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The Evolutionary Perspective
Daily Archives: April 13, 2020
Posted: April 13, 2020 at 11:48 am
The decoding of the genome was a sensation, although the announcement by Craig Venter on April 6, 2000, was somewhat premature. It actually took another year before the Human Genome Project (HGP), which was in competition with Venter, published its peer-reviewed research results in the scientific journal Science and Nature on February 15, 2001.
Battle for first place
The decoding of the genome was a race for scientific fame between the HGP, which is government-funded by the US, and Venter with his private company Celera Genomics. The government researchers lagged somewhat behind Celera Genomics in their work. By April 2000, they had been able to decode only 54% of the human genome.
The genome is made up of the genetic storage material deoxyribonucleic acid (DNA). It contains all hereditary information of life.
Read more:Blood test detects more than 50 types of cancer
Craig Venter 1998 in the laboratory of his company Celera Genomics. Venter invented the shotgun sequencing method.
Going after the genetic material with a shotgun
Venter used a different sequencing method than the HGP researchers: namely, the so-called shotgun method that he developed. In this method, the individual DNA fragments are generated randomly. This is similar to shooting at the long chain with a shotgun and then looking at and reading out the fragments individually.
However, Venter also used HGP data to achieve his goal. And that was an ambitious one: The human genome consists of 3.2 billion base pairs the letters of life, so to speak. Finding them all was a mammoth task for him and the competing researchers. But the design of this genetic chain is actually quite simple.
It consists of a sequence of only four different building blocks: the DNA bases cytosine (C), guanine (G), adenine (A) and thymine (T). It is the sequence of these bases that determines our eye or hair color or whether we have any hereditary diseases.
Read more:Stone-Age 'chewing gum' reveals human DNA
Many doors leading nowhere
Only a few sections of the entire genome are the genes that contain important instructions for building blocks of life such as proteins. "According to current knowledge, however, a large proportion of DNA is an evolutionary remnant and has no function whatsoever. This makes it clear that although the door to the code of life has been opened, countless new doors are hidden behind it," writes chemist Friederike Fehr from the Max Planck Institute for Dynamics and Self-Organization in Gttingen.
Many genes that were discovered in the genome sequence had been unknown until then. "So the effects or tasks associated with them must also be researched. The sequence of letters alone is of limited help in this regard," Fehr writes.
Long road to medical applications
It was only with the completion of sequencing that the project of decoding the human genome could bear practical fruit. Although Venter published his own personal genome in the scientific journal PLoS Biology in 2007, this, too, was of rather symbolic importance. Gene sequencing in itself was only a first step toward a fundamental change in our medicine.
Scientists still had to research and assign the respective functions of the individual building blocks of the genome, i.e. find out which building block is responsible for what. They did this with the help of mice. Their genome is largely identical to that of humans and thus provided a basis for understanding the functions of human genes.
Experts believe that it could take dozens, if not hundreds, of years to really understand the human genome.
Read more:Who's the daddy: Does it really matter where your DNA comes from?
What do we get out of this?
The genomes of two people differ. These differences are the basis for the genetic predisposition to certain diseases.
Increasingly, genetic tests are being offered that enable experts to identify some of these predispositions and thus determine whether or not a person carries an increased risk of disease. A saliva sample is sufficient for this.
The most important thing in all these tests is to interpret the results correctly, for example, to determine if there is the disposition for Alzheimer's or diabetes.
With the help of genome research, it is now possible to identify various gene functions. This in turn helps doctors to treat certain diseases, including in children with an immune deficiency that is hereditary. Doctors can even implant new genes into these children to treat the disease.
Breast and ovarian cancer become apparent in the alterations of two genes (BRCA1 and BRCA2). A genetic risk for a tumor disease can be detected only in a few cases by genetic analysis.
There is still much to be done
The human genome consists of roughly22,500genes. Researchers around the world were astonished at this result as, believe it or not, a water flea has 30,907.
How complex a living being is, therefore, not dependent only on the number of genes. US President Bill Clinton said on April 6, 2000: "Now we are learning the language with which God created life." We now know that we still need a lot more vocabulary before we master that language.
This article has been edited and correctedsince it's first publication on 5 April 2020
Read more:Barley geneticists toast to future of better beer
In 1891, a Croatian born, Argentine criminologist, Juan Vucetich, started building up the first modern-style fingerprint archive. Since then, fingerprints have become one of the main forms of evidence used to convict criminals. Here, a police officer spreads dust on the lock of a burglarized apartment. Fingerprints become visible.
He uses an adhesive film to capture the fingerprint. Then he glues it to a piece of paper. In the past, comparing fingerprints was a painstaking affair. Officers had to compare fingerprints found at the scene of a crime, one-by-one, with those of possible suspects. These days computers do the job.
Taking fingerprints used to be a messy affair - with ink and dirty hands. These days scanners have replaced the inky mess. And the data can immediately be sent to a database and turned into biometrical data.
The computer identifies typical spots within the ridge patterns of the fingerprint. These include forks in the lines, spots and the location of the center of the print. Fingerprints are never the same between two people - not even with identical twins.
No chance! Here, officials use fingerprint scanners during an election in Nigeria. It's how they make sure the people voting are registered voters and that they only vote once.
This is an important question for officials who have to decide about the refugee or asylum status of applicants. In the European Union all migrants are supposed to have their fingerprints taken at the first point of entry - provided, of course, the local police officers are equipped with the scanners.
Many smartphones now come with fingerprint recognition software, such as the iPhone's Touch-ID. The owner of the phone unlocks it with his fingerprint. If someone else finds or steals the phone, they have no way of getting at any encrypted data within.
This is an Automatic Teller Machine (ATM) in the Scottish town of Dundee. Customers wanting to withdraw money need to show biometric proof of identity - in the form of a fingerprint. Not good news for pickpockets.
Since 2005, German passports, and many other passports, contain a digital fingerprint as part of the biometric information stored on a RFID (radio-frequency controlled ID) chip. Other information on the chip includes a biometric passport photo. The facial image is similar to fingerprints: no two images are alike.
Facial recognition software, which uses biometrics, is well advanced. It is possible to identify suspects within large crowds, with surveillance cameras. Also internet services and private computer owners are increasingly making use of facial recognition software to sort holiday pictures and tagging them to names.
Alec Jeffreys discovered DNA-fingerprinting almost accidentally in 1984 during research at the University of Leicester. He identified a specific pattern on DNA segments, which were different for every human. He created a picture, which looks like a barcode at the supermarket.
Germany's Federal Criminal Police Office (BKA) started storing such barcodes in a federal database in 1998. Investigators have since solved more than 18,000 crimes, using genetic fingerprints.
It's not just criminals who get identified. Many innocent people can be cleared of criminal charges through good identification. For some, technology has saved their lives. Kirk Bloodsworth spent almost nine years on death row. The US Innocence Project has proved the false incarceration of more than 100 people using DNA evidence.
The first big test for DNA-fingerprinting came with the mass murder of Srebrenica. Bodies, exhumed from mass graves, were systematically identified using DNA techniques. They were then reburied by their loved ones. Here, five year old Ema Hasanovic pays last respects to her uncle. More than 6,000 victims of the massacre - mostly men - were identified using DNA-fingerprinting.
You may be surprised, but there's biometric information in sounds and other digital data. Voice recognition software can, for instance, identify people making threatening phone calls - the human voice is also unique. And don't forget: we leave all kinds of digital traces on the internet, which hold clues to who we really are.
Author: Fabian Schmidt
Posted: at 11:48 am
Two teams of scientists in Italy have collaborated on a project that further analyzed the SARS-CoV-2 genome from locally acquired samples. The analysis of the samples via next-generation sequencing (NGS) reveals a specific level of genetic variability that implies the SARS-CoV-2 genome is stable.The results are useful in the development of a safe and effective vaccine against SARS-CoV-2, as the more stable the virus's genome, the greater likelihood that a vaccine will be effective globally across populations.Technology Networks spoke with Professor Stefano Menzo, virologist, and Dr Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, to learn more about the findings.Molly Campbell (MC): For our readers that may be unfamiliar, please can you explain how next-generation sequencing (NGS) is utilized to explore the genome of the SARS-CoV-2 virus?Valerio Onofri (VO): NGS is a high-throughput method to sequence DNA or RNA. Unlike the classic Sanger sequencing method, NGS provides millions to billions of short nucleotide sequence reads in just a few hours and at lower costs. This method is routinely used to find pathogenetic variants that cause inherited disease or cancer. It is also useful to discover the sequence of an unknown viral, prokaryote or eukaryote genome.When a reference sequence becomes available, NGS labs can sequence a clinical or population sample, align the new sequence to the reference and annotate the differences to determine whether mutations have occurred. We are doing this work now to better understand the SARS-CoV-2 virus. The virus was first sequenced in December 2019 and in February 2020 in Wuhan, China where it originated. When the pandemic spread, many labs like ours began sequencing virus samples from local patients to detect variants and study their significance. NGS provides both fast whole genome sequencing and, thanks to sequencing redundancy, quasispecies analysis (analysis of both major and minor variants).MC: Please can you tell us about The Ion AmpliSeq SARS-COV-2 Research Panel?VO: This panel was designed by Thermo Fisher Scientific to provide an efficient, high-throughput workflow for analyzing the entire SARS-CoV-2 genome on the Ion Torrent platform. Based on the targeted approach by amplicons method, it consists of about 250 PCR cycles to amplify the full SARS-COV-2 genome. Drawing on our expertise from routinely using this method for forensic and medical genetics, we helped Thermo Fisher validate the panel in virus isolates as well as throat/nasal swabs. It is now widely available for NGS-based research to better understand COVID-19.MC: What have your analyses so far revealed about the genetic stability of the SARS-CoV-2 virus?Stefano Menzo (SM): So far, SARS-CoV-2 appears to be a relatively stable virus, meaning it does not display many variants in the quasispecies, compared to other known RNA viruses such as HCV or HIV.MC: What does the SARS-CoV-2 genome reveal about the evolutionary path of the coronavirus?SM: More sequencing of full-length genomes throughout the world will be necessary to better answer this question. For now, we can say the virus has started differentiating in the human population from a common ancestor at a slow/moderate pace.MC: How can this data be utilized in the development of preventatives/ therapeutics against the COVID-19 outbreak?SM: Any vaccine will work best throughout the world if the virus is relatively confined geographically to limit the generation of escape mutants. The same is true for any antiviral treatment.MC: What are your next steps in this research space?SM: We will continue to investigate the viruss evolution by sequencing samples from patients with different clinical outcomes.Professor Stefano Menzo, virologist, and Dr. Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, were speaking to Molly Campbell, Science Writer, Technology Networks.
See the article here:
Further Analysis of SARS-CoV-2 Genome Suggests It Is Stable - Technology Networks
Gundersen researchers sequence genomes of COVID-19, results help with tracking and possibly mitigating spread – La Crosse Tribune
Posted: at 11:48 am
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Just two weeks after developing a test for COVID-19, Gundersen Medical Foundation researchers have successfully sequenced the complete viral genomes of the virus, an achievement that will help researchers understand its origins and evolution during spread.
The Gundersen Medical Foundation cancer research team, directed by Dr. Paraic Kenny, has been utilizing the Foundations cancer genome sequencing equipment to examine COVID-19 infections in La Crosse County patients and how they correlate with the global pandemic.
To conduct the research, Kenny and his team secured Institutional Review Board approval to use specimens, remaining after the conducting of standard COVID-19 testing, from six of the La Crosse Countys earliest cases of the virus.
At the most basic level, the virus makes occasional spelling mistakes when it copies its genome during infection and these mutations are faithfully carried in all subsequent infections by that particular virus, Kenny says. By sequencing the whole viral genome, we have been able to map the different COVID-19 strains currently in La Crosse County. This allows us to go far beyond positive and negative test results to better understand how the virus spreads within our community and health-care system.
Through its local lab, Kennys research team has been able to document the independent appearance of COVID-19 strains in the Coulee Region, discovering several of the viruses sequenced share molecular fingerprints with viruses that traveled directly from China to Washington state, as well as strains that circulated about a month ago in France and one sub-strain present in community spread.
Trump wonders if COVID-19 genomes gave fake quotes to the NYT in bizarre Saturday outburst – Raw Story
Posted: at 11:48 am
President Donald Trump lashed out at The New York Times on Saturday.
So now the Fake News The New York Times is tracing the CoronaVirus origins back to Europe, NOT China. This is a first! I wonder where (sic) the Failing New York Times got for this one? Are there any NAMED sources? Trump wondered.
However, the reporting from The Times was not based on anonymous sources.
New research indicates that the coronavirus began to circulate in the New York area by mid-February, weeks before the first confirmed case, and that travelers brought in the virus mainly from Europe, not Asia, The Times reported on Wednesday.
The story cited now research by geneticists at the Icahn School of Medicine at Mount Sinai and the N.Y.U. Grossman School of Medicine.
Both teams analyzed genomes from coronaviruses taken from New Yorkers starting in mid-March, the newspaper noted. The research revealed a previously hidden spread of the virus that might have been detected if aggressive testing programs had been put in place.
Trump appeared bored on Saturday as he went for his second weekend without playing golf.
Trump spent the early evening praising a West Virginia resident for comments made when they called in to C-SPAN and complaining about Fox News hours before a Fox News interview.
then let us make a small request. The COVID crisis has cut advertising rates in half, and we need your help. Like you, we here at Raw Story believe in the power of progressive journalism. Raw Story readers power David Cay Johnstons DCReport, which we've expanded to keep watch in Washington. Weve exposed billionaire tax evasion and uncovered White House efforts to poison our water. Weve revealed financial scams that prey on veterans, and legal efforts to harm workers exploited by abusive bosses. And unlike other news outlets, weve decided to make our original content free. But we need your support to do what we do.
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Trump wonders if COVID-19 genomes gave fake quotes to the NYT in bizarre Saturday outburst - Raw Story
Posted: at 11:47 am
Investigators have identified genomic alterations that appear to be associated with prognosis in men with metastatic castration-sensitive prostate cancer (mCSPC).
Astudy of 424 patients with mCSPC treated at a tertiary care center revealedthat alterations in the androgen receptor (AR), TP53, cell-cycle, MYC oncogenicsignaling pathways occur more commonly in tumors with worse overall survivaland decreased time to castration-resistant disease, whereas alterations in theSPOP and MNT pathways occur more frequently in tumors with a better prognosis,according to findings published in ClinicalCancer Research.
Thegenomics of metastatic castration-sensitive prostate cancer have not been wellcharacterized in the literature, but it is now clear that upfront treatmentintensification with taxanes or next-generation AR-directed therapies offerbenefit in the overall patient population, said the studys co-senior authorWassim Abida, MD, a medical oncologist at Memorial Sloan Kettering CancerCenter in New York. The question remains whether treatment selection ortargeted therapies can be employed based on genomic characteristics.
Theassociation between alterations in cell-cycle genes and TP53 and MYC pathwaygenes and worse outcomes may pave the way for targeted therapy in thesehigher-risk groups, Dr Abida said.
Thestudy compared genomic alterations according to clinical phenotypes: high- vslow-volume disease and de novo vsmetastatic recurrence. Of the 424 patients in the study, 213 men (50%) hadhigh-volume disease (4 or more bone metastases or visceral metastases) and 211(50%) had low-volume disease; 65% had de novometastases and 35% had metastatic recurrence. At the time of sample collection, patients had a medianage of 66 years. The investigators conducted gene sequencing from May 2015 to September2018.
High- vs low-volume disease
Inadjusted analyses, men with higher-volume disease had significant 1.8- and3.7-fold increased risks of castration-resistant disease and death,respectively, compared with men who had low-volume disease. Tumor specimensfrom men with high-volume disease had more copy number alterations.
Amongmen with high-volume disease, the highest-ranking pathways were the NOTCH,cell-cycle, and epigenetic modifiers pathways.
Althoughthe prevalence of CDK12 alterations differed between patients with de novo metastatic and those with metastaticrecurrences, the groups had similar prognoses. I was actually surprised therewere not more dramatic genomic differences between de novo and relapsed disease, said study co-senior author PhilipKantoff, MD, a medical oncologist and Chair of the Department of Medicine atMemorial Sloan Kettering Cancer Center in New York.
Afteradjusting for disease volume and other genomic pathways, the researchers foundthat the rates of castration resistance differed by 1.5-fold and up to 5-fold accordingto alterations in the AR, SPOP (inverse), TP53, cell-cycle, WNT (inverse), andMYC pathways. Overall survival (OS) rates varied from 2- to 4-fold according toalterations in the AR, SPOP (inverse), WNT (inverse), and cell-cycle pathways.PI3K pathway alterations were not associated with prognosis.
Docetaxeland next-generation AR axis-directed therapies have been shown to prolong OS, butit remains uncertain which patients benefit the most from intensifiedtherapies. We did not find any obvious genomic reason to explain thedifferences in docetaxel sensitivity between high- and low-volume disease, DrKantoff said.
Theauthors pointed out that genomic landscape studies of tumor DNA profiling inprostate cancer in general have excluded metastatic castration-sensitive tumors.Instead, most studies have focus on localized disease or metastaticcastration-resistant disease.
DrAbida and his colleagues acknowledged that their study has inherent biases becauseit was hospital based and enrolled patients at an academic referral center.
Moleculardeterminants of castration resistance or survival in patients with mHSPC have beenunclear, but the new study sheds new light on molecular alterations associatedwith poor outcomes in men with mHSPC, particularly alterations in the AR, cellcycle genes, MYC, and TP53 genes, said Joshi Alumkal, MD, the Leader of theProstate/Genitourinary Medical Oncology Section and Associate Division Chieffor Basic Research in the Hematology-Oncology Division at the University ofMichigan School of Medicine.
Severalrandomized phase 3 clinical trials now show a benefit of escalating treatmentin men with mHSPC by adding novel AR-targeting agents or chemotherapy plusmedical castration versus medical castration alone, Dr Alumkal said. Whetherthe addition of any of these specific agents to medical castration isassociated with improved outcomes in patients with poor-risk molecularalterations identified by the new study is a critical next question, he said.
Urologiconcologist James Mohler, MD, Senior Vice President for Translational Researchat Roswell Park Comprehensive Cancer Center in Buffalo, New York, said the new study found relativelysmall differences among the clinical phenotypes, but that is not surprisingbecause the temporal differences in the evolution of tumor biology occur overlong periods of time, much of which precedes clinical presentation. The hazardratios for association between mutational analysis and oncologic outcome insome cases were statistically significant, but are so small as to not beclinically significant. Part of the reason for this may be that prostatecancer, once metastatic, is so complex that no single mutation or single genepathway is driving growth and hence targetable at a high rate beyond the long provenbenefit from androgen deprivation therapy, Dr Mohler said.
Theresults reported by these authors may be disappointing to many clinicians, butare important because they represent a comprehensive analysis of mCSPC. Theauthors appropriately acknowledge that better tumor sampling and morecomprehensive genetic analysis and larger numbers of patients may be requiredto find any benefit to genomic or somatic sequencing, Dr Mohler said. I amafraid that these limitations are not just of their work but a biologicallimitation of aggressive prostate cancer, which makes improving treatment ofadvanced prostate cancer in an individual patient extremely challenging.
Stopsack KH, Nandakumar S, Wibmer AG, et al. Oncogenic genomic alterations, clinical phenotypes, and outcomes in metastatic castration-sensitive prostate cancer [published online March 27, 2020]. Clin Cancer Res. doi: 10.1158/1078-0432.CCR-20-0168
See the rest here:
Genomic Alterations Linked to Outcomes in mCSPC - Renal and Urology News
Podcast: Nothing about me without meThe importance of involving patients in genomic research – Genetic Literacy Project
Posted: at 11:47 am
In this episode of Genetics Unzipped, recorded at the recent Festival of Genomics in London, Kat Arney finds out why its so important to make sure that both academic and commercial research studies are done with rather than on participants.
Research into genetic conditions relies on information from patients and their families, whether thats detailed health records or genomic data. As the tools and techniques for DNA and data analysis become cheaper and more organisations get in on this fast-growing field, its vital to make sure that the most valuable research resource human lives doesnt get overlooked in the rush.
Fiona Copelandis the chair of a support group for UK families affected by primary ciliary dyskinesia or PCD a rare genetic condition that affects the lungs and is the mother of two adult sons with the condition. Shes spent many years acting as a patient representative, engaging with academic and industry scientists looking to involve PCD patients in research into understanding and treating the condition. She explains what her role involves and shares her advice for how researchers can engage and involve patient groups more effectively. Her top tip? Dont make children cry!
Next Arney speaks with Patrick Short. Hes the CEO of Sano Genetics a Cambridge-based startup that aims to connect researchers with patients who want to take part in genomic research. While some companies using patients in research have come under scrutiny for poor handling of data and ethical compliance, Short is keen to help organizations do better and drive change in the fast-growing commercial genomics sector.
Finally, we hear from Shelley Simmonds, a disability rights campaigner and rare disease advocate whose son Fraser was initially given a diagnosis of Duchenne Muscular Dystrophy as a baby. When Fraser didnt seem to be progressing as might be expected for a child with the disease, she and her family got involved in Genomics Englands 100,000 Genomes Project in search of clarity but things turned out not to be quite so simple. Shelley talks what happens when the question Whats wrong with my child? has no answer.
Full transcript, links and references available online atGeneticsUnzipped.com
Genetics Unzippedis the podcast from the UKGenetics Society,presented by award-winning science communicator and biologistKat Arneyand produced byFirst Create the Media.Follow Kat on Twitter@Kat_Arney,Genetics Unzipped@geneticsunzip,and the Genetics Society at@GenSocUK
Listen to Genetics Unzipped onApple Podcasts(iTunes)Google Play,Spotify,orwherever you get your podcasts
Fighting the invisible: How science of genomics is helping us know novel coronavirus? – Northeast Now
Posted: at 11:47 am
As we enter 14th day of lock-down (April 7, 2020) in India, global death toll has reached more than 74,000, while as total Corona positive confirmed cases stands more than 13 lakh across the world, which is growing only, when you are reading this column. In India the tally stands at 4,281 people infected while as 111 deaths have been reported so far (April 7, 13:40).
The question is, how to deal with the new unseen villain. Is Science of Genomics helping us out? Lets dive a bit into what Genomics is and how it is helping us know this new actor in the epidemic world, SARS-Cov-2 virus, responsible for Covid-19 disease?
What is a Genome?
Genomes or genetic material of any organism are our guides to understanding how life works. Genomics (field which deals with study of Genomes) has revolutionized our understanding of human and pathogen (disease causing microbes) biology and also how the two interact.
Genome is an entire genetic material, containing hereditary information and present inside an organism such as human or bacteria or even virus. Genome consists of Genes. Genes themselves are small parts of larger molecules called DNA molecules (Deoxyribo Nucleic Acid) or RNA molecules (Ribo Nucleic Acid). DNA is a long molecule made up of a repeating string of just four different chemicals. (In scientific terminology these chemicals are also known as bases or nucelotides). Most genes are codes describing how to make different types of proteins. The information in genes is stored in order of these bases or chemicals only.
This digital like storage of information was one of the first big discoveries of modern science. Human genome is made of DNA. Same is the case with animals and plants or even bacteria or while as genome in some viruses is made of RNA only. Humans have an average of about 25,000 genes which control our various characteristic features and if there is some defect in our genes, they might result in diseases such as Haemophilia, Sickle Cell disease, Downss syndrome etc.
Similarly, bacteria have around 4000 genes. In the same way Viruses, which are much smaller than bacteria have genomes which contain information about their body biology and also the information required to make the virus and how they would work as well as interact with other organisms or hosts such as humans.
They also decide how a virus would respond if there is any change in its environment. How a virus would control the host cell (cells which they infect), is all coded in their genomes only. Some mutation or changes in genome of a virus renders him pathogenic or disease causing, which otherwise is non-toxic. Living organisms are mostly made of proteins and fats. Thus, to understand genes is to understand the organism itself.
Now why are viral or bacterial genomes important here?
Genome variations in bacteria and viruses give us a lot of information. For example, how they cause diseases, how they originate, how they interact with the host (organisms they cause diseases) and their pathogenicity or how toxic they are. By sequencing the genome of a bacteria or virus one can, not only determine which genes of bacteria and virus play a role in causing disease but through better understanding can help in creating possible solutions of how to stop them.
Thus, Genomic data is essential not only to build tests for identifying the villain (virus) but also to create drugs and vaccines against them. Whole genome sequencing (WGS) or complete genome sequencing is actually the process of determining the complete DNA sequence of an organisms genome at a single time.
Modern scientific methods such as WGS, enable us better examination of diversity and the analysis of virus populations, their origins as well as mutations they undergo during any epidemic. Genome sequencing has emerged as major and vital diagnostic tool for disease outbreak as well as identification of the disease-causing microbes.
What Novel Corona Virus (SARS-Cov-2) genome analysis has revealed so far?
Bacteria & Viruses differ from each other in two main aspects. One, bacteria are single celled organisms that are found throughout our body and in our environment while as viruses are much smaller than bacteria and live as long as they are inside a host organisms.
Second is antibiotics usually kill most of the bacteria but they arent effective against viruses. A virus has either a DNA or RNA genome. But vast majority of viruses have RNA genome. A virion is an entire virus particle consisting of an outer protein shell called a capsid or capsule and an inner core of nucleic acid (RNA or DNA). Thus, a genome in viruses is often packed within a protein capsule.
Now let us come to Novel Coronavirus, also known as SARS-Cov-2. Despite its similarity to other viruses in the coronavirus family, the virus is relatively unknown. It is thought to spread more easily and has higher mortality rates than some of its better-known counterparts, adding to the existing challenges of any public health crisis of this scale.
Scientific attempts to know the Novel Coronavirus, which causes Covid-19 disease, started with the study of its genetic material by using gene sequencing techniques. One amongst the first attempts of whole genome sequencing of SARS-Cov-2 virus outside China, was made by a group of scientists from Nepal, Colombia, Saudi Arabia, United Kingdom and Japan, from a strain which was taken from a Covid-19 patient in Nepal.
The patient was a Nepalese student of Wuhan University of Technology in Wuhan, China who had returned to Nepal and was showing symptoms such as mild fever, cough and throat congestion. The specimen was collected at the National Influenza Centre, National Public Health Lab-oratory in Kathmandu, Nepal and subsequently its genome was studied at WHO laboratory in University of Hong Kong, Hong Kong. This was done in February 2020 and then subsequently it got published in Microbiology Resource Announcements on 12th March 2020.
Similar attempts of isolation and sequencing of whole genome of the virus were done at many different laboratories of the world. For example genome sequencing was also carried out in African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer University, Nigeria. This was a preliminary attempt to reveal the sequence. Around 20th March 2020, the study of SARS-Cov-2 genome was carried out by ICGEB-Trieste, Italy, by a group of scientists, led by Alessandro Marcello.
Likewise, genome analysis was also carried out by a group of scientists from USA, UK and Australia. This particular study was led by Kristian G. Andersen of Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, USA and got published in Nature Medicine on 17th March 2020. These genome detailing procedures have revealed some important features about the virus such as its outer coating also known as Spike protein.
The analysis has shown the high affinity of the outer coating of the virus with humans and that this affinity is a result of natural selection process or evolution of this virus. This study done by Kristian G. Andersen and his colleagues, has revealed that the virus is not a product of any human manipulation, thus debunking many theories about its possible laboratory origins.
The study has also revealed that there have been some mutations in the virus which have changed its outer protein shell and thus facilitated its easy binding with with the human cells (e.g. Lung Cells). The virus has acquired few other mutations which make it so contagious as well as deadly for humans. The study has suggested two possibilities by which it could have evolved and acquired such features and traits which make it so deadly and resistant to all known vaccines & drugs. One is by natural selection in an animal host before it could jump into humans and second is natural selection in humans itself after it got transferred from animals.
More such studies are in progress across many different laboratories just to precisely determine how this animal virus sidestepped the species boundaries to infect humans to such an extent that it soon became a pandemic. The genomic studies would also help us reveal partly the spread and infectiousness in human population.
Genome sequencing of the virus (SARS-Cov-2), causing Covid-19 disease is currently going on in different research laboratories around the world to effectively understand the various strains, their biology and the mutations they undergo, which are causing the epidemic. Genome sequencing is also important in every country which is facing the epidemic to know the course of the disease and thus to explore effective ways which are needed to tackle it.
The war against Covid-19 is not over yet and there are still many unknowns regarding SARS-Cov-2 virus as well as Covid-19 disease, which need to be uncovered. It is just a matter of time before an effective vaccine is developed against the virus, and the villain, which has snatched many souls from their loved ones, is finally defeated by us. I dont know what better way to conclude than with this beautiful line from a play by Shakespeare, Health Shall Live Free and Sickness Freely Die.
Rayies Altaf is a science & technology writer and is currently consultant at Centre for Community Knowledge, Ambedkar University, New Delhi.
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Fighting the invisible: How science of genomics is helping us know novel coronavirus? - Northeast Now
Posted: at 11:44 am
With help from Eric Geller, Martin Matishak, Melissa Heikkil, Cristiano Lima and Daniel Lippman
Editors Note: Morning Cybersecurity is a free version of POLITICO Pro Cybersecuritys morning newsletter, which is delivered to our subscribers each morning at 6 a.m. The POLITICO Pro platform combines the news you need with tools you can use to take action on the days biggest stories. Act on the news with POLITICO Pro.
A coronavirus contact-tracing initiative from Apple and Google has some privacy and security landmines to navigate.
An advocacy group urged the Federal Energy Regulatory Commission to move ahead with cybersecurity standards despite calls to move back the timing.
A top U.N. official called for a digital cease-fire as the world contends with coronavirus, especially because of the need to safeguard health care organizations and employees.
HAPPY MONDAY and welcome to Morning Cybersecurity! So relatable. If a hacker gets a hold of a Zoom, what can they tell? Send your thoughts, feedback and especially tips to [emailprotected]. Be sure to follow @POLITICOPro and @MorningCybersec. Full team info below.
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TRACKING DOWNSIDES A joint Apple-Google project to track coronavirus exposure risks announced last week has sparked privacy and security fears even as some lawmakers are willing to give the tech giants some leeway. Tech companies new feature to contact trace coronavirus cases has positive potential, but we must ensure privacy concerns are considered, tweeted House Energy and Commerce Chairman Frank Pallone (D-N.J.). Ill be following this closely to ensure consumer privacy is protected. Rep. Jan Schakowsky (D-Ill.), who chairs E&Cs consumer protection subcommittee, echoed the sentiment.
Some security experts said that although the plan features safeguards, they arent adequate given the nature of the information at play. Phone data has NEVER been proven secure and the chance of release is above 0%, observed Sergio Caltagirone, vice president of threat intelligence for Dragos. In fact, this is so juicy I'd argue there will be lots of baddie[s] who are interested in finding ways to leak this. Matt Tait, a cyber fellow at the University of Texas at Austin, spelled out a slew of other potential problems.
Jennifer Granick, surveillance and cybersecurity council for the ACLU, credited the two companies for steps to mitigate risk but said there was room for improvement. These systems also cant be effective if people dont trust them, she said. People will only trust these systems if they protect privacy, remain voluntary, and store data on an individual's device, not a centralized repository.
Former Vice President Joe Biden, the presumptive Democratic nominee, broadly touched on the issue in his newly released proposal to safely reopen America. In a New York Times op-ed outlining his plan, Biden calls for a contact tracing strategy that protects privacy. And Apple and Google reportedly will work with the U.K., too.
NOT SO SLOW The coronavirus pandemic isnt a reason to significantly delay supply chain cybersecurity standards for electric grid utilities, the grid resilience advocacy group Protect Our Power told FERC late last week. The North American Electric Reliability Corp. wants FERC to delay the deadline for complying with the cyber rule and other new regulations, saying compliance could disrupt operations at a critical time. But in comments filed Thursday with FERC, Protect Our Power said NERCs requested three-month delay may not be justified or necessarily be in the public interest. Instead, it asked FERC to only grant a 30-day extension. This approach would acknowledge the time lost by utilities due to the coronavirus pandemic, the group said, but otherwise require the industry to continue to treat the supply chain security issue with the importance and seriousness it deserves.
In requesting a 90-day delay, NERC argued that the extra time would allow entities to recover from coronavirus-related strains, but Protect Our Power said such a long recovery window likely wasnt necessary. Given that FERC issued the supply chain standard 15 months ago, the group said, many or most utilities may already be prepared to comply with it by the current July 1 deadline. A shorter delay, it said, would also prevent us from having one crisis, the pandemic, unnecessarily cause us to lose focus and a sense of urgency about another crisis, supply chain risk.
CYBER CEASE-FIRE The United Nations undersecretary-general on Friday published an op-ed calling for a worldwide digital cease-fire during the coronavirus pandemic. When launched successfully, digital attacks are catastrophic and can lead to loss of life, wrote Fabrizio Hochschild. In particular, health care workers and hospitals battling Covid-19 shouldnt have to question whether their data and medical equipment is secure or worry about it being shut down. We must commit to an immediate digital cease-fire, and governments, civil society groups, and the private sector must set the tone. Without this step, our global response to the pandemic will be weakened, according to Hochschild.
ALL I WANNA DO IS ZOOM-A-ZOOM-ZOOM-ZOOM The top Republican on the House Oversight panel on Friday called for majority Democrats to abandon usage of the Zoom video conferencing service, citing security issues. Given the concerns surrounding Zooms security, it is clear Zoom is not an appropriate platform for Committee business, which may be particularly sensitive during the COVID-19 pandemic, wrote Rep. Jim Jordan (R-Ohio). Please immediately suspend any current or future use of Zoom systems for official committee activities and take immediate steps to evaluate the Committees internal cybersecurity preparedness to prevent hackers from accessing sensitive committee information through the Zoom platform.
Jordan cited the Senate sergeant at arms warning last week for offices to stop using it, broader hacking and malware concerns, and Zoom work done by employees in China as causes to suspend use. Jordan said House Oversight Democrats had been Zoom-bombed, something Democrats denied.
Rep. Jordans office was consulted directly and repeatedly about using Zoom and never raised any concerns, so its unfortunate that he is now putting out inaccurate information in this public letter, said Chairwoman Carolyn Maloney (D-N.Y.). Had his office consulted with us first, we could have clarified their misunderstandings and provided more information about the steps the Committee has already taken to address any potential issues. She said the committee would continue to use a number of different technologies to fulfill its responsibilities. The House was already reevaluating whether the chamber should switch to a government-specific form of Zoom.
EDGAR RIGHT The SEC announced last week that it has settled charges with two traders accused of profiting by exploiting sensitive corporate earnings information hacked from its EDGAR system. David Kwon of California settled for $165,474 that represented the profits from his alleged illegal trades, and $16,254 in interest; Igor Sabodakha of Ukraine settled for $148,804 in profits, prejudgment interest of $20,945 and a civil penalty of $148,804, plus the SEC said it would dismiss charges against his wife, Victoria Vorochek, whose accounts he allegedly used to conduct trades.
The EDGAR hack generated considerable interest from Congress when the SEC disclosed it in 2017, with some lawmakers pointing to their prior concerns about SEC vulnerabilities. The SEC charges against seven individuals and two entities filed in 2019 were accompanied by criminal charges against two other men.
CRITICAL SAFETY AND PRIVACY FLAWS IN CONNECTED CARS Drivers beware: Your rides are vulnerable to digital saboteurs. Some of Europes most popular connected car models have crucial security flaws that allow intruders to access personal data such as passwords and location history as well as components that control key functions such as collision-warning systems and tire air pressure, according to an investigation by British consumer group Which?.
By lifting the Volkswagen badge on the front of the car, researchers say they were able to access the vehicles front radar module, which controls its collision-warning system, according to our friends at POLITICO Europes Cyber Insights. Using a cheap laptop and a 25 gadget bought from online marketplace Amazon, the researchers also hacked into the Ford Focus system monitoring air pressure in tires. The investigators also got access to personal data such as Wi-Fi passwords, phone contacts and location history.
TWEET OF THE WEEKEND And then Zoom keeps doing stuff like this.
Kevin Zerrusen is now a managing director at EY where he works on cybersecurity and advisory services. He most recently was senior adviser to the chairman for cybersecurity policy at the SEC and is also a Goldman Sachs alum and served in the CIA for 30 years.
POLITICO: Small business loan effort might be less generous than advertised.
The Wall Street Journal: After Congress allowed surveillance tools to lapse, DOJ hasnt been able to obtain wiretaps or request business records between five and 10 times.
The Wall Street Journal: The FBI made errors in two FISA application filings last year.
Forbes: Cryptocurrency scammer revenue is down during the pandemic.
CyberScoop: Cyber criminal forums are also offering discounts during the pandemic.
Register: Cyber criminals leaked sensitive documents from contractors for Boeing, SpaceX, Tesla and other major companies in retaliation for an unpaid ransomware demand.
The Wall Street Journal: Travelex paid a $2.3 million ransom to hackers.
Bleeping Computer: San Francisco International Airport had a data breach.
gCaptain: Mediterranean Shipping Company may have suffered a cyberattack.
ZDNet: Online betting company SBTech will have to place $30 million in escrow as insurance for covering the fallout from a suspected ransomware infection.
Inside Cybersecurity: Two industry groups want more details from the Pentagon on its cybersecurity standards for contractors.
Forbes: Big data firm Palantir got some coronavirus emergency relief funds.
The New York Times: Burning Cell Towers, Out of Baseless Fear They Spread the Virus.
Thats all for today.
Stay in touch with the whole team: Eric Geller ([emailprotected], @ericgeller); Bob King ([emailprotected], @bkingdc); Martin Matishak ([emailprotected], @martinmatishak); and Tim Starks ([emailprotected], @timstarks).
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Posted: at 11:44 am
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Google has banned the popular videoconferencing software Zoom from its employees devices, BuzzFeed News has learned. Zoom, a competitor to Googles own Meet app, has seen an explosion of people using it to work and socialize from home and has become a cultural touchstone during the coronavirus pandemic.
Last week, Google sent an email to employees whose work laptops had the Zoom app installed that cited its security vulnerabilities and warned that the videoconferencing software on employee laptops would stop working starting this week.
We have long had a policy of not allowing employees to use unapproved apps for work that are outside of our corporate network, Jose Castaneda, a Google spokesperson, told BuzzFeed News. Recently, our security team informed employees using Zoom Desktop Client that it will no longer run on corporate computers as it does not meet our security standards for apps used by our employees. Employees who have been using Zoom to stay in touch with family and friends can continue to do so through a web browser or via mobile.
Headquartered in San Jose, California, Zoom went public in 2019, making its CEO Eric Yuan a billionaire. The companys videoconferencing service was aimed at enterprises to run webinars and meetings but is now being used by locked-down people around the world for gym sessions, education classes, cocktail parties, and more. In March, 200 million people used Zoom daily compared to just 10 million in December.
But Zooms growth has been marred by concerns around the services security and privacy. Last month, an investigation by Motherboard showed that Zooms app for iPhone and iPads sent data about users devices to Facebook, including people who did not have Facebook accounts.
Zoom stopped sending the data to Facebook just a day later, but more problems surfaced soon after. A former NSA hacker discovered a Zoom security issue that could allow bad actors to control users microphones and webcams and gain control of Apple iMacs. The Intercept showed that Zoom calls werent actually encrypted the way that the company claimed. Last week, the company said that some video calls were mistakenly routed through servers in China when they shouldnt have been. The offices of 27 attorneys general have also raised questions about the company.
Google isnt the first company to ban employees from using Zoom. Earlier this month, Elon Musks rocket company SpaceX also banned employees, citing significant privacy and security concerns, according to Reuters. And on Monday, New York Citys Department of Education urged schools to abandon Zoom and switch to a service from Microsoft.
[We] recognize that we have fallen short of the communitys and our own privacy and security expectations, Yuan wrote on a blog post earlier this month. For that, I am deeply sorry.
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Alphabet in the age of COVID-19: Google braved one recession, and now its more diversified – MarketWatch
Posted: at 11:44 am
This article is part of a series tracking the effects of the COVID-19 pandemic on major businesses, and will be updated. It was originally published on April 8.
Alphabet Inc.s Google lords over the online-advertising market, which is both a blessing and a curse in the age of coronavirus.
The core business of Alphabet GOOGL, -1.20% GOOG, -1.19% commands roughly 30% of the $110 billion digital-advertising market world-wide, and is expected to maintain that lead in 2021 and beyond, according to eMarketer. YouTube is a big reason why, as it is expected to haul in $9.33 billion in 2020 and $11.4 billion in 2021, according to eMarketer. In February, Alphabet disclosed it brought in $15.1 billion in ads through YouTube in 2019, and $8.9 billion via Google Cloud.
If there is one company that will initially be hit hardest by ad cutbacks, its Google. Up to 40% of its revenue comes from categories hard hit by COVID-19: in-person retail, restaurants, travel, automotive and small businesses. But it is also likely to be the first to rebound because of its market leadership.
Business in the age of COVID-19: Read profiles of how other large companies will be affected by the coronavirus
Google has been here before, when it wasnt named Alphabet. During the recession sparked by the subprime-loan crisis a decade ago, sales remained at single-digit growth for five quarters in a row. Googles revenue estimates declined at least 15% in 2009 and 2010, with a marginally greater earnings hit, according to analysis by MKM Partners.
Then again, Google had the field all to itself more than a decade ago, before Facebook Inc. FB, -2.55%, Snap Inc. SNAP, -1.71%, and Twitter Inc. TWTR, -3.74% emerged as online ad rivals.
Back then, I was told at the time the recovery is quicker than you think it is when you get there, and the strongest companies recover quicker than the weaker ones, former Google Chief Executive Eric Schmidt said in a Zoom ZM, +6.63% conference with business executives, investors and media on April 7.
Analysts seem to agree, painting a picture of short-term pain but a quick recovery for Google.
We are modeling a [year-over-year] decline in Google revenues in Q2 followed by a continued acceleration in revenues [in the second half], MKM Partners analyst Rohit Kulkarni said in an April 3 note. However, we do not expect Google to return to double-digit revenue growth until Q1 21.
To put this delicately, use the opportunity of the crisis to reconfigure and ensure the decisions you make now make you stronger when this lifts a year or maybe less, Schmidt said.
In 2008, for example, Google repriced stock options to employees to stabilize its workforce and retain talent.
It was the right decision at the time, Schmidt said.
Since the last recession, Google has also acted to diversify its business beyond search ads, with YouTube and Cloud accounting for more than 40% of incremental growth, MKM Partners reported.
Alphabet reports fiscal first-quarter results April 22.
Revenue: Average analyst expectations for the first quarter were $43.17 billion at the end of 2019, but have declined to $42.08 billion as of April 6. Estimates for Google websites, which account for most of Alphabets revenue, have declined from $30.32 billion to $29.73 billion in that time period, according to FactSet. For the full year, analysts expect revenue of $181.9 billion.
Earnings: Average analyst expectations from FactSet were $12.31 per share at the end of 2019. As of April 6, they were $11.24 per share. For the full year, analysts expect earnings of $48.90 as share.
Stock movement: During the first three months of 2020, Class A shares declined 13%. Google crested at $1,519.44 on Feb. 18, and closed at $1,183.19 on April 6.
Not much. Notoriously tight-lipped Alphabet executives havent said anything of note either in SEC filings, news releases or blog posts about the economic impact of coronavirus. What they have shared is mostly about a surge in traffic coursing over its network, prompting it to boost capacity to handle demands on its network and data centers.
April 3: Our priority now is how to meet the surge in demand, John Jester, vice president of customer experience at Google Cloud, told MarketWatch in a phone interview.
In a blog post on March 31, Google Cloud CEO Thomas Kurian said traffic on its premium videoconferencing property Meet has grown 60% day-over-day and is topping 2 billion minutes a day 25 times the traffic of a typical day.
Feb. 4: Until the last two quarters, Google was conspicuously silent about breaking out revenue figures by product division. During its fiscal fourth-quarter, it said YouTube was at $15 billion in annual ad revenue, and Cloud is on a $10 billion revenue run rate.
See also: YouTube, Google Cloud revenues finally revealed
Online advertising is half of global advertising, and Google has roughly 40% market share of online advertising. The math points toward an inevitable short-term disadvantage to Google, but a speedy recovery because of its clout, according to MKM Partners. We expect Google advertising revenues to decelerate from high teens (18% to 20%) during 2019 to 4% in 1Q:20, -1% in 2Q:20, and approx. +4% in 4Q20. We are raising our Google Cloud revenue assumptions as we expect continued acceleration in cloud, driven by sales force expansion and healthier end markets. MKM Partners analyst Rohit Kulkarni, maintained his buy rating while trimming Alphabets price target to $1,400 from $1,600 on April 3.
We expect Google to have a greater near-term disadvantage but also have a faster recovery as pandemic effects reduce... We believe Alphabet will be more resilient vs. Facebook in weathering the advertising decline due to its lower exposure to the [small business] advertiser base. As a result of these top-line changes, our 2020 GAAP EPS estimate is now $40.56 (vs. prior estimate of $53.47) and our 2021 GAAP EPS is now $54.30 (vs. prior estimate of $66. Citi analyst Jason Bazinet, maintained a buy rating while trimming Alphabets price target to $1,400 from $1,700 on April 1.
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