Category Archives: Genome

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

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.

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

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.

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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

By Express News Service

BENGALURU: Amidst concerns over the import of the new SARS-CoV-2 strain, Karnataka is awaiting genome sequence test results of 10-15 people who tested positive after returning from the UK.

Health Minister Dr K Sudhakar said that the samples of 10-15 Covid positive people had been sent to the National Institute of Mental Health and Neurosciences for a genome sequence test and the results would be out in two or three days. Once the report is out, we will know whether it is the second strain, and will follow necessary procedure for treatment, he said.

He said that researchers are studying new strains in other countries and according to initial studies, the SARS-CoV-2 variant of South African origin was more intensive than the one found in the UK. Based on the final reports from the Union Health Minister, we will take necessary steps. I have trust in the government.

Before we take any decision, we think a hundred times. Protecting the health of the people is our main priority, Sudhakar said.Local authorities are currently tracing the primary and secondary contacts of around 2,500 people who arrived in Karnataka from the UK between November 25 to December 22 on Air India and British Airways flights, and are now spread across the state.

Read this article:
Genome test results of UK returnees awaited - The New Indian Express

More News29 Dec 2020 | 10:50 AM

Kolkata, Dec 29 (UNI) West Bengal Governor Jagdeep Dhankhar on Tuesday will preside over in virtual mode Managing Committee of Ramakrishna Mission Institute of Culture.

Ambassa (Tripura), Dec 28(UNI) The Farmers' Act which has generated controversy after an almost month long dharna by the farmers in the national capital seems to have a completely different saga in the ever deprived north-eastern region of the country as the farmers here seem to be supporting this Act.

Patna, Dec 28 (UNI) Rajya Sabha MP and former Bihar Deputy chief minister Sushil Kumar Modi on Monday said that Congress leader Rahul Gandhi betrayed the farmers by leaving the country just ahead of their dialogue with the union government.

Bhagalpur, Dec 28 (UNI) Security at the NTPC power station of Kahalgaon in Bhagalpur was on Monday tightened following the arrest of a suspected person who was trying to enter the power station using fake documents.

Cuttack, Dec 28 (UNI) The police should look to the future as guardians of internal security in the country in order to face the challenges ahead, Chief of Defence Staff (CDS) General Bipin Rawat said here on Monday.

View post:
ILS Bhubaneswar to conduct genome sequencing - United News of India

Chennai: The result of genomic analysis of a sample from a United Kingdom returnee, who tested COVID-19 positive here, could be expected next week, according to the National Institute of Virology and Tamil Nadu has requested the research facility to expedite it, a senior health official said on Thursday.

The returnee from UK, who days ago tested positive, continues to be treated at the King's Institute for Preventive Medicine and Research and he is stable and doing well, Health Secretary J Radhakrishnan said here.

Asked on genomic analysis result of the sample sent to the Pune based NIV, he said institute authorities have indicated that it may be expected on December 28 and Tamil Nadu has requested it to expedite availability of result.

"We are talking with them (NIV) continously. This is genomic analysis. There are several mutations which has to be studied," he said.

The process involved in such an analysis is complex, something not seen in a routine test to detect coronavirus and hence it may consume more time, he noted.

The idea behind the test is to find out if the strain matched with the ones currently in circulation or whether it belonged to a different variant, like the one seen in the United Kingdom recently which is said to be more virulent.

Barring the young man, who tested positive on his arrival from the UK and being treated with drugs including anti-virals and antibiotics at state-run King's Institute, no other foreign returnee has tested positive, the official said citing test results of international returnees received.

Samples from 15 people-who travelled along with the man in the Delhi-Chennai connecting flight on Monday- have been taken and results are awaited. Seventy others on the domestic flight have also been asked to go for COVID-19 testing, he said.

A cargo flight arrived here hours ago from Britain and nine crew members have been tested for COVID-19 and they were sent to a hotel for institutional quarantine, the official said.

The cargo has been disinfected and instructions have been given to officials to not allow anyone to access the shipment as of now and a 'decision will be taken later on the cargo' after the results of the crew are known, he said.

While inspection of airports was on across Tamil Nadu, foreign returnees are allowed only if they have RT-PCR negative certificate and were being placed in home quarantine like those who arrive from other states. All the returnees were being monitored, the health official said.

Following inspection of the airport here, cargo handlers have been instructed to use Personal Protective Equipment and officials have been asked to focus more and increase visibility of advertisements on awareness about coronavirus at the premises,Radhakrishnan said.

Though flights from Britain have halted, officials have been instructed to intensify domestic surveillance as some could have travelled elsewhere from the UK and may arrive later in Tamil Nadu, he said. They were in touch with airline operators as well to ensure foolproof monitoring.

About 38,000 passengers who arrived from countries other than the UK recently were also being monitored in Tamil Nadu.

Instructions have been given to them to approach authorities if they have any symptoms and as regards returnees from the UK, their primary contacts were also being monitored.

Three people who arrived from Delhi allegedly did not cooperate with public health authorities and they proceeded to their destinations in the state and nearby Puducherry claiming that they tested negative for the virus in the national capital.

They were, however, subsequently traced and placed under insolation, he said and appealed to passengers and the general public to cooperate with officials to effectively tackle the pandemic.

If passengers prevent authorities from carrying out their duty like testing for the contagion, a complaint would be lodged against them with the police and action initiated, Radhakrishnan warned.

Read more:
Genomic analysis result of UK returnee's sample expected from NIV next week, says TN - Economic Times

The U.S. Food and Drug Administration has approved the first treatment for progeria, a rare and fatal pediatric disease, characterized by dramatic, rapid aging beginning in childhood. The treatment was made possible thanks in part to work at the National Institutes of Health over nearly two decades to identify and understand the function of the mutant gene and the protein it encodes (called progerin) with the goal of identifying new therapeutic drugs for the disorder.

In light of todays approval, NIH Director and Senior Investigator at the National Human Genome Research Institute (NHGRI), Francis S. Collins, M.D., Ph.D., is available to discuss his labs research activities on progeria, including its involvement in the discovery of the gene responsible for the disease, the development of a mouse model, and the demonstration that this drug class could provide benefit.

Progeria, also known as Hutchinson-Gilford progeria syndrome, is a rare, multisystemic disease that causes premature aging and premature death in children. Progeria is caused by a genetic mutation in the LMNA (lamin A) gene, which helps maintain the normal structure and function of a cells nucleus. About 400 children worldwide have been diagnosed with progeria.

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Decades of NIH research help lead to first FDA-approved treatment for progeria - National Human Genome Research Institute