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A fast, accurate, equipment-free diagnostic test for SARS-CoV-2 and its variants

More than two years into the pandemic, the virus that causes COVID—SARS-CoV-2—continues to spread worldwide. Testing for the virus and its variants…

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More than two years into the pandemic, the virus that causes COVID—SARS-CoV-2—continues to spread worldwide. Testing for the virus and its variants can help limit transmission and inform treatment decisions, and is therefore an important pillar of the public health response.

Credit: Jon Arizti Sanz, Broad Institute of MIT and Harvard

More than two years into the pandemic, the virus that causes COVID—SARS-CoV-2—continues to spread worldwide. Testing for the virus and its variants can help limit transmission and inform treatment decisions, and is therefore an important pillar of the public health response.

Now, a team of researchers from Princeton University and the Broad Institute of MIT and Harvard have created an easy-to-use diagnostic test for COVID infection that is more sensitive than the commonly used at-home antigen tests, and that also allows for the rapid and specific detection of SARS-CoV-2 variants in point-of-care settings. The study was published May 30, 2022 in the journal Nature Biomedical Engineering.

“Viral infections are often challenging to detect – as we all realized in the early days of the SARS-CoV-2 pandemic,” said Cameron Myhrvold, an assistant professor in the Department of Molecular Biology at Princeton.

The improved test detects virus using a different mechanism than the more familiar clinic-based PCR or at-home antigen tests. Instead, the test detects virus using a technology known as CRISPR, which has found widespread use in gene editing. CRISPR originated from a system used by bacteria to detect and defend against viral infections, and is uniquely suited to rapidly identifying specific genetic sequences.

Myhrvold previously worked with Broad Institute member and Harvard University professor Pardis Sabeti to develop a CRISPR-based test that could be tailored to diagnose specific viral infections. In the wake of the pandemic’s first wave in 2020, Myhrvold’s team of researchers modified their test, which they called SHINE, to detect SARS-CoV-2 with remarkable sensitivity.

“The original version of SHINE was more of a lab-based test,” said Myhrvold. “We wanted to make it possible to perform outside of a lab, with the ultimate goal of enabling people to self-test or test at home.”

Jon Arizti-Sanz, a graduate student in medical engineering in the joint Harvard-MIT Health Sciences and Technology department and whom Myhrvold is mentoring, spearheaded a collaborative effort between the two scientists’ research teams to improve SHINE. First, the group focused on eliminating the need for specialized equipment to prepare patient samples for testing. Next, they optimized the test so that its reagents don’t need to be kept in a freezer, which ensures that the test can be easily transported long distances.

They dubbed the improved test “SHINEv.2.” After confirming that the altered test worked well in their own laboratory, the group sent a test kit to a laboratory in Nigeria to see whether it could survive a long period in transit and still retain its accuracy and sensitivity. It did. But then a new challenge arose for the team to address.

“While we were working on SHINEv.2, new SARS-CoV-2 variants emerged, so we wanted to make tests for them,” said Myhrvold.

The team was able to quickly adapt SHINEv.2 to discern between infections mounted by the Alpha, Beta, Delta or Omicron SARS-CoV-2 variants in patient samples, and say the test can be rapidly modified to pick up on any other variants that may arise.

“The data indicating this approach can be used to distinguish SARS-CoV-2 variants of concern by differential detection of genomic mutations could enable us to better prepare for the appearance of the next mutation,” said Tony Hu, director of the Center for Intelligent Molecular Diagnostics and Weatherhead Presidential Chair at Tulane University. Hu reviewed the manuscript for Nature Biomedical Engineering.

Because it tests for the different variants all at once, this version of the test needs one special, but relatively inexpensive, piece of equipment to read out its results. Nonetheless, SHINEv.2 is much faster to perform, and requires much less equipment and expertise, than current approaches used to identify SARS-CoV-2 variants. The team envisions that it would mainly be used at doctors’ offices, even ones with limited resources in remote locations, to help physicians determine which viral variant is afflicting their patient, and tailor therapies appropriately.

The team also wanted to create a version of their test that would be usable by people at home, which meant optimizing it so that it can be performed without any special equipment.

“We created a fully equipment-free version that can be performed by incubating the reaction using body heat—holding it in the underarm—or at room temperature,” said Myhrvold. “Our goal was to minimize the need for heating as much as possible.”

“The approach reported by authors could be a significant contribution for pandemic control by providing a method that requires minimal sample processing or heating,” Hu said.

The home test doesn’t discern between the different viral variants, but the minimal sample processing involved in this version of SHINEv.2 would be a boon to the home user—especially with a test that can accurately detect an infection with high sensitivity, picking up on cases that might be missed by other types of home tests. Myhrvold is optimistic that SHINEv.2 will soon be joining the front lines in the battle against SARS-CoV-2, and any other new pathogen that arises in the future.

Funding for this study was provided by DARPA, Flu Lab, ELMA Foundation, MacKenzie Scott, TED’s Audacious Project, Skoll Foundation, Open Philanthropy, ‘la Caixa’ Foundation, Princeton University, Battelle National Biodefense Institute, Department of Homeland Security Science and Technology Directorate for the management and operation of the National Biodefense Analysis and Countermeasures Center, National Institutes of Health, Howard Hughes Medical Institute, Merck KGaA Future Insight Prize


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We can turn to popular culture for lessons about how to live with COVID-19 as endemic

As COVID-19 transitions from a pandemic to an endemic, apocalyptic science-fiction and zombie movies contain examples of how to adjust to the new norm…

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An endemic means that COVID-19 is still around, but it no longer disrupts everyday life. (Shutterstock)

In 2021, conversations began on whether the COVID-19 pandemic will, or even can, end. As a literary and cultural theorist, I started looking for shifts in stories about pandemics and contagion. It turns out that several stories also question how and when a pandemic becomes endemic.


Read more: COVID will likely shift from pandemic to endemic — but what does that mean?


The 2020 film Peninsula, a sequel to the Korean zombie film, Train to Busan, ends with a group of survivors rescued and transported to a zombie-free Hong Kong. In it, Jooni (played by Re Lee) spent her formative years living through the zombie epidemic. When she is rescued, she responds to being informed that she’s “going to a better place” by admitting that “this place wasn’t bad either.”

Jooni’s response points toward the shift in contagion narratives that has emerged since the spread of COVID-19. This shift marks a rejection of the push-for-survival narratives in favour of something more indicative of an endemic.

Found within

Contagion follows a general cycle: outbreak, epidemic, pandemic and endemic. The determinants of each stage rely upon the rate of spread within a specified geographic region.

Etymologically, the word “endemic” has its origins with the Greek words én and dēmos, meaning “in the people.” Thus, it refers to something that is regularly found within a population.

Infectious disease physician Stephen Parodi asserts that an endemic just means that a disease, while still prevalent within a population, no longer disrupts our daily lives.

Similarly, genomics and viral evolution researcher Aris Katzourakis argues that endemics occur when infection rates are static — neither rising nor falling. Because this stasis occurs differently with each situation, there is no set threshold at which a pandemic becomes endemic.

Not all diseases reach endemic status. And, if endemic status is reached, it does not mean the virus is gone, but rather that things have become “normal.”

Survival narratives

We’re most likely familiar with contagion narratives. After all, Steven Soderbergh’s 2011 film Contagion, was the most watched film on Canadian Netflix in March 2020. Conveniently, this was when most Canadian provinces went into lockdown during the early stages of the COVID-19 pandemic.

A clip from the film Contagion showing the disease spreading throughout the world.

In survival-based contagion narratives, characters often discuss methods for survival and generally refer to themselves as survivors. Contagion chronicles the transmission of a deadly virus that is brought from Hong Kong to the United States. In response, the U.S. Centers for Disease Control is tasked with tracing its origins and finding a cure. The film follows Mitch Emhoff (Matt Damon), who is immune, as he tries to keep his daughter safe in a crumbling Minneapolis.

Ultimately, a vaccine is successfully synthesized, but only after millions have succumbed to the virus.

Like many science fiction and horror films that envision some sort of apocalyptic end, Contagion focuses on the basic requirements for survival: shelter, food, water and medicine.

However, it also deals with the breakdown of government systems and the violence that accompanies it.

A “new” normal

In contrast, contagion narratives that have turned endemic take place many years after the initial outbreak. In these stories, the infected population is regularly present, but the remaining uninfected population isn’t regularly infected.

A spin-off to the zombie series The Walking Dead takes place a decade after the initial outbreak. In the two seasons of The Walking Dead: World Beyond (2020-2021) four young protagonists — Hope (Alexa Mansour), Iris (Aliyah Royale), Silas (Hal Cumpston) and Elton (Nicolas Cantu) — represent the first generation to come of age within the zombie-infested world.

The four youth spent their formative years in an infected world — similar to Jooni in Peninsula. For these characters, zombies are part of their daily lives, and their constant presence is normalized.

The trailer for the second season of AMC’s The Walking Dead: World Beyond.

The setting in World Beyond has electricity, helicopters and modern medicine. Characters in endemic narratives have regular access to shelter, food, water and medicine, so they don’t need to resort to violence over limited resources. And notably, they also don’t often refer to themselves as survivors.

Endemic narratives acknowledge that existing within an infected space alongside a virus is not necessarily a bad thing, and that not all inhabitants within infected spaces desire to leave. It is rare in endemic narratives for a character to become infected.

Instead of going out on zombie-killing expeditions in the manner that occurs frequently in the other Walking Dead stories, the characters in World Beyond generally leave the zombies alone. They mark the zombies with different colours of spray-paint to chronicle what they call “migration patterns.”

The zombies have therefore just become another species for the characters to live alongside — something more endemic.

The Walking Dead, Fear the Walking Dead (2015-), Z Nation (2014-18), and many other survival-based stories seem to return to the past. In contrast, endemic narratives maintain a present and sometimes even future-looking approach.

Learning from stories

According to film producer and media professor Mick Broderick, survival stories maintain a status quo. They seek a “nostalgically yearned-for less-complex existence.” It provides solace to imagine an earlier, simpler time when living through a pandemic.

However, the shift from survival to endemic in contagion narratives provides us with many important possibilities. The one I think is quite relevant right now is that it presents us with a way of living with contagion. After all, watching these characters survive a pandemic helps us imagine that we can too.

Krista Collier-Jarvis does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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Has the pandemic changed our personalities? New research suggests we’re less open, agreeable and conscientious

COVID-related changes in our personalities could go some way to explaining the widespread decrease in wellbeing.

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Lightspring/Shutterstock

For many of us, some personality traits stay the same throughout our lives while others change only gradually. However, evidence shows that significant events in our personal lives which induce severe stress or trauma can be associated with more rapid changes in our personalities.

A new study, published in PLOS ONE, suggests the COVID pandemic has triggered much greater shifts in personality than we would expect to have seen naturally over this period. In particular, the researchers found that people were less extroverted, less open, less agreeable and less conscientious in 2021 and 2022 compared with before the pandemic.


Read more: How we discovered that VR can profile your personality


This study included more than 7,000 participants from the US, aged between 18 and 109, who were assessed before the pandemic (from 2014 onwards), early in the pandemic in 2020, and then later in the pandemic in 2021 or 2022.

At each time point, participants completed the “Big Five Inventory”. This assessment tool measures personality on a scale across five dimensions: extroversion versus introversion, agreeableness versus antagonism, conscientiousness versus lack of direction, neuroticism versus emotional stability, and openness versus closedness to experience.

There weren’t many changes between pre-pandemic and 2020 personality traits. However, the researchers found significant declines in extroversion, openness, agreeableness and conscientiousness in 2021/2022 compared with before the pandemic. These changes were akin to a decade of normal variation, suggesting the trauma of the COVID pandemic had accelerated the natural process of personality change.


Read more: Languishing: what to do if you're feeling restless, apathetic or empty


Interestingly, younger adults’ personalities changed the most in the study. They showed marked declines in agreeableness and conscientiousness, and a significant increase in neuroticism in 2021/2022 compared with pre-pandemic. This may be due in part to social anxiety when emerging back into society, having missed out on two years of normality.

Personality and wellbeing

Many of us became more health-conscious during the pandemic, for example by eating better and doing more exercise. A lot of us sought whatever social connections we could find virtually, and tried to refocus our attention on psychological, emotional and intellectual growth – for example, by practising mindfulness or picking up new hobbies.

Nonetheless, mental health and wellbeing decreased significantly. This makes sense given the drastic changes we went through.

Notably, personality significantly impacts our wellbeing. For example, people who report high levels of conscientiousness, agreeableness or extroversion are more likely to experience the highest level of wellbeing.

So the personality changes detected in this study may go some way to explaining the decrease in wellbeing we’ve seen during the pandemic.

A young woman looks out the window.
Personality changed the most for younger people. fizkes/Shutterstock

If we look more closely, the pandemic appears to have negatively affected the following areas:

  • our ability to express sympathy and kindness towards others (agreeableness);

  • our capacity to be open to new concepts and willing to engage in novel situations (openness);

  • our tendency to seek out and enjoy other people’s company (extraversion);

  • our desire to strive towards our goals, do tasks well or take responsibilities towards others seriously (conscientiousness).

All of these traits influence our interaction with the environment around us, and as such, may have played a role in our wellbeing decline. For example, working from home may have left us feeling demotivated and as though our career was going nowhere (lower conscientiousness). This in turn may have affected our wellbeing by making us feel more irritable, depressed or anxious.

What next?

Over time, our personalities usually change in a way that helps us adapt to ageing and cope more effectively with life events. In other words, we learn from our life experiences and this subsequently impacts our personality. As we age, we generally see increases in self-confidence, self-control and emotional stability.

However, participants in this study recorded changes in the opposite direction to the usual trajectory of personality change. This is understandable given that we faced an extended period of difficulties, including constraints on our freedoms, lost income and illness. All these experiences have evidently changed us – and our personalities.


Read more: Personality can predict who's a rule-follower and who flouts COVID-19 social distancing guidelines


This study provides us with some very useful insights into the impacts of the pandemic on our psyche. These impacts may subsequently influence many aspects of our lives, such as wellbeing.

Knowledge allows us to make choices. So you might like to take the time to reflect on your experiences over the past few years, and how these personality changes may have affected you.

Any changes may well have protected you during the height of the pandemic. However, it’s worth asking yourself how useful these changes are now that the acute phase of the pandemic is behind us. Do they still serve you well, or could you try to rethink your perspective?

Jolanta Burke does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

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Coalesce lands fresh capital to transform data at ‘enterprise scale’

Coalesce is a startup that offers data transformation tools geared mainly toward enterprise customers. Today the company closed a $26 million Series A…

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Coalesce is a startup that offers data transformation tools geared mainly toward enterprise customers. Today the company closed a $26 million Series A funding round led by Emergence Capital with participation from 11.2 Capital and GreatPoint Ventures, bringing the company’s total raised to $31.92 million. Co-founder and CEO Armon Petrossian tells TechCrunch that the cash will be put toward building out Coalesce’s product and ecosystem.

Petrossian met Coalesce’s other co-founder, Satish Jayanthi, at WhereScape, where the two were responsible for solving data warehouse problems for large organizations. (In computing, a “data warehouse” refers to systems used for reporting and data analysis — analysis usually germane to business intelligence.) Their clients often encountered challenges in transforming data, Petrossian says, as well as documenting these transformations in a way that made intuitive sense.

To Petrossian’s point, a survey commissioned by data integration platform Matillion found that as much as 57% of the time involved in analytics projects is spent tackling data transformation hurdles. Moreover, 75% percent of data teams feel that outdated migration and maintenance processes are costing them productivity and capital.

“Companies have been struggling with data transformation and optimization since the early days of data warehousing, and with the enormous growth of the cloud, that challenge has only increased,” he told TechCrunch via email. “We are on a mission to radically improve the analytics landscape by making enterprise-scale data transformations as efficient and flexible as possible.”

Coalesce offers tools designed to simplify modeling, cleansing and governance of data primarily in the Snowflake cloud, powered by what Petrossian describes as a “column-aware” architecture that leverages metadata to manage data transformations with an understanding of how the data is related or connected. Users can take advantage of data transformation automation templates that can be edited, packaged and shared, either with code or a visual design tool.

Image Credits: Coalesce

Often, companies approach Coalesce with specific problems, Petrossian said, like needing to transform data from different databases, apps and systems to follow a certain spec or standard. Other customers seek to speed up business intelligence queries by removing the need to search across multiple data sources and formats.

“Our product solves the largest bottleneck in analytics today by combining the speed of an intuitive graphical user interface with the flexibility of code, plus a healthy dose of automation, to enable rapid data transformations,” Petrossian continued. “With Coalesce, the data can be organized in an easy to access and read fashion while using automation to streamline the process and limit the amount of time needed by highly skilled engineers to code manually.”

Petrossian sees Coalesce competing with “extract, transform, and load” data integration vendors, including Informatica and Talend. The aforementioned Matillion also occupies that space, as does Incorta and Etleap.

Fortunately for Coalesce, the ETL market is massive, with one estimate putting it at $10.75 million as of early 2021. While demurring when asked about revenue, Petrossian claimed that Coalesce’s business is quite strong, with “multiple” Fortune 500 customers paying for the startup’s services.

“Our company was born during the pandemic and has given us an opportunity to serve enterprise Fortune 500 companies that are resilient to the potential looming recession,” Petrossian added. “The Coalesce platform is easing the burden of companies struggling to find talented data engineers or architects by providing them with a tool that empowers their existing teams to be much more efficient without compromising flexibility at scale.”

Coalesce currently has 40 salaried employees, spread across locations in four different countries. Petrossian wouldn’t commit to hiring a certain number this year but said the plan is to invest generally in Coalesce’s marketing, sales and engineering operations.

Coalesce lands fresh capital to transform data at ‘enterprise scale’ by Kyle Wiggers originally published on TechCrunch

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