Category Archives: Transhuman News

The National Task Force on COVID-19 also recommended the setting up of a Genomic Surveillance Consortium to map the various strains circulating in India.

A meeting of the National Task Force (NTF) on COVID-19, convened by the Indian Council of Medical Research, has concluded that while there was no need to change the existing treatment protocol in view of the mutations emerging in the SARS-CoV-2 strain, 5% of the positive cases from all the States and Union Territories would now be sent for whole genome sequencing (WGS).

This is in addition to the more than 50 samples of U.K. returnees which are currently under sequencing at the designated laboratories, the NTF said.

Coronavirus | U.K. scientists explore drug for COVID-19

The NTF also recommended the setting up of a Genomic Surveillance Consortium (INSACOG) to map the various strains circulating in India.

As per the earlier direction of the Union Health Ministry, all passengers who arrived from the U.K. between December 21 and 23 were tested at the airports. Only those testing negative in the RT-PCR test are permitted to exit the airports.

The NTF recommended that in addition to the existing surveillance strategies, it is critical to conduct enhanced genomic surveillance for SARS-CoV-2 specially in incoming passengers from the U.K.

Coronavirus | EU begins vaccine rollout as new virus strain spreads

Besides, it will also be critical to conduct genome sequencing in samples where there is dropout of the S gene in lab diagnosis, proven cases of re-infections etc. Routine genomic surveillance of SARS-CoV-2 from representative samples all across the samples needs to be a continuous and well planned activity, it said.

Since ICMR has always advocated use of two or more gene assays for testing SARS-CoV-2, it is unlikely to miss infected cases using the current testing strategy, said a release issued by the Health Ministry on Saturday.

The meeting was convened to discuss evidence-based modifications in testing, treatment and surveillance strategies with the emergence of the new virus variant in the U.K.

Coronavirus | A.P. gears up to conduct COVID-19 vaccine dry run

The Ministry noted that the variant has 14 non-synonymous (amino acid altering) mutations, 6 synonymous (non amino-acid altering), and 3 deletions. Eight mutations are present in the Spike (S) gene which carries the binding site (Receptor Binding Domain) of the ACE2 receptors, which are the point of entry of the virus into the human respiratory cells.

NTF recommended that in addition to the existing surveillance strategies, it is critical to conduct enhanced genomic surveillance for SARS-CoV-2 specially in incoming passengers from UK.

Besides, it will also be critical to conduct genome sequencing in samples where there is dropout of the S gene in lab diagnosis, proven cases of re-infections etc. Routine genomic surveillance of SARS-CoV-2 from representative samples all across the samples needs to be a continuous and well planned activity, it said.

Coronavirus | 150 soldiers in Delhi for Republic Day parade test positive for COVID-19

The Ministry said it is important to understand that like all other RNA viruses, SARS-CoV-2 will continue to mutate.

The mutated virus can also be contained by measures like social distancing, hand hygiene, wearing masks and also by an effective vaccine, as and when available, it said.

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Coronavirus | 5% of COVID-19 cases to be tested for genome sequence - The Hindu

SAN DIEGO, Dec. 28, 2020 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO), announced today that Praxis Genomics, LLC received accreditation from the College of American Pathologists (CAP), making it the first CAP-accredited, CLIA-certified diagnostic lab in the United States to offer a laboratory developed test (LDT) based on whole genome analysis with Saphyr. The LDT is designed for postnatal patients suspected of a constitutional genetic disorder. Praxis uses optical genome mapping (OGM) with Bionanos Saphyr System as an alternative to traditional methods of chromosomal microarray (CMA) and karyotyping (KT), as they seek to improve the rate of clinical diagnosis for patients with genetic disease. CMA and KT together typically diagnose 30-50% of patients tested. Recent studies have found that OGM with Saphyr is concordant with CMA and KT and also diagnoses a significant fraction (18-25%) of the patients who could not be diagnosed with traditional methods.

Medical guidelines recommend successive rounds of analysis with CMA, KT, repeat expansion testing, single gene or gene panel testing and whole exome sequencing until a pathogenic variant is identified or until the different techniques have been exhausted. At Praxis, this tiered approach is replaced by whole genome analysis using OGM with Saphyr for structural variants (SVs) and, when requested, whole genome analysis by next-generation sequencing (NGS) for single nucleotide variants (SNVs). This workflow eliminates costly and time-consuming steps like cell culture and tedious manual data analysis across multiple platforms and provides a streamlined approach for detection of all types of genomic aberrations designed to achieve a higher rate of diagnosis faster, easier, and at a lower economic cost to labs and payors.

Several diagnostic labs in the U.S. such as PerkinElmer Genomics and the University of Iowa Hospitals and Clinics have already launched Saphyr based LDTs targeting a specific clinical indication, a form of muscular dystrophy called FSHD1. While development of whole genome clinical tests with Saphyr have been in progress in Europe for various clinical applications including inherited genetic disorders and leukemias, the Praxis clinical service is the first to provide whole genome analysis in the U.S.

Erik Holmlin, PhD, CEO of Bionano Genomics commented: We want to congratulate Praxis Genomics and its founder Dr. Peter L. Nagy on their CAP accreditation, making their Saphyr-based test the first whole genome analysis LDT in the U.S. in a CAP/CLIA setting. We believe this accreditation is a key step on the path to reimbursement of Saphyr-based LDTs by third party payors. While Praxis is first, we expect several other U.S. laboratories to offer whole genome LDTs for various clinical applications in the future, establishing Saphyr as a key tool for next generation cytogenomics. By adding whole genome sequencing, Praxis intends to demonstrate that Saphyr and NGS complement each other to provide answers to patients and families affected with genetic disorders. As more Saphyr-based tests enter the LDT stage worldwide, we believe it is possible to create a paradigm shift for cytogenomic applications in cancer and genetic disease that have the potential to improve patient outcomes.

Dr. Peter L. Nagy, Founder and CEO of Praxis Genomics will present case studies of diagnoses made with OGM at Bionanos Next-Generation Cytogenomics Symposium on January 11, 2021. Register for the event here: https://bit.ly/3fPULzs

About Bionano GenomicsBionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing, and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools, and genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visitwww.bionanogenomics.com or http://www.lineagen.com.

Forward-Looking StatementsThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the capability of Praxis Genomics LDT to replace the tiered approach for detection of pathogenic variants currently recommended by medical guidelines; our expectations regarding reimbursement for Saphyr-based LDTs by third party payors; Saphyrs potential as a powerful new tool in cytogenetics and its potential contribution to improvements in traditional cytogenetics; Praxis Genomics intended use of the Saphyr system and our services, including to demonstrate Saphyrs capabilities in comparison to NGS; the ability to integrate data from the Saphyr system into other offerings by Praxis Genomics; expanded adoption and utilization of the Saphyr system for various clinical applications; improvements in patient outcomes driven by increased use of Saphyr-based tests in the LDT arena; and Saphyrs potential as an indispensable tool for personalized medicine and furthering understanding of cancer in the medical community. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the loss of key members of management and our commercial team; and the risks and uncertainties associated withour business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2019 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations Contact:Ashley R. RobinsonLifeSci Advisors, LLC+1 (617) 430-7577arr@lifesciadvisors.com

Media Contact:Darren Opland, PhDLifeSci Communications+1 (617) 733-7668darren@lifescicomms.com

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Bionano Customer Praxis Genomics Accredited by College of American Pathologists, Completing First LDT in US for Constitutional Genetic Disorders that...

In view of the new UK strain that has shown a higher enough degree of infectiousness to have drawn fresh international travel restrictions from several countries, Indias national task force on Covid-19 has recommended the whole genome sequencing of 5% of positive cases from all states and UTs as part of prospective surveillance. While at this stage the new strain is not known to either cause more severe disease or require fresh treatment protocols, the importance of tracking it properly cannot be overstated. Throughout the pandemic it has been seen again and again that any negligence in testing takes a painfully high toll.

One reason why the UK was able to alert the world to the worrying mutation is that a genetic consortium there systematically sequences 10% of all positive samples. Most countries dont even sequence 1%. In India the sequences of less than 5,000 novel coronavirus samples are in the public domain. The goal of now seeking to sequence 5% of all positive cases means that there can be no letup in testing even though overall infection has been trending downwards, with only 18,732 new Covid-19 cases reported in the Sunday update, the lowest daily rise in nearly six months. The new ask also depends on molecular tests that have the requisite sensitivity.

Meanwhile the way in which many recent UK returnees are untraceable reminds of costly lapses in the early days of the pandemic and underlines the challenges going forward. There is also learning for ongoing domestic trials from how Pfizer and Moderna are launching new studies for their vaccines effectiveness against the new strain. Overall this new scare stresses that constant vigilance will be needed right until herd immunity is achieved through widespread and effective vaccinations. And India must not fritter away its hard won gains against the virus.

This piece appeared as an editorial opinion in the print edition of The Times of India.

END OF ARTICLE

Excerpt from:
Battling the mutant Indias testing regime has to rise to a new challenge: 5% whole genome sequencing - The Times of India Blog

Every living thing has a genetic code within its cells, called a genome, written in DNA. Scientists first figured out how to read or "sequence" DNA in 1977, and since then, they've sequenced the whole genomes of thousands of species, including animals, viruses, and humans.

While genome sequencing itself is cool (hidden code revealed!) being able to analyze those genomes is even cooler within the code are insights that can help us treat diseases, understand pathogens, and even combat pandemics.

Today, scientists have access to handheld sequencing devices, which they're using to sequence living genomes everywhere from under the sea to up in space. However, they still need to rely on specialized laptops for their genome analysis, which can be a burden when working in these challenging locations.

Now, a team of scientists from Cold Spring Harbor Laboratory (CSHL) has developed the world's first mobile app for genome analysis turning any scientist with a handheld sequencer and a smartphone into a mobile genetics laboratory.

Eight years ago, when Aspyn Palatnick was a 14-year-old high school student interning at CSHL, he and researcher Michael Schatz noticed that, while sequencers were getting smaller, the devices used for genome analysis weren't.

Palatnick, who's now a software engineer at Facebook, got to work, programming what would eventually become iGenomics a free, open-source app for genome analysis.

In a paper published in the journal Gigascience, Palatnick and his collaborators report that the app can analyze the sequenced genomes of viruses and microbes about as quickly, accurately, and reliably as popular laptop-based systems.

Specifically, the app can map a newly sequenced genome to a reference genome, a common genome analysis process known as "read alignment." This can tell you what an organism is or how closely related it is to others. It can also identify places where the sequenced genome differs from the reference that's known as "variant calling."

The app does all of its processing on the device a major plus if a researcher is somewhere with unreliable internet access. However, this does limit the size of the genomes the app can analyze viruses and microbes are doable, but something larger, like a human genome, isn't.

Still, being able to analyze the genomes of germs can reveal insights, such as mutations, that could be key to treating infections and now, scientists will be able to conduct this genome analysis without having to lug an expensive laptop around with them.

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First-of-Its-Kind App Lets Scientists Analyze DNA on the Move - Freethink

Aditi Tandon

Tribune News Service

New Delhi, December 24

COVID positive UK returnees have moved to nine states including Punjab, the government said today, asking all these states to track these travellers as the genome sequencing of samples progresses.

The Centre also said so far no UK mutant strain has been detected in India.

Also read: England halts flights after more infectious Covid strain from South Africa spreads in UK

Union Health Secretary Rajesh Bhushan reviewed status of these travellers with the states where they went. The states are Maharashtra, Karnataka, Telangana, Tamil Nadu, West Bengal, Goa, Punjab, Gujarat and Kerala.

Six government labs have been asked to conduct genome sequences and states have been advised to follow up.

The States/UTs have been l advised to access the details of passengers from UK to India from the online portal AIR-SUVIDHA and Bureau of Immigration.

States/UTs were also asked to send the samples of those found positive to the laboratories identified for genome sequencing, Health Ministry said.

The six labs conducting genome sequencing to look for any signs of the UK mutant COVID strain in travellers are CSIR-Institute of Genomics and Integrative BiologyNew Delhi; CSIR- Centre for Cellular and Molecular Biology, Hyderabad; DBT- Institute of Life Sciences, Bhubaneswar; DBT-InStem-NCBS, Bangalore;DBT-National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal; ICMR- National Institute of Virology, Pune.

The number of such designated labs would increase over time and their details would be shared with the States/UTs.

If found positive with old COVID strain the passengers will be allowed to home isolate.

If positive with mutant strain they would have to go to institutional quarantine.

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Covid-positive UK returnees went to 9 states, including Punjab; genome sequencing of samples under way - The Tribune India

Representational image.  |  Photo Credit: Twitter

Only weeks after vaccine breakthroughs sparked hopes of an end to the pandemic, Britain has sounded the alarm over a new highly contagious variant of COVID-19 circulating within the country. Prime Minister Boris Johnson has responded to the threat by implementing Tier 4 restrictions the most stringent in large parts of southern and eastern England while over forty countries have already suspended entry of flights from the UK into their borders.

Since China published the full genomic sequence of the virus found in Wuhan, geneticists have been hard at work identifying the various strains of COVID-19 across the world and comparing them with their Wuhan ancestor discovered in mid-November 2019.

When a virus passes between one carrier to another, there may only be very subtle changes in the genome that take place. However, as it travels over larger numbers of carriers and across distances, these genomic differences become larger and more noticeable. By analysing the changes in the genome, researchers can create a high-resolution picture of how the virus has evolved in real-time and, perhaps, more importantly, identify the key transmission chains along which it has travelled. This information can prove vital in informing policy decisions and appropriate safety protocols.

As far as mutations go, SARS-CoV-2, being an RNA virus, behaves similarly to other viruses that cause Ebola, Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and influenza. These viruses are typically more prone to replication errors mutations than DNA viruses. Scientists have determined that SARS-CoV-2 has a fairly predictable evolution rate, mutating on average twice a month. Through sequencing, researchers can identify sub-lineages of the viruses much like outlining the branches of a tree.

Epidemiological experts agree that most mutations are unlikely to change the nature of the virus much, if at all, as it relates to transmissibility and severity of the symptoms caused. But there always remained a risk of a mutation which could make a real difference to the way the virus that causes COVID-19 behaves.

Early data indicates that, with, reportedly, 20 different mutations, the new variant found in Britain could, in fact, be what they have warned about. It is difficult to identify exactly how such variants come about. In some cases, it could just be through sheer luck.

But as immunity within populations builds either through vaccination or otherwise, researchers expect the virus to gain further practical mutations that enable it to spread more rapidly or hide from our immune systems. The viral strain now prevalent in Britain is particularly worrying in that its mutations affect the way the virus attaches itself to human cells and infects them. It is important to note though, that currently there is no evidence to suggest that it causes more severe symptoms.

Similarly, experts have been quick to reassure communities that there is little to suggest that the new variant may be more resistant to the vaccines developed, or in development. While it is important to pay close attention to these mutations, researchers have noted that it often takes years, not months, for a virus to mutate to a point where vaccines are rendered ineffective. However, with the virus, reportedly, spreading more aggressively through the UK's population than previous strains, this may warrant a redoubling of vaccination efforts.

Continue reading here:
How genome sequencing helps track viral evolution and where the UK COVID variant fits in - Times Now

Indian researchers have found 19 coronavirus variants circulating in India with "escape mutations" that allow them to evade the antibodies generated by immune systems and one such variant is spreading fast in Andhra Pradesh.

The genetically tweaked variant with a mutation named N440K has been found in nearly 34% of the 272 SARS-CoV-2 genomes analysed from Andhra Pradesh. The variant has also been seen in Karnataka, Maharashtra and Telangana.

Read: Where are we in the Covid-19 vaccine race?

At least one case of Covid-19 reinfection confirmed by genetic sequencing and reported in a hospital at Noida was caused by this variant.

"Andhra Pradesh has a population of 4.5 crore. If one of the Covid-19 genomes isolated from this state carry this variant, then we should watch out for the strain, Vinod Scaria, one of the scientists at CSIRs Institute for Genomics and Integrative Biology, Delhi and a member of the team that found the new strain told DH. The paper has been uploaded in a preprint server and yet to be peer-reviewed.

The team analysed 6,370 Indian Covid-19 genomes and found that 2% of the genome all over the country was carrying the N440K mutation that originated around July-August in Asia.

On Saturday, a national task force on Covid-19 suggested doing genome sequencing of 5% of all Covid-19 cases nationwide. India carried out far less gene mapping compared to the UK (more than 157,000 sequencing) and the USA (in excess of 50,000).

IGIB has inked an agreement with the Kerala government to carry out a detailed genetic study of the Covid-19 in each of the 14 districts of Kerala.

Also Read | Oxford-AstraZeneca vaccine should be effective against new variant: Report

The new variants clinical significance is yet to be understood with scientists observing that further data and analysis would be required to investigate the potential impact of such variants on the efficacy of different vaccines.

We don't know anything about this mutations clinical significance. We only saw its accumulation at one site and would be on the look-out to see if it reproduces elsewhere, said Sridhar Sivasubbu, another IGIB scientist.

Another variant N501Y that made global headlines as the new mutated UK strain was present in 290 genomes, including genomes from the United Kingdom, Australia, South Africa, USA, Denmark and Brazil.In Australia, one mutation (S477N) was found in 67% of 14,000 plus genomes that were analysed.

The researchers studied more than 240,000 genomes from 133 nations and spotted 126 variants with immune-escape provisions. Eighty six of such variants were seen in 63 countries and 19 variations have been found in India.

Besides the N440K, other escape mutations have been seen in Andhra Pradesh, Maharashtra, Karnataka, West Bengal, Telangana, Uttarakhand, Haryana, Gujarat and Delhi.

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Indian Covid-19 mutation 'N440k' found in one-third of Andhra Pradesh's coronavirus genomes - Deccan Herald

Global Whole Genome Amplification Market

The global Whole genome amplification market report provides analysis and insights on Whole genome amplification kits and consumables. Commercially availableWhole genome amplification kitsare based on Single cell WGA kits, Complete WGA Kit, WGA Reamplification Kit, WGA & Chip DNA Kit and others. Increasing demand for technologically advanced methods in sample preparation, extraction, amplification and testing for nucleic acid and the strategic agreements of manufacturers with leading research institutes to boost research activities in molecular biology field play a vital role for fueling the demand of Whole genome amplification. These Whole genome amplification kits can be used in both clinical diagnostics as well as for research applications. Applications such as agricultural and veterinary animal cell DNA testing, viral and bacterial infectious diseases, drug discovery & development, cancerous diseases, forensic testing, genetically related diseases and paternity testing/HLA typing coupled with rising awareness is predicted to increase usages of whole genome amplification worldwide. This is expected to bolster growth of the Whole genome amplification market over the forecast period.

To Get Sample Copy of Report visit @https://www.futuremarketinsights.com/reports/sample/rep-gb-1873

Global Healthcare Sector Outlook

Despite the economic and political uncertainty in the recent past, the global healthcare industry has been receiving positive nudges from reformative and technological disruptions in medical devices, pharmaceuticals and biotech, in-vitro diagnostics, and medical imaging. Key markets across the world are facing a massive rise in demand for critical care services that are pushing global healthcare spending levels to unimaginable limits.

A rapidly multiplying geriatric population; increasing prevalence of chronic ailments such as cancer and cardiac disease; growing awareness among patients; and heavy investments in clinical innovation are just some of the factors that are impacting the performance of the global healthcare industry. Proactive measures such as healthcare cost containment, primary care delivery, innovation in medical procedures (3-D printing, blockchain, and robotic surgery to name a few), safe and effective drug delivery, and well-defined healthcare regulatory compliance models are targeted at placing the sector on a high growth trajectory across key regional markets.

Research Methodology

FMI utilizes a triangulation methodology that is primarily based on experimental techniques such as patient-level data, to obtain precise market estimations and insights on Molecule and Drug Classes, API Formulations and preferred modes of administration. Bottom-up approach is always used to obtain insightful data for the specific country/regions. The country specific data is again analysed to derive data at a global level. This methodology ensures high quality and accuracy of information.

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Secondary research is used at the initial phase to identify the age specific disease epidemiology, diagnosis rate and treatment pattern, as per disease indications. Each piece of information is eventually analysed during the entire research project which builds a strong base for the primary research information.

Primary research participants include demand-side users such as key opinion leaders, physicians, surgeons, nursing managers, clinical specialists who provide valuable insights on trends and clinical application of the drugs, key treatment patterns, adoption rate, and compliance rate.

Quantitative and qualitative assessment of basic factors driving demand, economic factors/cycles and growth rates and strategies utilized by key players in the market is analysed in detail while forecasting, in order to project Year-on-Year growth rates. These Y-o-Y growth projections are checked and aligned as per industry/product lifecycle and further utilized to develop market numbers at a holistic level.

On the other hand, we also analyse various companies annual reports, investor presentations, SEC filings, 10k reports and press release operating in this market segment to fetch substantial information about the market size, trends, opportunity, drivers, restraints and to analyse key players and their market shares. Key companies are segmented at Tier level based on their revenues, product portfolio and presence.

Please note that these are the partial steps that are being followed while developing the market size. Besides this, forecasting will be done based on our internal proprietary model which also uses different macro-economic factors such as per capita healthcare expenditure, disposable income, industry based demand driving factors impacting the market and its forecast trends apart from disease related factors.

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Market Taxonomy

By Product Type

By Application

By End User

By Region

1. Executive Summary

1.1. Market Overview

1.2. Market Analysis

1.3. FMI Analysis and Recommendations

1.4. Wheel of Fortune

2. Market Introduction

2.1. Market Taxonomy

2.2. Market Definition

2.3. Company Description and Whole Genome Amplification Market Research Coverage

3. Whole Genome Amplification Market Opportunity Analysis

3.1. Macro-Economic Factors

3.2. Opportunity Analysis

so on..

About FMI

Future Market Insights (FMI) is a leading provider of market intelligence and consulting services, serving clients in over 150 countries.FMIis headquartered in Dubai, the global financial capital, and has delivery centers in the U.S. and India. FMIs latestmarket research reportsand industry analysis help businesses navigate challenges and make critical decisions with confidence and clarity amidst breakneck competition. Our customized and syndicated market research reports deliver actionable insights that drive sustainable growth. A team of expert-led analysts at FMI continuously tracks emerging trends and events in a broad range of industries to ensure that our clients prepare for the evolving needs of their consumers.

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Whole Genome Amplification Market To Make Great Impact In Near Future By 2028 - PharmiWeb.com