- Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk Nature.com
- Scientists discover evidence of 4 more breast cancer genes—and potentially many others: ‘The risks can be significant for women who carry them Fortune
- Unraveling the Genetic Code: New Suspects in Breast Cancer Identified SciTechDaily
- Thousands more women could discover they’re at increased risk of breast cancer as scientists identify 4 n… The US Sun
- Blood test may spot women at risk of breast cancer as scientists discover another four genes linked to disease Daily Mail
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Tag Archives: Sequencing
Genome sequencing trial to test benefits of identifying genetic diseases at birth | Genetics
Genomics England is to test whether sequencing babies’ genomes at birth could help speed up the diagnosis of about 200 rare genetic diseases, and ensure faster access to treatment.
The study, which will sequence the genomes of 100,000 babies over the next two years, will explore the cost-effectiveness of the approach, as well as how willing new parents are to accept it.
Although researchers will only search babies’ genomes for genetic conditions that surface during early childhood, and for which an effective treatment already exists, their sequences will be held on file. This could open the door to further tests that could identify untreatable adult onset conditions, or other genetically determined traits, in the future.
“One challenging thing with newborn genomes is that they will potentially accompany people from cradle to grave,” said Sarah Norcross, director of the Progress Educational Trust (PET), an independent charity that improves choices for people affected by infertility and genetic conditions.
Ensuring the privacy of this data is therefore essential. “People must be able to trust that any data collected will only be used in the agreed way, and for the stated purpose,” Norcross said.
Each year, approximately 3,000 children are born in the UK with a treatable rare condition that could be detected using genome sequencing. Although newborn babies are currently offered a heel-prick test to screen their blood for signs of nine rare but serious conditions, such as sickle cell disease and cystic fibrosis, whole genome sequencing could enable hundreds more such conditions to be diagnosed at birth.
Currently, such diseases are usually only diagnosed once a child develops symptoms, often after months or years of tests. One such condition is biotinidase deficiency, an inherited disorder in which the body is unable to recycle the vitamin biotin. Affected children may experience seizures and delays in reaching developmental milestones, and have problems with vision or hearing, but early diagnosis and treatment with biotin supplements can prevent this deterioration and keep them healthy.
Dr Richard Scott, chief medical officer at Genomics England, said: “At the moment, the average time to diagnosis in a rare disease is about five years. This can be an extraordinary ordeal for families, and it also puts pressure on the health system. The question this programme is responding to is: ‘is there a way that we can get ahead of this?’”
The study aims to recruit 100,000 newborn children to undergo voluntary whole genome sequencing over the next two years, to assess the feasibility and effectiveness of the technology – including whether it could save the NHS money by preventing serious illness.
It will also explore how researchers might access an anonymised version of this database to study people as they grow older, and whether a person’s genome might be used throughout their lives to inform future healthcare decisions. For instance, if someone develops cancer when they are older, there may be an opportunity to use their stored genetic information to help diagnose and treat them.
According to research commissioned by PET earlier this year, 57% of the UK public would support the storage of genetic data in a national database, provided it were only accessible to the sequenced individual and healthcare professionals involved in their care. Only 12% of people opposed this.
Of greater concern would be the storage of a person’s genetic data for use by government authorities including the police, with the person being identifiable to those authorities. This was supported by 40% of people, and opposed by 25%. Norcross said that while Genomics England has good safeguards in place for providing research access to genomic data, “this risk can never be eliminated completely”.
Scott stressed that the purpose of the trial was to explore whether the potential benefits of newborn sequencing stack up, and engage in a genuine national debate about whether the technology is something people feel comfortable with. “The bottom line here is about us taking a cautious approach, and developing a view jointly nationally about what the right approach is, and what the right safeguards are,” he said.
Others raised concerns about the potential for false or uncertain results. Frances Flinter, emeritus professor of clinical genetics at Guy’s & St Thomas NHS foundation trust, and a member of the Nuffield council on bioethics, said: “Using whole genome sequencing to screen newborn babies is a step into the unknown. Getting the balance of benefit and harm right will be crucial. The potential benefits are early diagnosis and treatment for more babies with genetic conditions. The potential harms are false or uncertain results, unnecessary anxiety for parents, and a lack of good follow-up care for babies with a positive screening result.
“We must not race to use this technology before both the science and ethics are ready. This research programme could provide new and important evidence on both. We just hope the question of whether we should be doing this at all is still open.”
World’s Largest Autism Whole Genome Sequencing Study Reveals 134 Autism-Linked Genes
Summary: Researchers have identified 134 genes associated with autism and a range of genetic alterations associated with ASD. Notably, the study identified changes in copy number variations with likely associations with ASD, including autism-associated variants in 14% of people on the autism spectrum.
Source: Hospital for Sick Children
Researchers from The Hospital for Sick Children (SickKids) have uncovered new genes and genetic changes associated with autism spectrum disorder (ASD) in the largest autism whole genome sequencing analysis to date, providing better understanding into the ‘genomic architecture’ that underlies this disorder.
The study, published today in Cell, used whole genome sequencing (WGS) to examine the entire genomes of over 7,000 individuals with autism as well as an additional 13,000 siblings and family members.
The team found 134 genes linked with ASD and discovered a range of genetic changes, most notably gene copy number variations (CNVs), likely to be associated with autism, including ASD-associated rare variants in about 14 per cent of participants with autism.
The majority of data was drawn from the Autism Speaks MSSNG database, the world’s largest autism whole genome dataset, which provides autism researchers with free, open access to thousands of sequenced genomes.
“By sequencing the entire genome of all participants, and with deep involvement from the participating families in MSSNG on forming our research priorities, we maximize the potential for discovery and allow analysis that encompasses all types of variants, from the smallest DNA changes to those that affect entire chromosomes,” says Dr. Stephen Scherer, Senior Scientist, Genetics & Genome Biology and Chief of Research at SickKids and Director of the McLaughlin Centre at the University of Toronto.
Dr. Brett Trost, lead author of the paper and a Research Associate in the Genetics & Genome Biology program at SickKids, notes the use of WGS allowed researchers to uncover variant types that would not have otherwise been detectable.
These variant types include complex rearrangements of DNA, as well as tandem repeat expansions, a finding supported by recent SickKids research on the link between autism and DNA segments that are repeated many times.
The role of the maternally inherited mitochondrial DNA was also examined in the study and found to account for two percent of autism.
The paper also points to important nuances in autism genetics in families with only one individual with autism compared with families that have multiple individuals with autism, known as multiplex families.
Surprising to the team was that the “polygenic score” – an estimation of the likelihood of an individual having autism, calculated by aggregating the effects of thousands of common variants throughout the genome – was not higher among multiplex families.
“This suggests that autism in multiplex families may be more likely to be linked to rare, highly impactful variants inherited from a parent. Because both the genetics and clinical traits associated with autism are so complex and varied, large data sets like the ones we used are critical to providing researchers with a clearer understanding of the genetic architecture of autism,” says Trost.
The research team says the study data can help expand inquiries into the range of variants that might be linked to ASD, as well as efforts to better understand contributors to the 85 percent of autistic individuals for which the genetic cause remains unresolved.
In a linked study of 325 families with ASD from Newfoundland published this same month in Nature Communications, Dr. Scherer’s team found that combinations of spontaneous, rare-inherited, and polygenic genetic factors coming together in the same individual can potentially lead to different sub-types of autism.
Dr. Suzanne Lewis, a geneticist and investigator at the BC Children’s Hospital Research Institute who diagnosed many of the families enrolled in the study said, “Collectively, these latest findings represent a massive step forward in better understanding the complex genetic and biological circuitry linked with ASD.
“This rich data set also offers an opportunity to dive deeper into examining other factors that may determine an individual’s chance of developing this complex condition to help individualize future treatment approaches.”
Funding: Funding for this study was provided by the University of Toronto McLaughlin Centre, Genome Canada/Ontario Genomics, Genome BC, Government of Ontario, Canadian Institutes of Health Research, Canada Foundation for Innovation, Autism Speaks, Autism Speaks Canada, Brain Child, Kids Brain Health Network, Qatar National Research Fund, Ontario Brain Institute, SFARI and SickKids Foundation.
See also
About this genetics and autism research news
Author: Jelena Djurkic
Source: Hospital for Sick Children
Contact: Jelena Djurkic – Hosptial for Sick Children
Image: The image is in the public domain
Original Research: Closed access.
“Genomic architecture of autism from comprehensive whole-genome sequence annotation” by Stephen Scherer, et al. Cell
Abstract
Genomic architecture of autism from comprehensive whole-genome sequence annotation
Highlights
- New MSSNG release contains WGS from 11,312 individuals from families with ASD
- Extensive variant data available, including SNVs/indels, SVs, tandem repeats, and PRS
- Annotation reveals 134 ASD-associated genes, plus SVs not detectable without WGS
- Rare, dominant variation has a prominent role in multiplex ASD
Summary
Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312).
Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%).
Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants.
Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.
Transcriptome variation in human tissues revealed by long-read sequencing
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Single-Cell DNA Sequencing Offers a New Angle on the Causes of Alzheimer’s Disease
Summary: An abundance of newly acquired mutations in the mutations that occur at an accelerated speed is a telling pattern of Alzheimer’s disease, researchers report.
Source: Boston Children’s Hospital
Alzheimer’s disease is marked by a loss of functional neurons in the brain. But what causes this loss?
Through single-cell genome sequencing, researchers at Boston Children’s Hospital, Brigham and Women’s Hospital, and the Broad Institute show that people with Alzheimer’s have an abundance of newly acquired mutations in their neurons — more than people of the same age without Alzheimer’s, and enough to disable genes important to brain function. Findings were published in Nature on April 20.
“Cells have repair pathways to undo DNA damage, but our work shows that in Alzheimer’s disease, neurons can’t keep up with the repairs, so the damage is permanent and cumulative,” says Christopher Walsh, MD, PhD, chief of Genetics and Genomics at Boston Children’s Hospital and an Investigator of the Howard Hughes Medical Institutes, and co-senior investigator on the study. “This work provides a new way of thinking about neurodegenerative diseases such as Alzheimer’s, suggesting that they impair the ability of neurons to use their genome. “
The study may also help connect the dots between loss of neurons and the well-documented accumulation of amyloid-β and tau proteins in Alzheimer’s disease. The pattern of mutations the team found suggests that they are caused by reactive oxygen species (ROS), chemicals that can oxidize and damage DNA. Both amyloid-β and tau can induce the production of ROS, and ROS have been found to be increased in the brains of people with Alzheimer’s.
Miller, Huang and colleagues analyzed single-cell whole-genome sequencing data from 319 neurons from the prefrontal cortex and hippocampus of individuals with Alzheimer’s disease and neurotypical people of similar age. These areas are important in cognitive functioning.
They not only found more mutations in those with Alzheimer’s, but differences in the pattern of mutations compared with normally aging brains. These changes — switches in certain bases or “letters” that make up DNA — were of a kind known to be induced by ROS, unlike mutations in normally aging brains. The team also found direct evidence of increased oxidation in the neurons of people with Alzheimer’s.
In addition to amyloid-β and tau, inflammation caused by microglia could also contribute to ROS production, notes August Yue Huang, PhD, an Instructor co-mentored by Walsh and Alice Lee, PhD, and co-first author on the paper with Michael B. Miller, MD, PhD, of Boston Children’s Hospital and Brigham and Women’s Hospital. Microglia are immune cells in the brain that can interact with neurons, and have shown to be abnormally activated in Alzheimer’s.
“Neuroinflammation introduced by microglia might be one cause of oxidative damage to the genome,” Huang says.
The researchers note that genes important to brain function may be especially vulnerable to mutations. Essential genes used by the brain tend to be larger than average, presenting a bigger target that is more likely to be “hit” and disrupted. They are also more often turned on.
“Genes with a higher level of expression in the brain — and are therefore more likely to have critical functions — had a higher mutation burden,” says Huang.
Treatment implications?
It’s tempting to speculate that antioxidants could have value in Alzheimer’s, but the researchers want to further investigate how oxidation of the genome occurs and the role that inflammation and immune reactions may play.
“We want to look at other neurodegenerative diseases like frontotemporal dementia, ALS, and chronic traumatic encephalopathy to see whether there’s a limit to the number of mutations in brain that a neuron can tolerate,” says Walsh. “We’ve demonstrated that in Alzheimer’s disease, neurons cannot tolerate widespread oxidation of the genome, which results in permanent damage that can’t be fixed.”
Funding: Walsh was co-senior investigator on the study with Eunjung Alice Lee, both of Boston Children’s Hospital, and Michael Lodato from the University of Massachusetts Chan Medical School. The study was funded by the National Institutes of Health (K08 AG065502,T32 HL007627, T32 GM007753, T15 LM007098, R00 AG054748, K01 AG051791, R01 NS032457-20S1, R01 AG070921, DP2 AG072437), the Brigham and Women’s Hospital Program for Interdisciplinary Neuroscience, the BrightFocus Foundation (A20201292F), the Doris Duke Charitable Foundation (2021183), the Suh Kyungbae Foundation, the F616 Prime Foundation, and the Allen Discovery Center program of the Paul G. Allen Family Foundation. Walsh is a Howard Hughes Medical Institute Investigator.
Walsh is a paid consultant to Third Rock Ventures and Flagship Pioneering and is on the Clinical Advisory Board of Maze Therapeutics. These companies did not fund and had no role in the current study.
About this Alzheimer’s disease and genetics research news
Author: Bethany Tripp
Source: Boston Children’s Hospital
Contact: Bethany Tripp – Boston Children’s Hospital
Image: The image is in the public domain
Original Research: Closed access.
“Somatic genomic changes in single Alzheimer’s disease neurons” by Christopher Walsh et al. Nature
Abstract
See also
Somatic genomic changes in single Alzheimer’s disease neurons
Dementia in Alzheimer’s disease progresses alongside neurodegeneration, but the specific events that cause neuronal dysfunction and death remain poorly understood. During normal aging, neurons progressively accumulate somatic mutations at rates similar to those of dividing cells which suggests that genetic factors, environmental exposures or disease states might influence this accumulation.
Here we analysed single-cell whole-genome sequencing data from 319 neurons from the prefrontal cortex and hippocampus of individuals with Alzheimer’s disease and neurotypical control individuals. We found that somatic DNA alterations increase in individuals with Alzheimer’s disease, with distinct molecular patterns.
Normal neurons accumulate mutations primarily in an age-related pattern (signature A), which closely resembles ‘clock-like’ mutational signatures that have been previously described in healthy and cancerous cells. In neurons affected by Alzheimer’s disease, additional DNA alterations are driven by distinct processes (signature C) that highlight C>A and other specific nucleotide changes. These changes potentially implicate nucleotide oxidation, which we show is increased in Alzheimer’s-disease-affected neurons in situ.
Expressed genes exhibit signature-specific damage, and mutations show a transcriptional strand bias, which suggests that transcription-coupled nucleotide excision repair has a role in the generation of mutations.
The alterations in Alzheimer’s disease affect coding exons and are predicted to create dysfunctional genetic knockout cells and proteostatic stress. Our results suggest that known pathogenic mechanisms in Alzheimer’s disease may lead to genomic damage to neurons that can progressively impair function.
The aberrant accumulation of DNA alterations in neurodegeneration provides insight into the cascade of molecular and cellular events that occurs in the development of Alzheimer’s disease.
Huge Project Is Now Underway to Sequence The Genome of Every Complex Species on Earth
The Earth Biogenome Project, a global consortium that aims to sequence the genomes of all complex life on earth (some 1.8 million described species) in ten years, is ramping up.
The project’s origins, aims and progress are detailed in two multi-authored papers published today. Once complete, it will forever change the way biological research is done.
Specifically, researchers will no longer be limited to a few “model species” and will be able to mine the DNA sequence database of any organism that shows interesting characteristics. This new information will help us understand how complex life evolved, how it functions, and how biodiversity can be protected.
The project was first proposed in 2016, and I was privileged to speak at its launch in London in 2018. It is currently in the process of moving from its startup phase to full-scale production.
The aim of phase one is to sequence one genome from every taxonomic family on earth, some 9,400 of them. By the end of 2022, one-third of these species should be done. Phase two will see the sequencing of a representative from all 180,000 genera, and phase three will mark the completion of all the species.
The importance of weird species
The grand aim of the Earth Biogenome Project is to sequence the genomes of all 1.8 million described species of complex life on Earth. This includes all plants, animals, fungi, and single-celled organisms with true nuclei (that is, all “eukaryotes”).
While model organisms like mice, rock cress, fruit flies and nematodes have been tremendously important in our understanding of gene functions, it’s a huge advantage to be able to study other species that may work a bit differently.
Many important biological principles came from studying obscure organisms. For instance, genes were famously discovered by Gregor Mendel in peas, and the rules that govern them were discovered in red bread mold.
DNA was discovered first in salmon sperm, and our knowledge of some systems that keep it secure came from research on tardigrades. Chromosomes were first seen in mealworms and sex chromosomes in a beetle (sex chromosome action and evolution has also been explored in fish and platypus). And telomeres, which cap the ends of chromosomes, were discovered in pond scum.
Answering biological questions and protecting biodiversity
Comparing closely and distantly related species provides tremendous power to discover what genes do and how they are regulated. For instance, in another PNAS paper, coincidentally also published today, my University of Canberra colleagues and I discovered Australian dragon lizards regulate sex by the chromosome neighborhood of a sex gene, rather than the DNA sequence itself.
Scientists also use species comparisons to trace genes and regulatory systems back to their evolutionary origins, which can reveal astonishing conservation of gene function across nearly a billion years. For instance, the same genes are involved in retinal development in humans and in fruit fly photoreceptors. And the BRCA1 gene that is mutated in breast cancer is responsible for repairing DNA breaks in plants and animals.
The genome of animals is also far more conserved than has been supposed. For instance, several colleagues and I recently demonstrated that animal chromosomes are 684 million years old.
It will be exciting, too, to explore the “dark matter” of the genome, and reveal how DNA sequences that don’t encode proteins can still play a role in genome function and evolution.
Another important aim of the Earth Biogenome Project is conservation genomics. This field uses DNA sequencing to identify threatened species, which includes about 28 percent of the world’s complex organisms – helping us monitor their genetic health and advise on management.
No longer an impossible task
Until recently, sequencing large genomes took years and many millions of dollars. But there have been tremendous technical advances that now make it possible to sequence and assemble large genomes for a few thousand dollars. The entire Earth Biogenome Project will cost less in today’s dollars than the human genome project, which was worth about US$3 billion in total.
In the past, researchers would have to identify the order of the four bases chemically on millions of tiny DNA fragments, then paste the entire sequence together again. Today they can register different bases based on their physical properties, or by binding each of the four bases to a different dye. New sequencing methods can scan long molecules of DNA that are tethered in tiny tubes, or squeezed through tiny holes in a membrane.
Why sequence everything?
But why not save time and money by sequencing just key representative species?
Well, the whole point of the Earth Biogenome Project is to exploit the variation between species to make comparisons, and also to capture remarkable innovations in outliers.
There is also the fear of missing out. For instance, if we sequence only 69,999 of the 70,000 species of nematode, we might miss the one that could divulge the secrets of how nematodes can cause diseases in animals and plants.
There are currently 44 affiliated institutions in 22 countries working on the Earth Biogenome Project. There are also 49 affiliated projects, including enormous projects such as the California Conservation Genomics Project, the Bird 10,000 Genomes Project and UK’s Darwin Tree of Life Project, as well as many projects on particular groups such as bats and butterflies.
Jenny Graves, Distinguished Professor of Genetics and Vice Chancellor’s Fellow, La Trobe University.
This article is republished from The Conversation under a Creative Commons license. Read the original article.
DNA sequencing solves mystery of earliest hybrid animal’s identity
Descriptions and imagery in Mesopotamian art and texts portray a powerful animal that pulled war wagons into battle and royal vehicles in parades. Its true identity, however, had long puzzled and divided archaeologists. Domesticated horses didn’t arrive in the region, sometimes referred to as the Fertile Crescent, until 4,000 years ago.
Intact skeletons of the creatures were buried alongside high-status people — the upper crust of Bronze Age society — at the burial complex of Umm el-Marra in northern Syria, suggesting the animals occupied a very special position. Analysis of kunga teeth showed that they wore bits in their mouths and were well fed.
However, the bones of horses, donkeys, asses, mules and other equids are very similar and difficult to tell apart, making it impossible to definitively ID the animal merely by examining the skeletons.
Now, analysis of DNA extracted from the bones buried at Umm el-Marra has revealed the animal was a cross between a donkey, which was domesticated at the time, and the now-extinct Syrian wild ass, sometimes called hemippe or an onager.
This makes it the earliest evidence of hybrid animal breeding with parents from two different species, according to the research published in the journal Science Advances Friday. It was likely intentionally created, trained and then exchanged among the elites of the day.
“Since hybrids are usually sterile, it means there was a remarkable level of energy devoted to constantly capturing and raising wild onagers, breeding them with domestic donkeys and then training these teams of prestigious kungas (which would only last for one generation),” said Benjamin Arbuckle, an anthropological archaeologist at the University of North Carolina at Chapel Hill, via email. He wasn’t involved with the research.
“It really shows the innovative and experimental nature of ancient people which I think some people only associate with the modern world and also their willingness to invest a lot of resources in the artificial creation of an expensive animal used only by and for elites.”
War animal
Before the arrival of the horse, finding an animal willing to charge into battle was a challenge, said Eva-Maria Geigl, head of research at CNRS (French National Center for Scientific Research) at the Université de Paris and author of the study.
While cattle and donkeys could pull wagons, they wouldn’t run toward an adversary, she said.
“They were not used for making war, and there were no domestic horses at the time. The Sumerians, who wanted to make war because they were really very powerful city states, they had to find another solution.”
She thinks the first kunga came into being naturally — a Syrian wild ass mated with a female donkey.
“They must have seen that the animal was more robust and more trainable. They must have observed the result of this natural crossing and then they said OK, we will do that. For the first time in human history, we will bioengineer an animal.”
However, it wouldn’t have been easy. The Syrian wild ass was thought to be aggressive and moved extremely quickly, she said.
Geigl said an earlier study of mitochondrial DNA , which revealed the female line, had found that the kunga was a hybrid. It was only with analysis of the nuclear DNA that the scientists were able to pinpoint the paternity of the animal.
To reach their findings, the researchers sequenced and compared the genomes of a 4,500-year-old kunga buried at Umm el-Marra in Syria, an 11,000-year-old Syrian wild ass found at Gobekli Tepe (the earliest known human-made place of worship in modern-day Turkey) and two of the last surviving Syrian wild asses, which went extinct in the early 20th century.
Arbunkle said that most texts referring to kungas date from the mid-2,000s BC, and it was unlikely they were bred earlier than 3,000 BC — when donkeys appear in the archaeological record. By 2,000 BC, he said, they had been replaced as pulling animals by horses and mules — a cross between a male donkey and female horse.
“This work settles the idea that hybrids were in fact created by ancient Mesopotamians, which is very cool,” Arbuckle said.
“But we still don’t know how widespread this animal was and it also doesn’t address additional questions relating to other types of hybrid equids created in the Bronze Age. So there are plenty more questions.”
Swift Sequencing of Omicron Sample at UCSF Highlights Challenges of Tracking Variant’s Spread
Keeping track of where the Omicron variant has already spread and how quickly it may be multiplying is just the latest challenge for scientists and public health officials — and perhaps the only reason the first U.S. case was found in SF is because of the caliber of the health system here, not because it isn’t already in other places in the country.
A person sick with COVID landed at SFO before Thanksgiving, on Monday, November 22. That person had been in South Africa, and within days began feeling ill. A lab at UCSF would not receive the person’s “suspicious” test sample until Tuesday afternoon, November 30, eight days after their arrival in the country, and after an unknown number of encounters with friends and family. The sample appears to have been taken by a Color Lab in SF on Monday the 29th, and other samples may still be being processed from the person’s close contacts — but the CDC said those contacts have so far tested negative.
It wouldn’t be until 4 a.m. Wednesday that researchers at UCSF could confirm with certainty that this was indeed an Omicron sample, and that was after working through the night with special urgency.
An earlier report by CNN reported that the positive test had come in on November 29, but now we are learning just how long it took for that test to be flagged and have its genetics sequenced.
“This particular sample, I heard about it yesterday at about 3 p.m.,” said UCSF’s Dr. Charles Chiu at Wednesday’s news conference at SF City Hall, per KPIX. “We were able to receive the sample in the laboratory by 8 p.m. We ran a very fast molecular test which looks for spike gene dropout. What this test can tell you that you may have detected omicron, but it’s not conclusive.”
It would be a total of 30 hours between the time of the Color test being administered to it being sequenced and fully confirmed, as the Chronicle reports — though that timeline seems odd if 4 a.m. was the final confirmation, which would put the test at 10 p.m. on Monday night. Maybe 10 p.m. Monday was when the test positivity was first confirmed?
“We were able to confirm the detection of Omicron in five hours and had nearly the entire genome in eight hours,” Chiu said. “At 4 a.m. last night we were able to conclusively demonstrate that this was an infection of the Omicron variant.”
It’s likely that within days, or even before today is out, we will hear of other cases in the U.S. — and given the efforts described above to sequence a single sample, is it any wonder that this should take a little time after the world first heard about Omicron just five days ago?
The US is better than many countries at detecting and sequencing variants, and it has only become so in the last six months or so. Still, as Kristian Andersen, a professor of immunology and microbiology at California’s Scripps Research Institute, tells Vox, it’s still an ad hoc network of labs that is doing the heavy lifting. “A lot of it is still hacked together,” Andersen says of the system.
Andersen further explained that it was both the high prevalence of Omicron in South Africa as well as South Africa’s better-than-average system of surveillance for variants, that led to its discovery there.
CDC Director Rochelle Walensky said Tuesday that the U.S. is now running genetic sequencing on one out of every seven positive COVID cases in the country — though this global database is still saying that the U.S. only runs 29 sequences per 1,000 cases, which would be one out of every 34 cases. That still puts us in the top 20 countries globally, as Vox reports, but it highlights how many variant cases could be slipping through each day, with the U.S. now finding about 50,000 to 120,000 new COVID cases each day.
The fact remains that no one knows if Omicron is better at evading vaccines or spreading more easily than Delta, it just appears it might be. Evolutionary selection is likelier to have given rise to a variant that is successful at something, however as the New York Times reported Monday, experts caution that mutations can also work against each other, and it’s still early days with this variant.
The infected U.S. individual, a San Francisco resident, had two doses of the Moderna vaccine, likely more than six months ago — but we don’t know the dates. That person had not yet received a booster.
Related: Breed, Colfax Say No New Restrictions Because of Omicron Variant, While Heckler Tries to Steal the Show