated from those who are not sick, while quarantine restricts the movement of people who are exposed to a contagious disease to monitor if they become sick, according to Luis Ostrosky, MD, professor of infectious diseases at The University of Texas Health Science Center at Houston (UTHealth).

So, what does self-quarantine look like? Susan Wootton, MD, an infectious disease pediatrician at McGovern Medical School at UTHealth, explains.

Wash your hands
  • Separate yourself from other people and animals in your home
  • Stay home except to get medical care
  • Call ahead before visiting your doctor
  • Wear a face mask if you are sick
  • Cover your coughs and sneezes
  • Wash your hands often
  • Avoid sharing personal household items
  • Clean all “high-touch” surfaces daily
  • Monitor your symptoms
  • Receive a green light from health care providers before discontinuing quarantine

Household members, intimate partners, and caregivers who may have close contact with a person exposed to or symptomatic with COVID-19 should monitor their health closely. Call your health care provider right away if you develop symptoms suggestive of COVID-19 including fever, cough, and trouble breathing.

For those who have been to an affected area or exposed to someone who is sick with COVID-19 in the last 14 days, you may have some limitations on your movement or activity. If you develop symptoms during that period, seek medical advice immediately. Call the office of your health care provider before you go, and tell them about your recent travel history and your symptoms. They will give you instructions on how to get care without exposing other people to your illness.

“Infection control and prevention efforts by patients with COVID-19, their household members, and their health care providers, in combination with contact tracing activities, are key to limiting the community spread of disease,” Wootton said.

Stay informed by following updates on Harris County Public HealthTexas Department of State Health ServicesCDC, and World Health Organization.

How to prepare in the event of a pandemic

As COVID-19, also known as coronavirus, becomes more prevalent around the world, University of Alabama at Birmingham experts share tips to help you prepare yourself, your family and your home should the virus continue to gain momentum.

Photo by Pixabay on Pexels.com

What is COVID-19?

Human coronaviruses are the second most common cause of colds and generally cause mild to moderate symptoms. Sometimes, coronaviruses that infect animals can evolve and become a new human coronavirus, as in the case of Severe Acute Respiratory Syndrome (SARS) in 2003 or the novel coronavirus, COVID-19, which first appeared in late 2019.

“This has become dangerous because this is a first-of-its-kind type of coronavirus, and all humans do not have immunity built up to fight it,” said Rachael Lee, M.D., UAB Medicine’s health care epidemiologist and assistant professor in the Division of Infectious Diseases

The Centers for Disease Control and Prevention (CDC) is closely monitoring the evolving epidemic of respiratory illness caused by the novel coronavirus, which was first identified in Wuhan, Hubei Province, China. To date, Chinese health officials have reported thousands of infections with the virus in China, as well as community spread in other locations such as South Korea, Italy and Iran.  To date, the United States has had a minimal number of cases. The CDC anticipates that the virus could spread and affect countries worldwide, including the United States. 

Based on early reports of COVID-19, symptoms typically include fever, runny nose, headache, cough and a general feeling of being unwell; these are the same symptoms of the common flu virus.

If you begin to experience flu-like symptoms, UAB doctors recommend seeking medical care as soon as possible.

Wash your hands

Caroline Cartledge, a nurse practitioner with UAB Student Health Services, details the right way to make sure your hands are as clean as possible. 

 “Wash your hands as much as you can,” she said. “We always recommend handwashing before you eat anything, before you make food for other people and after you use the restroom. I wash my hands anytime I touch a doorknob; if there is hand-sanitizer around, I always use it.

People touch their faces more often than they realize. Every time you touch a door handle and then scratch your nose, you are susceptible to contracting viruses.” 

Cartledge recommends lathering your hands with soap and water for at least 20 seconds. 

“A good rule of thumb is to sing or hum ‘Happy Birthday’ to yourself twice,” she said. 

Traveling and more

Lee says to follow the CDC and local health care authorities’ guidance regarding travel to areas with active disease. She recommends using common sense to be safe and careful in traveling. 

“As with any respiratory virus, the main recommendations hold true with the novel coronavirus,” Lee said. “Wash your hands, cover your cough with your arm, and stay home if you feel sick. Wearing surgical masks out in public is not recommended, as brief exposure to the virus in public is unlikely to make a person sick. Most cases have occurred when there has been prolonged contact, such as with health care professionals or family members serving as a caregiver. Use of masks is recommended for health care professionals, caregivers and those with disease symptoms.” 

Lee adds that, in the United States, we have seen very few cases of COVID-19. However, we are still seeing a large number of influenza cases that are causing many hospitalizations across the United States. 

“It’s important at this time to get to your flu shot if you have not already done so,” Lee said. 

She also suggests that, if you have symptoms and need to see a health care professional, call ahead to your health care provider, so that they can take appropriate precautions to treat you and safeguard themselves and others in the clinic or hospital when you arrive. 

Building immunity

While washing your hands is always recommended, Jessica Grayson, M.D., assistant professor with the UAB Department of Otolaryngology, says certain foods and supplements can help boost your immune system, potentially protecting your body from germs. 

“Foods that contain indole-3-carbinols have been found to reduce the number of viral infections — while this hasn’t been specifically tested in coronaviruses, the prevention of any viral illnesses that may weaken your immune system is and will be important,” Grayson said. “These foods include leafy greens like kale, spinach, collard greens, turnip greens, mustard greens, etc. They can be cooked or raw.”

Grayson adds that elderberry has certain compounds that have been approved by the FDA for use in flavoring of food. 

“There are many studies on the antiviral and antimicrobial activity of elderberry,” Grayson said. “It has been shown in some studies to bind to some subtypes of the flu virus to prevent cell entry. However, there are still more studies needed to confirm whether this is true substantial benefit.” 

You can also boost your immune system by maintaining a healthy lifestyle, says Lee. Eat a balanced diet, get plenty of rest, and avoid stress. 

Grayson also says there is no data to support that increased Vitamin C helps prevent or shorten viral illnesses. In fact, studies looking at this have shown no benefit. Utilizing the leafy greens above in a smoothie can be an easy way to increase intake, but strictly drinking orange or pineapple juice does not have proof of benefit. 

Protect your home and loved ones

Ian McKeag, M.D., a family and community medicine physician at UAB, says now is the time to disinfect and clean your home. Use isopropyl alcohol, or disinfecting wipes, to wipe down countertops and common areas. 

“Keep the surfaces of your home clean, especially areas where you eat and spend the most time,” McKeag said. “Use soap and water to wash your hands after you touch contaminated areas, such as doorknobs, toilet and faucet handles, and any cooking items. If you do not have access to soap and water, use hand-sanitizer.” 

McKeag adds that it is also a good idea to avoid shaking hands with others right now. If you do, wash your hands or use sanitizer right away, especially before touching your face. 

Grayson says you should limit the amount of time spent in public places and avoid people who are sick, including those who are coughing or presenting symptoms. 

“If you have a fever or other symptoms, stay home,” Grayson said. “If your children have a fever, do not send them to school. Consider working from home if your workplace allows it.” 

Finally, she recommends planning ahead for your daily medications.

“Be sure that you have plenty of the medicines that you routinely take so that if ill you can avoid going out in public to retrieve these things,” Grayson said. “In the case of a pandemic or major outbreak in the U.S., it is a good idea to stock up on non-perishable foods should your community be quarantined.”