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From delta to omicron, here’s how scientists know which coronavirus variants are circulating in the US

A nationwide genomic surveillance system analyzes positive COVID-19 tests to build a picture of which variants are spreading in the population.

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A positive COVID-19 test is the first step in the process. Paul Hennessy/SOPA Images/LightRocket via Getty Images

The omicron variant quickly took over the global coronavirus landscape after it was first reported in South Africa in late November, 2021. The U.S. became the 24th country to report a case of omicron infection when health officials announced on Dec. 1, 2021, that the new strain had been identified in a patient in California.

How do scientists know what versions of the coronavirus are present? How quickly can they see which viral variants are making inroads in a population?

Alexander Sundermann and Lee Harrison are epidemiologists who study novel approaches for outbreak detection. Here they explain how the genomic surveillance system works in the U.S. and why it’s important to know which virus variants are circulating.

What is genomic surveillance?

Genomic surveillance provides an early warning system for SARS-CoV-2. The same way a smoke alarm helps firefighters know where a fire is breaking out, genomic surveillance helps public health officials see which coronavirus variants are popping up where.

Labs sequence the genome in coronavirus samples taken from patients’ COVID-19 tests. These are diagnostic PCR tests that have come back positive for SARS-CoV-2. Then scientists are able to tell from the virus’s genome which coronavirus variant infected the patient.

By sequencing enough coronavirus genomes, scientists are able to build up a representative picture of which variants are circulating in the population overall. Some variants have genetic mutations that have implications for prevention and treatment of COVID-19. So genomic surveillance can inform decisions about the right countermeasures – helping to control and put out the fire before it spreads.

For example, the omicron variant has mutations that diminish how well existing COVID-19 vaccines work. In response, officials recommended booster shots to enhance protection. Similarly, mutations in omicron reduce the effectiveness of some monoclonal antibodies, which are used both to prevent and treat COVID-19 in high-risk patients. Knowing which variants are circulating is therefore crucial for determining which monoclonal antibodies are likely to be effective.

masked men hold plastic tube rack in front of lab machinery
The authors load samples for genomic sequencing in their lab. Nathan Langer/UPMC, CC BY-ND

How does genomic surveillance work in the US?

The U.S. Centers for Disease Control and Prevention leads a consortium called the National SARS-CoV-2 Strain Surveillance (NS3) system. It gathers around 750 SARS-CoV-2-positive samples per week from state public health labs across the U.S. Independent of CDC efforts, commercial, university and health department laboratories sequence additional specimens.

Each type of lab has its own strengths in genomic surveillance. Commercial laboratories can sequence a high number of tests, rapidly. Academic partners can provide research expertise. And public health laboratories can supply insight into local transmission dynamics and outbreaks.

Regardless of the source, the sequence data is generally made publicly available and therefore contributes to genomic surveillance.

What data gets tracked?

When a lab sequences a SARS-CoV-2 genome, it uploads the results to a public database that includes when and where the coronavirus specimen was collected.

The open-access Global Initiative on Sharing Avian Influenza Data (GISAID) is an example of one of these databases. Scientists launched GISAID in 2008 to provide a quick and easy way to see what influenza strains were circulating across the globe. Since then, GISAID has grown and pivoted to now provide access to SARS-CoV-2 genomic sequences.

The database compares a sample’s genetic information to all the other samples collected and shows how that particular strain has evolved. To date, over 6.7 million SARS-CoV-2 sequences from 241 countries and territories have been uploaded to GISAID.

Taken together, this patchwork of genomic surveillance data provides a picture of the current variants spreading in the U.S. For example, on Dec. 4, 2021, the CDC projected that omicron accounted for 0.6% of the COVID-19 cases in the U.S. The estimated proportion rose to 95% by Jan. 1, 2022. Surveillance gave a stark warning of how quickly this variant was becoming predominant, allowing researchers to study which countermeasures would work best.

It’s important to note, however, that genomic surveillance data is often dated. The time between a patient taking a COVID-19 test and the viral genome sequence getting uploaded to GISAID can be many days or even weeks. Because of the multiple steps in the process, the median time from collection to GISAID in the U.S. ranges from seven days (Kansas) to 27 days (Alaska). The CDC uses statistical methods to estimate variant proportions for the most recent past until the official data has come in.

How many COVID-19 samples get sequenced?

Earlier in 2021, the CDC and other public health laboratories were sequencing about 10,000 COVID-19 specimens per week total. Considering that hundreds of thousands of cases have been diagnosed weekly during most of the pandemic, epidemiologists considered that number to be too small a proportion to provide a complete picture of circulating strains. More recently, the CDC and public health labs have been sequencing closer to around 60,000 cases per week.

Despite this improvement, there is still a wide gap in the percentages of COVID-19 cases sequenced from state to state, ranging from a low of 0.19% in Oklahoma to a high of 10.0% in North Dakota within the past 30 days.

Moreover, the U.S. overall sequences a much smaller percentage of COVID-19 cases compared to some other countries: 2.3% in the U.S. compared to the 7.0% in the U.K., 14.8% in New Zealand and 17% in Israel.

Which COVID-19 tests get sequenced?

Imagine if researchers collected COVID-19 tests from only one neighborhood in an entire state. The surveillance data would be biased toward the variant circulating in that neighborhood, since people are likely transmitting the same strain locally. The system might not even register another variant that is gaining steam in a different city.

That’s why scientists aim to gather a diverse sample from across a region. Random geographically and demographically representative sampling gives researchers a good sense of the big picture in terms of which variants are predominant or diminishing.

Fauci and Biden on a set for a COVID-19 briefing
Tracking the rise and fall of different variants keeps officials on top of changes in the coronavirus – and implications for prevention and treatment. Win McNamee/Getty Images News via Getty Images

Why don’t patients in the US get variant results?

There are a few reasons patients are generally not informed about the results if their specimen gets sequenced.

First, the time lag from specimen collection to sequence results is often too long to make the information clinically useful. Many patients will have progressed far into their illness by the time their variant is identified.

Second, the information is often not relevant for patient care. Treatment options are largely the same regardless of what variant has caused a COVID-19 infection. In some cases, a doctor might select the most appropriate monoclonal antibodies for treatment based on which variant a patient has, but this information can often be gleaned from faster laboratory methods.

As we begin 2022, it is more important than ever to have a robust genomic surveillance program that can capture whatever the next new coronavirus variant is. A system that provides a representative picture of current variants and fast turnaround is ideal. Proper investment in genomic surveillance for SARS-CoV-2 and other pathogens and data infrastructure will aid the U.S. in fighting future waves of COVID-19 and other infectious diseases.

The authors do not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.

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Commodities

Saudi Arabia Signals Backing For Russia In OPEC+

Saudi Arabia Signals Backing For Russia In OPEC+

Authored by Tom Ozimek via The Epoch Times,

Saudi Arabia has signaled its support for Russia as…

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Saudi Arabia Signals Backing For Russia In OPEC+

Authored by Tom Ozimek via The Epoch Times,

Saudi Arabia has signaled its support for Russia as a continued member of the OPEC+ oil cartel, which comes amid ongoing Western pressure to sanction and isolate Moscow over the Ukraine invasion.

Saudi energy minister Prince Abdulaziz bin Salman told the Financial Times in an interview published on May 22 that he sees Russia as an integral part of the OPEC+ group of oil producers, adding that politics should be kept out of the alliance.

He said Saudi Arabia hopes “to work an agreement with OPEC+ … which includes Russia,” referring to a new crude production deal. Oil pumping quotas under the current OPEC+ agreement struck in 2020 are set to expire in several months.

While the United States banned oil imports from Russia in March, member states of the European Union remain divided on phasing out Russian crude imports.

OPEC and its allies are unwinding record output cuts put in place during the worst of the pandemic in 2020, although they have rebuffed Western pressure to raise output at a faster pace as energy consumers grapple with the highest oil prices in years.

Oil prices surged above $130 per barrel in March over concerns of disrupted supplies from Russia, although they have since eased.

Brent crude futures rose by 22 cents to $112.77 a barrel by midafternoon on May 23, while the U.S. benchmark West Texas Intermediate crude fell 49 cents to $109.79.

High crude prices have translated into pain at the pump for drivers. The average price of regular-grade gasoline in the United States spiked 33 cents over the past two weeks to $4.71 per gallon, according to the Lundberg Survey, while JPMorgan analysts expect prices to climb above $6 a gallon by the end of the summer.

In his interview with the Financial Times, Prince Abdulaziz blamed soaring gasoline prices on taxes and a lack of global refining capacity.

The U.S. Energy Information Administration (EIA) said that the Russia–Ukraine conflict has injected greater volatility into oil markets.

“Sanctions on Russia and other independent corporate actions contributed to falling oil production in Russia and continue to create significant market uncertainties about the potential for further oil supply disruptions,” EIA said in the outlook, noting that Russia sanctions came against a backdrop of persistent upward oil price pressures and low oil inventories.

Global oil inventory levels in April in developed countries stood at 2.63 billion barrels, up marginally from February, when they fell to their lowest level since April 2014, EIA said.

“Because oil inventories are currently low, we expect downward oil price pressures will be limited and market conditions will exist for significant price volatility,” EIA noted.

The agency predicts Brent will average $103 per barrel in the second half of 2022, before falling to $97 per barrel in 2023.

In its most recent monthly report, OPEC cut its forecast for growth in world oil demand in 2022, citing the impact of the Ukraine war, surging inflation, and pandemic curbs in China.

Tyler Durden Tue, 05/24/2022 - 05:00

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International

Pandas wants to give Latin American businesses buying power in Asia

Pandas connects Latin America’s small businesses directly with Asian manufacturers to reduce logistical problems and high fees often imposed by importers…

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Access to global supply chains can be difficult for small businesses in Latin America, but companies like Meru, which raised funding in March to source and import goods between Mexico and China, and now more recently Pandas, are tapping into overseas relationships and technology to make this easier.

In Pandas’ case, the company is doing something similar to Meru, but starting in Colombia, connecting small businesses directly with Asian manufacturers, so that they can reduce the high fees often imposed by half a dozen importers and intermediaries as well as logistical problems that all businesses are facing right now where inventory is now taking many more months to arrive than during pre-pandemic times.

Co-founders Rio Xin and Marcos Esterli started Pandas just three months ago to provide Asian-origin inventory to micro-businesses in Latin America. Their collective background includes careers at McKinsey and Treinta for Esterli, and McKinsey, with more than seven years spent in China, for Xin, where he told TechCrunch he developed a strong network in the region.

“The main issue that we’ve seen is people who don’t understand the Chinese language or how Chinese manufacturers work and then you add in the logistical problems,” Xin added. “We are able to bridge the breach, while at the same time having our team in China to overcome all these logistics problems.”

Pandas B2B marketplace. Image Credits: Pandas

Here’s how it works: Businesses order products via the Pandas marketplace, touting lower pricing, in which the business can make purchases in a few clicks. Pandas takes it from there, offering one-day-delivery and customer support.

Esterli explained that people in Latin America have been using smartphones for their personal finances and other tasks, but that has not translated as quickly to the business side.

“A lot of customers told us Alibaba was something they wanted to use, but that it was very complicated to figure out,” he added. “We wanted to build an easy solution that was super intuitive because business owners don’t have that time to spend.”

Initially providing basic electronics products — think headphones, accessories and cables — and with a new round of funding, $5.8 million pre-seed, Pandas will move into categories like textiles and home accessories. The company touts the pre-seed investment as “the largest pre-seed financial in Spanish-speaking LatAm to date.”

Third Kind Venture Capital led the round and was joined by Acequia Capital, Picus Capital, Tekton Ventures, Partech, Liquid2 Ventures, Clocktower Technology Ventures, Gaingels and a host of individual investors, including Tul’s Juan Carlos Narvaez, Jose Jair Bonilla from Chiper, Treinta’s Man Hei and Lluís Cañadell, Pablo Viguera from Belvo, Nowports’ Alfonso de los Rios, Sujay Tyle from Merama and Ironhack’s Gonzalo Manrique.

So far in its young journey, the company is growing 100% month over month and has amassed a supplier network of about 300 out of 5,000 in China, Xin said.

In addition to moving into those new inventory categories, the new capital will enable Pandas to scale its operations, technology and product development and make new hires.

Xin expects to be in most of the main markets across Latin America in the next three years. In the meantime, new features coming down the pipeline in the next 12 months include a suite of fintech and analytics tools like financing.

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Government

Monkeypox cases are rising. Should we be worried?

The World Health Organization has said the current outbreak of monkeypox is the largest ever recorded outside sub-Saharan
The post Monkeypox cases are…

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The World Health Organization has said the current outbreak of monkeypox is the largest ever recorded outside sub-Saharan Africa, with cases rising above the 100-mark a few days ago and the UK top of the table with 56 as of yesterday.

Top of the list of concerns is how the virus – which does not spread easily between humans and requires skin-to-skin contact – is spreading so quickly in so many countries in Europe, the Americas and Australia where the disease is not endemic.

There is speculation that monkeypox may be being spread between sexual partners, even though it is not normally considered a sexually-transmitted infection. Thankfully, there have been no deaths reported so far, although the WHO notes monkeypox has a fatality rate of between 3% and 6%.

While health authorities are on alert, the WHO said it thinks the outbreak can be contained and that the overall risk to the population remains low. It also stressed there is no evidence that a viral mutation is responsible for the unusual pattern of infections.

Monkeypox is considered less likely to mutate quickly because it is a DNA virus rather than an RNA virus like influenza or COVID-19.

Several countries including Belgium and the UK are already advising a three-week quarantine period for anyone who contracts the virus and their close contacts.

The increasing case numbers in the current monkeypox outbreak are certainly concerning,” commented Dr Charlotte Hammer, an expert in emerging infectious diseases based at the University of Cambridge in the UK.

“It is very unusual to see community transmission in Europe – previous monkeypox cases have been in returning travellers with limited ongoing spread. However, based on the number of cases that were already discovered across Europe and the UK in the previous days, it is not unexpected that additional cases are now being and will be found, especially with the contact tracing that is now happening.”

Vaccines and drugs are available

Meanwhile, attention is now being turned to other measures to control the outbreak, including the use of vaccines against smallpox – a related virus – in a ‘ring vaccination’ approach designed to control the spread among contacts.

Vaccines used during the smallpox eradication programme can provide around 85% protection against monkeypox, according to the WHO, which notes that one newer vaccine – Bavarian Nordic’s Jyneos – has been approved by the FDA for prevention against both viruses.

There’s also a licensed antiviral drug for monkeypox. SIGA Technologies’ oral drug Tpoxx (tecovirimat) is approved for smallpox, monkeypox and cowpox in Europe, and in the US and Canada for smallpox, although it can be used off-label for the other disease. The US FDA also approved a new intravenous form of the drug last week.

The WHO says there is no need for widespread vaccination, as other control measures like isolation of patients should be enough to curb the spread and in any case supplies of vaccines are limited.

Monkeypox causes symptoms similar to but milder than smallpox, typically beginning with fever, headache, muscle aches and exhaustion. It is transmitted to people from various wild animals, such as rodents and primates, and is usually a self-limited disease with symptoms lasting from two to four weeks.

In 2003, the US experienced an outbreak of monkeypox, which was the first time human monkeypox was reported outside of Africa. The Centers for Disease Control and Prevention (CDC) is making some Jyneos vaccine reserves available for close contact inoculations, including healthcare workers tending to patients.

The UK Health Security Agency (UKHSA) said yesterday it had identified 36 additional cases of monkeypox in England, and that vaccination of high-risk contacts of cases is already underway.

“A notable proportion of recent cases in the UK and Europe have been found in gay and bisexual men so we are particularly encouraging these men to be alert to the symptoms,” said the agency’s chief medical advisor Dr Susan Hopkins.

“Because the virus spreads through close contact, we are urging everyone to be aware of any unusual rashes or lesions and to contact a sexual health service if they have any symptoms.”

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