Respiratory virus sequencing provides new insights into coinfection, virus spread, and COVID

Dr. Rabindra Korhe.Credits: Michael Holahan, Augusta University

With the wearing of masks and reduced social distance, the cold and flu season, researchers have developed a virus panel that allows simultaneous testing of SARS-CoV-2 and a number of common respiratory viruses. In the play of a patient who was hit hard by COVID.

With this new genetic epidemiology tool, which provides detailed genetic information about the virus that exists when packaged with a molecular immunology model called Nextstrain, researchers are able to see new viral variants circulating in the state or country. And its spread pattern can also be evaluated and assisted. Dr. Ravindra Korhe, director of the Georgia Esoteric and Molecular Laboratory (GEM Lab) at Augusta University’s Medical College of Georgia, said it would predict and mitigate future outbreaks.

Deficiencies in SARS-CoV-2 monitoring and monitoring of other co-circulatory respiratory viruses were public health challenges during the pandemic, Kolhe and his colleagues report in the journal. virus..

Coinfection is a reality, Kolhe says with these respiratory viruses when coughing, sneezing, and even talking, especially when staying close for long periods of time, such as in hospitals, geriatric homes, schools, and potentially at work. , Unknowingly infects the air.

Another reality is that coinfection can have a combined effect that exacerbates symptoms and outcomes, as we all hear that comorbidities such as diabetes and high blood pressure can result. ..

Looking for other respiratory viruses in the new panel may help provide insights into why and perhaps new directions on how to help, especially when patients are not doing well, he says. Kolhe predicts that the larger panel will be more expensive than the straight COVID test, which continues to be the front-line test of this pandemic.

In the cold Influenza season Last year, there were COVID preventive measures such as wearing a mask, so it was basically cleaning. In fact, the coinfection rate in the group surveyed was less than 1%. He and others are concerned that the cold and flu seasons will vary significantly, even with vaccination efforts. For both COVID and influenza.

“Most of us are no longer wearing masks or social distances and are resuming our normal schedule, so we are concerned that one outcome will result in more co-infections,” Kolhe said. Mr. says. “I think this is a good tool to prepare for the flu and cold season.”

Working with a San Diego-based biotechnology company Illumina, Researchers have developed 41-virus A panel containing four common human coronaviruses that have caused people colds for years, SARS-CoV-2, and other players like RSV, RS virus, This also causes a typically mild cold, and more than a dozen flu viruses.

They produced 483 patient samples and 12 saliva samples collected primarily by nasopharyngeal swabs that were positive for SARS-CoV-2 from across Georgia between June and the end of December 2020. I looked it up.

While the standard SARS-CoV-2 test can use the polymerase chain reaction (PCR) to check for the presence of the virus, the technique used in the panel actually sequences the viral genome. Determines and enables detection of potentially deadly variants such as deltas. Variants that have been talked about in recent months.

It also details the changes in the larger storage areas of the virus that essentially occur each time the virus propagates. This indicates that we have discovered a host organism such as a human. These small changes in the virus’s storage area do not affect clinical outcome, but provide a kind of genomic stamp that indicates where the virus came from. However, benign changes in the conserved areas, the next changes to appear in about 100 infected people in the savanna.

“There is no molecular coincidence that the exact same sequence appears in the savanna,” he says. “This is a way to identify the starting point and monitor how people’s movements actually move the virus and which counties are affected.”

The unique molecular signature is also a way to know which cases are not relevant. One of the questions he wants to answer is whether the repetition of this virus will experience more of these changes when it infects others.

COVID-19, coronavirus

This scanning electron microscope image shows cells in which SARS-CoV-2 (yellow) (2019-nCoV, also known as the virus that causes COVID-19) was isolated from the patient and cultured in the laboratory (blue /). It indicates that it is emerging from the surface of (pink). Credit: NIAID-RML

The interactive visualization model they use to monitor the spread of the virus can also track the movement of variants such as Delta that have direct clinical consequences such as the degree of infectivity and the resulting disease. I can do it.

Kolhe states that some of the human movements can occur before an individual realizes that he or she is positive.

It is important to know exactly which virus is present. Respiratory viruses have some things in common, because treatments tend to be different, but there is not much crossover data on the amount so far. As an example, patients with COVID-19 co-infected with the influenza virus are treated with monoclonal antibodies, artificial antibodies that target the virus, or corticosteroids that help reduce the hyperimmune response that can destroy the lungs. What happens if I do? A process called a cytokine storm. Although there is some evidence that monoclonal antibodies and corticosteroids may also be effective against some influenza, Monoclonal antibody Made specifically for the COVID virus. There is some evidence that influenza and COVID vaccines appear to have no overlap in defense.

According to the Disease Center, respiratory viruses are known to exist in pairs, for example, a common rhinovirus associated with another cause of a common cold, including other common coronaviruses, is a runny nose. Control and prevention that may increase the associated misery, such as headaches and coughs.

It is also possible to test for the virus that causes the flu, but often the patient is not tested for SARS-CoV-2 and the most mild cold and flu since the start of the current data reporting system. It seems to be one of the seasons. 1997 — Kolhe says that possibility has diminished even more recently.

Stanford University reported in late March 2020 that about one in five people with COVID-19 was infected with others. Respiratory virus In addition, 1 in 10 people with symptoms of respiratory illness diagnosed as a common respiratory virus were co-infected with the COVID-19 virus SARS-CoV-2. Coinfection of bacteria and fungi also occurs.

Much has been learned about SARS-CoV-2 in the last two years, but there is insufficient documentation on changes in the viral genome, some of which contribute to the action of the virus and other viruses. There is little insight into co-infection. People, Kolhe says.

New studies show that genomic epidemiology is essential for prediction Disease transmission Researchers have written patterns of infection, including the possibility of recognizing possible resurrections.

Their findings included identifying the most prevalent virus version in the early days of the pandemic in Georgia. It is a branch group of Pangolin line B.

The co-authors of this study include Dr. Tedros, director of the Center for Vaccine Immunology, an influenza expert, a prominent scholar at the University of Georgia and a professor of infectious diseases, and director of the Georgia Research Alliance. A center with expertise in ecology, modeling, infectious diseases and virology. Ross leads one of the new Joint Influenza Vaccine Innovation Centers, an initiative funded by the National Institutes of Health to develop single-dose vaccines that can protect against multiple strains of the influenza virus.

According to the CDC, the respiratory virus can spread by touching it, such as by shaking hands or touching the surface on which the virus is present and then touching the nose, mouth, or eyes. According to the CDC, both cold and flu viruses are basically always present, but autumn and winter are generally considered the flu season, with late August to early spring being the main cold season. Also, people with underlying health conditions who are older or pregnant are considered to be at increased risk of serious illness and complications from both COVID-19 and influenza.

The vaccine is a region that can have a significant impact on the flu virus, as Nextstrain is routinely used by the CDC to more accurately predict what the flu virus will look like next season. Can be targeted more appropriately.

The panel, already developed by Kolhe and his colleagues, is available to other researchers through Illumina. A process to verify the validity of the panel is also available.

The nasal microflora has clues as to who develops symptoms from SARS-CoV-2

For more information:
Nikhil S. Sahajpal et al, High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruss, virus (2021). DOI: 10.3390 / v13102063

Quote: Respiratory virus sequence is coinfection, virus spread, obtained from on November 1, 2021. And provides new insights into COVID (2021, November 1st).

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Respiratory virus sequencing provides new insights into coinfection, virus spread, and COVID

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