One of the major hurdles to combating the COVID-19 pandemic and fully reopening communities across the country is the availability of mass rapid testing. Knowing who is infected would provide valuable insights about the potential spread and threat of the virus for policymakers and citizens alike.

Yet, people must often wait several days for their results, or even longer when there is a backlog in processing lab tests. And, the situation is worsened by the fact that most infected people have mild or no symptoms, yet still carry and spread the virus.

In a new study published in the scientific journal Cell, the team from Gladstone, UC Berkeley, and UCSF has outlined the technology for a CRISPR-based test for COVID-19 that uses a smartphone camera to provide accurate results in under 30 minutes.

“It has been an urgent task for the scientific community to not only increase testing, but also to provide new testing options,” says Melanie Ott, MD, PhD, director of the Gladstone Institute of Virology and one of the leaders of the study. “The assay we developed could provide rapid, low-cost testing to help control the spread of COVID-19.”

The technique was designed in collaboration with UC Berkeley bioengineer Daniel Fletcher, PhD, as well as Jennifer Doudna, PhD, who is a senior investigator at Gladstone, a professor at UC Berkeley, president of the Innovative Genomics Institute, and an investigator of the Howard Hughes Medical Institute. Doudna recently won the 2020 Nobel Prize in Chemistry for co-discovering CRISPR-Cas genome editing, the technology that underlies this work.

Not only can their new diagnostic test generate a positive or negative result, it also measures the viral load (or the concentration of SARS-CoV-2, the virus that causes COVID-19) in a given sample.

“When coupled with repeated testing, measuring viral load could help determine whether an infection is increasing or decreasing,” says Fletcher, who is also a Chan Zuckerberg Biohub Investigator. “Monitoring the course of a patient’s infection could help health care professionals estimate the stage of infection and predict, in real time, how long is likely needed for recovery.”

A Simpler Test through Direct Detection

Current COVID-19 tests use a method called quantitative PCR — the gold standard of testing. However, one of the issues with using this technique to test for SARS-CoV-2 is that it requires DNA. Coronavirus is an RNA virus, which means that to use the PCR approach, the viral RNA must first be converted to DNA. In addition, this technique relies on a two-step chemical reaction, including an amplification step to provide enough of the DNA to make it detectable. So, current tests typically need trained users, specialized reagents, and cumbersome lab equipment, which severely limits where testing can occur and causes delays in receiving results.

As an alternative to PCR, scientists are developing testing strategies based on the gene-editing technology CRISPR, which excels at specifically identifying genetic material.

All CRISPR diagnostics to date have required that the viral RNA be converted to DNA and amplified before it can be detected, adding time and complexity. In contrast, the novel approach described in this recent study skips all the conversion and amplification steps, using CRISPR to directly detect the viral RNA.

“One reason we’re excited about CRISPR-based diagnostics is the potential for quick, accurate results at the point of need,” says Doudna. “This is especially helpful in places with limited access to testing, or when frequent, rapid testing is needed. It could eliminate a lot of the bottlenecks we’ve seen with COVID-19.”

Parinaz Fozouni, a UCSF graduate student working in Ott’s lab at Gladstone, had been working on an RNA detection system for HIV for the past few years. But in January 2020, when it became clear that the coronavirus was becoming a bigger issue globally and that testing was a potential pitfall, she and her colleagues decided to shift their focus to COVID-19.

“We knew the assay we were developing would be a logical fit to help the crisis by allowing rapid testing with minimal resources,” says Fozouni, who is co-first author of the paper, along with Sungmin Son and María Díaz de León Derby from Fletcher’s team at UC Berkeley. “Instead of the well-known CRISPR protein called Cas9, which recognizes and cleaves DNA, we used Cas13, which cleaves RNA.”

In the new test, the Cas13 protein is combined with a reporter molecule that becomes fluorescent when cut, and then mixed with a patient sample from a nasal swab. The sample is placed in a device that attaches to a smartphone. If the sample contains RNA from SARS-CoV-2, Cas13 will be activated and will cut the reporter molecule, causing the emission of a fluorescent signal. Then, the smartphone camera, essentially converted into a microscope, can detect the fluorescence and report that a swab tested positive for the virus.

“What really makes this test unique is that it uses a one-step reaction to directly test the viral RNA, as opposed to the two-step process in traditional PCR tests,” says Ott, who is also a professor in the Department of Medicine at UCSF. “The simpler chemistry, paired with the smartphone camera, cuts down detection time and doesn’t require complex lab equipment. It also allows the test to yield quantitative measurements rather than simply a positive or negative result.”

The researchers also say that their assay could be adapted to a variety of mobile phones, making the technology easily accessible.

“We chose to use mobile phones as the basis for our detection device since they have intuitive user interfaces and highly sensitive cameras that we can use to detect fluorescence,” explains Fletcher. “Mobile phones are also mass-produced and cost-effective, demonstrating that specialized lab instruments aren’t necessary for this assay.”

Accurate and Quick Results to Limit the Pandemic

When the scientists tested their device using patient samples, they confirmed that it could provide a very fast turnaround time of results for samples with clinically relevant viral loads. In fact, the device accurately detected a set of positive samples in under 5 minutes. For samples with a low viral load, the device required up to 30 minutes to distinguish it from a negative test.

“Recent models of SARS-CoV-2 suggest that frequent testing with a fast turnaround time is what we need to overcome the current pandemic,” says Ott. “We hope that with increased testing, we can avoid lockdowns and protect the most vulnerable populations.”

Not only does the new CRISPR-based test offer a promising option for rapid testing, but by using a smartphone and avoiding the need for bulky lab equipment, it has the potential to become portable and eventually be made available for point-of-care or even at-home use. And, it could also be expanded to diagnose other respiratory viruses beyond SARS-CoV-2.

In addition, the high sensitivity of smartphone cameras, together with their connectivity, GPS, and data-processing capabilities, have made them attractive tools for diagnosing disease in low-resource regions.

“We hope to develop our test into a device that could instantly upload results into cloud-based systems while maintaining patient privacy, which would be important for contact tracing and epidemiologic studies,” Ott says. “This type of smartphone-based diagnostic test could play a crucial role in controlling the current and future pandemics.”

About the Research Project

The study entitled “Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy,” was published online by Cell on December 4, 2020.

Other authors of the study include Gavin J. Knott, Michael V. D’Ambrosio, Abdul Bhuiya, Max Armstrong, and Andrew Harris from UC Berkeley; Carley N. Gray, G. Renuka Kumar, Stephanie I. Stephens, Daniela Boehm, Chia-Lin Tsou, Jeffrey Shu, Jeannette M. Osterloh, Anke Meyer-Franke, and Katherine S. Pollard from Gladstone Institutes; Chunyu Zhao, Emily D. Crawford, Andreas S. Puschnick, Maira Phelps, and Amy Kistler from the Chan Zuckerberg Biohub; Neil A. Switz from San Jose State University; and Charles Langelier and Joseph L. DeRisi from UCSF.

The research was supported by the National Institutes of Health (NIAID grant 5R61AI140465-03 and NIDA grant 1R61DA048444-01); the NIH Rapid Acceleration of Diagnostics (RADx) program; the National Heart, Lung, and Blood Institute; the National Institute of Biomedical Imaging and Bioengineering; the Department of Health and Human Services (Grant No. 3U54HL143541-02S1); as well as through philanthropic support from Fast Grants, the James B. Pendleton Charitable Trust, The Roddenberry Foundation, and multiple individual donors. This work was also made possible by a generous gift from an anonymous private donor in support of the ANCeR diagnostics consortium.

The study — recently published online in JAMA Network Open — is, according to its authors, one of the first to examine the impact of comorbid conditions and neighborhood socioeconomic status (SES) on outcomes for Black, Hispanic and Asian patients hospitalized for COVID-19. Findings indicate that Black and Hispanic populations are not inherently more susceptible to poor COVID-19 outcomes compared to other groups, and that once hospitalized, their outcomes are equal to or better than their White counterparts.

“We know that Black and Hispanic populations account for a disproportionate share of COVID-19-related deaths relative to their population size in New York and major cities across the country,” says Gbenga Ogedegbe, MD, MPH, Dr. Adolph and Margaret Berger Professor of Medicine and Population Health at NYU Langone Health, and the study’s lead author. “We were, however, surprised to find that Black and Hispanic patients were no more likely to be hospitalized across NYU Langone than White patients, which means we need to look at other structural factors at play that are negatively affecting outcomes in these communities. These factors include poor housing conditions, unequal access to health care, differential employment opportunities, and poverty — and they must be addressed,” says Ogedegbe, who is also director of NYU Langone’s Institute for Excellence in Health Equity.

How the Study Was Conducted

The team of investigators obtained all data from NYU Langone Health’s electronic health record (EHR) of 9,722 patients tested for COVID-19 at the health system’s 260 outpatient office sites and four acute care hospitals in Manhattan, Brooklyn, and Long Island between March 1, 2020 and April 8, 2020, and followed them through May 13, 2020. The patients’ race and ethnicity data was self-reported.

For every patient who tested positive for COVID-19 , the researchers compiled race/ethnicity data, patient characteristics such as body mass index (BMI), age and sex, and neighborhood socioeconomic (SES) data contained in a weighted index of seven indicators (including median household income, level of education and housing value, among others).

Study Findings

• Among the 4,843 patients who tested positive for COVID-19, 39 percent were White, 15.7 percent were Black, 25.9 percent were Hispanic, 7 percent were Asian, and 7.4 percent were multiracial/other; 2,623 patients were hospitalized.
• Of 2,623 patients hospitalized, 39.9 percent were White, 14.3 percent were Black, 27.3 percent were Hispanic, 6.9 percent were Asian, and 7.9 percent were multiracial/other. Hospitalized patients were older and had higher comorbidity than patients who tested positive but were not hospitalized. 70.8 percent were discharged, 36.3 percent experienced critical illness, 24.7 percent died or were discharged to hospice, and 4.5 percent remained hospitalized as of May 13, 2020.
• Black and Hispanic patients had a lower risk of critical illness and were less likely to die or be discharged to hospice compared to White patients. After adjusting for age, sex, insurance status and comorbidity, Black patients continued to have lower risk of death compared to White patients, while Hispanics and Asian patients had similar rates to White patients.
• After adjusting for all the above factors, Asian patients had higher odds of being hospitalized than White patients even though they were less likely to test positive for COVID-19.

“Our findings provide more evidence that the social determinants of health play a critical role in determining patient outcomes, particularly for Black patients, before they ever get to the hospital,” said Joseph Ravenell, MD, associate professor in the Department of Population Health and associate dean for Diversity Affairs and Inclusion at NYU Langone.

“However, we do see a bit of a paradox,” said Ravenell. “In keeping with other research, we’ve found that once Black patients with COVID-19 make it to the hospital — despite coming from lower-income neighborhoods — their odds of dying are similar to or lower than White patients. Meanwhile, we also know that Black and Hispanic people are disproportionately contracting and dying of COVID-19 across the country.”

According to Ogedegbe and Ravenell, Black populations are more likely to be uninsured and underinsured than White populations and thus more likely to die at home as opposed to in hospital due to poorer access to care. Another predictor of poor outcomes for patients hospitalized with COVID-19 is male sex. In this particular study cohort, 62 percent of Black hospitalized patients were female, which could explain their relatively better outcomes. The study population may also not be representative of the overall New York City population, they said.

Study senior author Leora Horwitz, MD, associate professor in the Departments of Population Health and Medicine and director of the Center for Healthcare Innovation and Delivery Science at NYU Langone, says that future studies need to better examine the direct impact of structural inequities on racial and ethnic disparities in COVID-19 related hospitalization, morbidity, and mortality.

In addition to Ogedegbe, Horwitz, and Ravenell, additional co-authors from NYU Langone Health are Samrachana Adhikari, PhD, Mark Butler, PhD, Tiffany Cook, MA, Fritz Francois, MD, Eduardo Iturrate, MD, Girardin Jean-Louis, PhD, Simon Jones, PhD, Deborah Onakomaiya, MPH, Christopher Petrilli, MD, Claudia Pulgarin, MS, Seann Reagan, MA, Harmony Reynolds, MD, Azizi Seixas, PhD, and Frank Michael Volpicelli, MD.

Led by Edward S. Peters, DMD, SM, ScD, FACE, the team at LSU Health New Orleans School of Public Health sought to find more definitive answers about what contributed to the nation’s highest per capita rate of COVID-19 cases in New Orleans during the summer of 2020 and the disproportionate number of African Americans affected. Few studies in the US had assessed the role of social determinants of health on COVID-19 disease. The studies that existed examined only a couple of specific risk factors, such as overcrowding and income. The LSU Health New Orleans team took a much more comprehensive approach to examine the relationship between neighborhood deprivation and COVID-19 in Louisiana.

The authors explain, “Risk factors leading to COVID-19 disease, hospitalization, and mortality exist not only at the individual or biological level; neighborhood-level factors and their interactions with individual-level factors are also responsible for the observed disparities. Lack of access to health care, unemployment, less education, and poor housing conditions significantly increase the risk of COVID-19 infection. These determinants of health can be studied collectively as neighborhood or area deprivation.”

“We used a measurement called the Area Deprivation Index (ADI) to look at how relative deprivation of Louisiana neighborhoods is associated with the rate of COVID-19 cases,” notes Dr. Peters, Professor and Chair of Epidemiology at LSU Health New Orleans School of Public Health. “The ADI uses 17 census-derived measures of poverty, education, housing, and employment indicators at the census tract level to classify neighborhoods. It is a robust metric measuring many relevant social determinants of health that may help explain the socio-biologic mechanisms of disease. We obtained the cumulative number of Louisiana COVID-19 case counts from the Louisiana Department of Health on July 31, 2020. We estimated COVID-19 risk for five categories of deprivation, ranging from least to most deprived neighborhoods.”

The authors noted that non-Hispanic African Americans are more likely to have vulnerable and low-paying jobs that do not allow remote work, are more likely to rely on public transportation and to live in crowded housing or work in crowded worksites that place them an increased risk for COVID-19. African Americans exhibit a greater burden of chronic medical conditions such as hypertension, diabetes, heart disease, chronic disease, and obesity that increase the severity of COVID-19 illness. In Louisiana, 2.9 million people have at least one chronic condition, and 68% of Louisiana adults are overweight or obese. Furthermore, the poverty rate is much higher among African Americans compared to Non-Hispanic Whites, and African Americans tend to live in neighborhoods with high poverty. Neighborhood socioeconomic status is linked to access to health care services, and people residing in low socioeconomic status neighborhoods are less likely to have access to health care services, which further increases the risk of adverse health outcomes related to COVID-19, such as a higher rate of hospitalizations and mortality.

“We observed a great disparity in deprivation among Louisiana neighborhoods,” Peters says. “We also found an association between neighborhood deprivation and cumulative COVID-19 cases per 1,000 persons in Louisiana. Neighborhoods with greater deprivation should be especially targeted with public health prevention measures such as wearing a mask while in public, social distancing, and considered as a priority for COVID-19 vaccine delivery.”

The research team also included Drs. Evrim Oral, Susanne Straif-Bourgeois, and Ariane L. Rung, along with PhD student Madhav KC, all at LSU Health New Orleans School of Public Health.

Scientific evidence for abrupt climate change in the past finally achieved

During the last glacial period, app. 10,000 — 110,000 years ago the northern hemisphere was covered in glacial ice and extensive sea ice, covering the Nordic seas. The cold glacial climate was interrupted by periods of fast warmup of up to 16.5 degrees Celsius over the Greenland ice sheet, the so called Dansgaard Oeschger events (D-O).

These rapid glacial climate fluctuations were discovered in the Greenland ice core drillings decades ago, but the cause of them have been hotly contested. D-O events are of particular significance today as the rate of warming seems to be very much like what can be observed in large parts of the Arctic nowadays. The new results show that the abrupt climate change in the past was closely linked to the quick and extensive decline in sea ice cover in the Nordic seas. Very important knowledge as sea ice is presently decreasing each year.

“Our, up until now, most extensive and detailed reconstruction of sea ice documents the importance of the rapid decrease of sea ice cover and the connected feedback mechanisms causing abrupt climate change,” says Henrik Sadatzki, first author of the study.

Sediment core and ice core data were combined in order to achieve the result

The Norwegian researchers investigated two sediment cores from the Norwegian sea and the Danish researchers investigated an ice core from East Greenland for changes in the sea ice cover. Both sediment and ice cores were meticulously dated and further linked to one another through several volcanic layers of ash (tephra) identified in both.

Past sea ice cover was reconstructed in the marine cores by observing the relation between specific organic molecules produced by algea living in sea ice and others by algea living in ice free waters. In the Renland ice core from East Greenland the researchers looked at the content of Bromin. This content is connected to newly formed sea ice, since Bromin contents increase when sea ice is formed. A robust chronology and sea ice information in both sediment cores and the ice core could be established and used to investigate the extent of the sea ice changes in the Nordic seas during the last glacial period.

“We have investigated how the sea ice cover changed during the last glacial period in both marine cores and ice cores. With the high resolution in our data sets we are able to see that the Nordic seas, during the rapid climate changes in the glacial period, change from being covered in ice all year round to having seasonal ice cover. This is knowledge we can apply in our improved understanding of how the sea ice decline we observe today may impact the climate in the Arctic,” says Helle Astrid Kjær, Associate professor at the Ice, Climate and Geophysics section at the Niels Bohr Institute.

Sea ice changes in the past show how the climate today can change abruptly

The data the group of researchers present shows that the Nordic seas were covered by extensive sea ice in cold periods, while warmer periods are characterized by reduced, seasonal sea ice, as well as rather open ice free oceans. “Our records show that the extensive decline in sea ice could have happened during a period of 250 years or less, simultaneously with a phase in which the water in the oceans to the north mixed with the Nordic sea, and that this situation led to sudden changes in atmospheric warming,” says Henrik Sadatzki.

As the Nordic seas changed abruptly from ice covered to open sea, the energy from the warmer ocean water was released to the cold atmosphere, leading to amplification of sudden warming of the climate. The result of the study documents that sea ice is a “tipping element” in the tightly coupled ocean-ice-climate system. This is particularly relevant today, as the still more open ocean to the north can lead to similar abrupt climate change.

Story Source:

Materials provided by University of Copenhagen. Note: Content may be edited for style and length.

Because of this amplified impact, they are urging policymakers to prioritize these individuals for COVID-19 vaccination. Their findings were published in Diabetes Care, the journal of the American Diabetes Association.

While studies have suggested that those with type 2 diabetes are at higher risk for more serious complications and being hospitalized if they get COVID-19, little is known about the risk for individuals with type 1 diabetes. In the U.S. alone, an estimated 1.6 million individuals have type 1 diabetes.

“I think these data support prioritizing individuals with type 1 or individuals with type 2 diabetes for immunization alongside other high-risk medical conditions that increase the risk of getting very sick with COVID-19, such as heart or lung disease,” said Justin Gregory, MD, MSCI, lead investigator for the study.

The team of investigators identified electronic health records (EHRs) of more than 6,000 patients across 137 Vanderbilt Health clinical sites who had a COVID-19 diagnosis during the period from mid-March until the first week of August. The team then closely reviewed the patients’ medical records and contacted many individuals by telephone to identify additional risk factors and gather more information on how COVID-19 had impacted their health.

They compared the overall impact of COVID-19 for three populations: individuals with type 1 diabetes, individuals with type 2 diabetes and those who did not have diabetes. The study was a prospective cohort study, meaning researchers identified the study subjects soon after their infection with COVID-19 and followed these individuals as they progressed through the illness. Prospective studies have lower risk of investigator bias as the outcome is not known when study subjects are identified.

“People with type 1 diabetes don’t need to live in fear and have undue anxiety, but they need to be really diligent in doing the things we all should be doing,” Gregory said. “All of us should be washing our hands and staying 6 feet apart. We should be conscientious about limiting the time spent with people outside our household. I’m not asking people with type 1 diabetes to do anything that all of us shouldn’t already be doing. I just think they need to be the most diligent about doing it day in and day out.”

Story Source:

Materials provided by Vanderbilt University Medical Center. Note: Content may be edited for style and length.

In a new paper in the journal Nature, Barouch, Director of BIDMC’s Center for Virology and Vaccine Research, and colleagues shed light on the role of antibodies and immune cells in protection against SARS-CoV-2, the virus that causes COVID-19, in rhesus macaques. “In this study, we define the role of antibodies versus T cells in protection against COVID-19 in monkeys. We report that a relatively low antibody titer (the concentration of antibodies in the blood) is needed for protection,” said Barouch. “Such knowledge will be important in the development of next generation vaccines, antibody-based therapeutics, and public health strategies for COVID-19.”

Building on previous findings that SARS-CoV-2 infection protects rhesus monkeys from re-exposure, Barouch and colleagues purified and collected antibodies from animals that had recovered from infection. They administered the antibodies at various concentrations to 12 uninfected macaques and observed that protection against SARS-CoV-2 challenge was dose dependent. Animals that received higher amounts of antibodies were protected more completely, while animals that received lower amounts of antibodies were protected less well. Similarly, when the researchers administered various concentrations of the purified antibodies to 6 macaques with active SARS-CoV-2 infection, those given higher doses demonstrated more rapid viral control.

In a second set of experiments, Barouch and colleagues evaluated the role of specific immune cells — CD8+ T cells — in contributing to protection against the virus by removing these cells from animals that had recovered from SARS-CoV-2 infection. Removal of these immune cells left the animals vulnerable to infection after re-exposure to SARS-CoV-2.

“Our data define the role of antibodies and T cells in protection against COVID-19 in monkeys. Antibodies alone can protect, including at relatively low levels, but T cells are also helpful if antibody levels are insufficient,” said Barouch, who is also Professor of Medicine at Harvard Medical School, and a member of the Ragon Institute of MGH, MIT, and Harvard. “Such correlates of protection are important given the recent successful vaccine results from human trials, and the likelihood that these and other vaccines will become widely available in the spring; as a result future vaccines may need to be licensed based on immune correlates rather than clinical efficacy.”

Co-authors include co-first author Katherine McMahan, co-first author Jingyou Yu, co-first author Noe B. Mercado, co-first author Lisa H. Tostanoski, co-first author Abishek Chandrashekar, co-first author Jinyan Liu , co-first author Lauren Peter, Esther A. Bondzie, Gabriel Dagotto, Makda S. Gebre, Catherine Jacob-Dolan, Zhenfeng Li, Felix Nampanya, and Shivani Patel of BIDMC; co-first author Carolin Loos, Caroline Atyeo, Alex Zhu, and Galit Alter, of Ragon Institute of MGH, MIT, and Harvard; Laurent Pessaint, Alex Van Ry, Kelvin Blade, Jake Yalley-Ogunro, Mehtap Cabus, Renita Brown, Anthony Cook, Elyse Teow, Hanne Andersen, Mark G. Lewis, of Bioqual; and Douglas A. Lauffenburger of Massachusetts Institute of Technology.

This work was supported by the Ragon Institute of MGH, MIT, and Harvard, Mark and Lisa Schwartz Foundation, Massachusetts Consortium on Pathogen Readiness (MassCPR), the Bill & Melinda Gates Foundation (INV-006131), and the National Institutes of Health (OD024917, AI129797, AI124377, AI128751, AI126603, CA260476).

The authors declare no financial conflicts of interest. Barouch is a co-inventor on provisional SARS-CoV-2 vaccine patents (62/969,008; 62/994,630).