Category Archives: Genome

When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them.

The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you're susceptible to.

There is pronounced variation in the microbial composition and diversity of the gut microbiome between people living in different countries around the world. Although researchers are starting to understand what factors affect microbiome composition, such as diet, there is still limited understanding on why different groups have different strains of the same species of microbes in their guts.

We are researchers who study microbial evolution and microbiomes. Our recently published study found that not only did microbes diversify with their early modern human hosts as they traveled across the globe, they followed human evolution by restricting themselves to life in the gut.

We hypothesized that as humans fanned out across the globe and diversified genetically, so did the microbial species in their guts. In other words, gut microbes and their human hosts "codiversified" and evolved together just as human beings diversified so that people in Asia look different from people in Europe, so too did their microbiomes.

To assess this, we needed to pair human genome and microbiome data from people around the world. However, data sets that provided both the microbiome data and genome information for individuals were limited when we started this study. Most publicly available data was from North America and Western Europe, and we needed data that was more representative of populations around the world.

So our research team used existing data from Cameroon, South Korea and the United Kingdom, and additionally recruited mothers and their young children in Gabon, Vietnam and Germany. We collected saliva samples from the adults to ascertain their genotype, or genetic characteristics, and fecal samples to sequence the genomes of their gut microbes.

For our analysis, we used data from 839 adults and 386 children. To assess the evolutionary histories of humans and gut microbes, we created phylogenetic trees for each person and as well as for 59 strains of the most commonly shared microbial species.

When we compared the human trees to the microbial trees, we discovered a gradient of how well they matched. Some bacterial trees didn't match the human trees at all, while some matched very well, indicating that these species codiversified with humans. Some microbial species, in fact, have been along for the evolutionary ride for over hundreds of thousands of years.

We also found that microbes that evolved in tandem with people have a unique set of genes and traits compared with microbes that had not codiversified with people. Microbes that partnered up with humans have smaller genomes and greater oxygen and temperature sensitivity, mostly unable to tolerate conditions below human body temperature.

In contrast, gut microbes with weaker ties to human evolution have traits and genes characteristic of free-living bacteria in the external environment. This finding suggests that codiversified microbes are very much dependent on the environmental conditions of the human body and must be transmitted quickly from one person to the next, either passed down generationally or between people living in the same communities.

Confirming this mode of transmission, we found that mothers and their children had the same strains of microbes in their guts. Microbes that were not codiversified, in contrast, were more likely to survive well outside of the body and may be transmitted more widely through water and soil.

Our discovery that gut microbes evolved right along with their human hosts offers another way to view the human gut microbiome. Gut microbes have passed between people over hundreds to thousands of generations, such that as humans changed, so did their gut microbes. As a result, some gut microbes behave as though they are part of the human genome: They are packages of genes that are passed between generations and shared by related individuals.

Personalized medicine and genetic testing are starting to make treatments more specific and effective for the individual. Knowing which microbes have had long-term partnerships with people may help researchers develop microbiome-based treatments specific to each population. Clinicians are already using locally sourced probiotics derived from the gut microbes of community members to treat malnutrition.

Our findings also help scientists better understand how microbes transition ecologically and evolutionarily from "free-living" in the environment to dependent on the conditions of the human gut. Codiversified microbes have traits and genes reminiscent of bacterial symbionts that live inside insect hosts. These shared features suggest that other animal hosts may also have gut microbes that codiversified with them over evolution.

Paying special attention to the microbes that share human evolutionary history can help improve understanding of the role they play in human well-being.

Taichi A. Suzuki, Postdoctoral Research Associate in Microbiome Science, Max Planck Institute for Biology and Ruth Ley, Director, Department of Microbiome Science, Max Planck Institute for Biology

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Like genes, your gut microbes pass from one generation to the next - Salon

Genetics can influence the development of major depressive disorder (MDD) in affected individuals who were previously exposed to trauma, according to new study appearing in JAMA Psychiatry this week. Self-reported trauma exposure, particularly that occurring in childhood, has an established role in depression, and research has indicated that higher levels of trauma are linked to MDD. However, the interplay between genetics and trauma on depression has not been fully explored. In their new paper, researchers from the University of Edinburgh analyzed genomic and other data on roughly 150,000 adult participants in the UK Biobank who showed depressive symptoms and/or neuroticism and reported exposure to a range of different traumas. They find that genome-by-trauma exposure interactions can explain up to 20 percent of variation in MDD and more often in males versus females. The study results, the authors write, suggest that "exploring mechanisms underlying genome-by-trauma exposure interactions may be useful in identifying at-risk individuals and intervention targets ... [and] may provide explanations for depression prevalence differences across the different sexes."

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Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds - GenomeWeb

Academics and biotech research organisations with corporate interests have been leading the lobby campaign to deregulate new genomic techniques in the EU using 'climate-friendly' and 'science-based' narratives, a new report revealed on Thursday (29 September).

The findings come just a few days after the Czech EU Council presidency voiced support to loosen regulations for genetically-modified food and seed technologies in the EU.

"Advocacy is an acceptable part of democracy, but presenting stakeholders as neutral scientists is not," reads the report by the Greens in the European Parliament, which builds on Corporate Europe Observatory's (CEO) previous research.

Political pressure to change current rules for genetically-modified organisms (GMOs) has been mounting since 2018 when the European Court of Justice ruled that new techniques like CRISPR-Cas still fall under the current framework dealing with genetic-engineering products.

Current legislation imposes a pre-market authorisation on any GMO sold to consumers, following a risk assessment, as well as traceability, labelling, and monitoring obligations.

Following a request by EU member states, the commission published a study last year arguing that the current regulation is not "fit for purpose" and needs to be amended to contribute to sustainable food systems.

A legislative proposal on "plants produced by certain new genomic techniques" is due in spring 2023. What this will look like is still unclear.

But environmental groups and green MEPs fear that the upcoming commission proposal will lower standards for risk assessment and monitoring, or even forgo labelling requirements.

Industry players want to see GM plants that have no 'foreign DNA' intentionally added to their genome excluded from the EU GMO legislation. They argue that such DNA changes could also occur in nature and that gene-edited crops are key to achieving EU green goals.

The report shows how the lobby platform EU-SAGE, founded by the Flemish Biotech Institute (VIB), the European Plant Science Organisation (EPSO) working group and the European Federation of Academies of Sciences and Humanities (ALLEA) network have made similar claims.

It also notes that several academics involved in these three organisations have "strong links" with the seed industry and hold patents or patent applications in this area which are not publicly disclosed.

The debate about the deregulation of new genomic techniques has increased in recent months, due to fears over food security but the commission has acknowledged the risks of the hype.

In a briefing for a meeting between the commission's agricultural department and the lobby group Euroseed, representing companies like Syngenta and Bayer, the commission said that linking new genomic techniques to food security is "not helpful".

"This was done with GMOs in the past and ultimately the premises made were counterproductive. It is important not to promise more than what the technology can deliver," reads the briefing.

Meanwhile, many fear that the upcoming commission proposal will undermine consumers' rights.

Nina Holland, a researcher at CEO, warned that getting rid of labelling requirements would not only hinder consumers' rights but also organic farming as people will struggle to spot GMO-free products.

Green MEPs and environmentalists have urged the commission to implement the 2018 court ruling, voicing concerns over the influence that organisations with vested interests have on policy-making.

"Our decisions must be based on independent scientific advice. We cannot take scientific advice from scientists who have vested interests in the commercialisation of these products," said Green MEP Martin Husling.

Lobby groups, for their part, have slammed the 2018 court ruling for being a setback for the application of new genomic techniques which are already well-established in markets outside the EU, like the US.

"It [the ruling] created a situation in which the application of the GMO legislation would block many applications of genome-edited organisms, while at the same time the scientific community saw an enormous potential in this technology to contribute to a more sustainable agriculture and food production and help mitigate climate change," the chairman of EU-SAGE Dirk Inz told EUobserver.

Moreover, EU-SAGE and the Czech branch of ALLEA have managed to gain the support of the Czech EU Council presidency for one of their high-profile conferences on gene editing taking place in Prague on 13-14 October.

The conference, which features the logo of the EU presidency, will address "how the potential of genome-edited crops for more sustainable agriculture in Europe can be established with broader societal support".

EU agriculture commissioner Janusz Wojciechowski has been invited to take part in the programme.

Read more here:
Deregulation of new GMO crops: science or business? - EUobserver

DUBLIN--(BUSINESS WIRE)--Horizon Therapeutics plc (Nasdaq: HZNP) today announced the presentation of new data defining molecular patterns in TED and further implicating the role of insulin-like growth factor-1 (IGF-1) in patients with low CAS. These data were presented during the American Academy of Ophthalmology Annual Meeting (AAO 2022), Sept. 30 Oct. 3 in Chicago.

TED is a progressive and potentially vision-threatening rare autoimmune disease, which has been historically characterized as biphasic: acute, which is traditionally believed to be patients with high CAS and earlier in their TED journey; and chronic, traditionally believed to be patients with low CAS and later in the course of their disease.1 This analysis reveals that in patients with both high and low CAS, there is clear activation of IGF-1 and related pathways, as well as the extracellular matrix (ECM) organization, a structural network that supports cellular processes.2

By demonstrating that disease activity remains in patients with low CAS, this analysis may help explain why many patients who have lived with Thyroid Eye Disease for several years are still struggling with challenging symptoms that can be debilitating, said Shoaib Ugradar, M.D., The Jules Stein Eye Institute at University of California, Los Angeles (UCLA). It is important for physicians to be aware of the continued activation of IGF-1 throughout the course of the disease and its potential impact on treatment decisions.

The study analyzed genome ribonucleic acid (RNA) sequencing and pathway analysis in orbital tissue from patients with a CAS of 3 and patients with a CAS 2, as well as five control subjects. Though high CAS patients are often distinguished by activation of immune system pathways, which remain largely unaffected in low CAS patients, IGF-1 and its related pathways were found to be upregulated in both stages of disease. Additional analysis suggests that IGF-1 activity plays a central role in linking immune and ECM pathways in people with TED.2

The upregulation of IGF-1 found in low CAS patients with extended disease duration is further supported by a growing body of evidence that outlines the impact of TED on people who have lived with it for several years.3 One assessment published in the journal Ophthalmology and Therapy in 2021 found that disease burden continues well into the chronic phase, affecting daily lives with appearance and persistent visual changes, increasing risk for anxiety and depression.4

This study, which represents one of the first molecular analyses of the continuum of Thyroid Eye Disease, confirms this challenging disease may not simply subside after a few years of obvious symptoms, said Jeffrey W. Sherman, M.D., FACP, executive vice president, chief medical officer, Horizon. We are committed to pioneering research like this to better understand drivers of the evolution of this disease in order to better support patients living with Thyroid Eye Disease across the course of their lifetimes.

About Thyroid Eye Disease (TED)

TED is a serious, progressive and potentially vision-threatening rare autoimmune disease.1 TED often occurs in people living with Graves disease, but is a distinct disease that is caused by autoantibodies activating an IGF-1R-mediated signaling complex on cells within the retro-orbital space.5,6 This leads to a cascade of negative effects, which may cause long-term, irreversible damage, including blindness. Early signs and symptoms of TED may include dry eyes and grittiness; redness, swelling and excessive tearing; eyelid retraction; proptosis; pressure and/or pain behind the eyes; and diplopia.7,8

About Horizon

Horizon is a global biotechnology company focused on the discovery, development and commercialization of medicines that address critical needs for people impacted by rare, autoimmune and severe inflammatory diseases. Our pipeline is purposeful: We apply scientific expertise and courage to bring clinically meaningful therapies to patients. We believe science and compassion must work together to transform lives. For more information on how we go to incredible lengths to impact lives, visit http://www.horizontherapeutics.com and follow us on Twitter, LinkedIn, Instagram and Facebook.

References

Original post:
New Data Reveal Molecular Drivers of Thyroid Eye Disease (TED) May Remain Activated In Patients with Low Clinical Activity Score (CAS) - Business Wire

News Release

Tuesday, September 27, 2022

The Molecular Phenotypes of Null Alleles in Cells program will first look at protein-coding genes.

The National Institutes of Health is launching a program to better understand the function of every human gene and generate a catalog of the molecular and cellular consequences of inactivating each gene. The Molecular Phenotypes of Null Alleles in Cells (MorPhiC) program, managed by the National Human Genome Research Institute, aims to systematically investigate the function of each gene through multiple phases that will each build upon the work of the previous.

The program will be funded initially for five years for a total of $42.5 million, pending the availability of funds. Phase 1 of the program will focus on 1,000 protein-coding genes and serve as a pilot phase and has three goals: exploring multiple methods of inactivating, or knocking out, gene function; developing molecular and cellular systems that model multiple human tissues and developmental stages; and developing molecular and cellular approaches to catalog gene function that other researchers can reproduce.

The function of thousands of genes is still a mystery, and they likely serve vital biological roles," said Colin Fletcher, Ph.D., NHGRI program director in the Division of Genome Sciences. Understanding fundamental biology can help us figure out why certain diseases occur and how can we develop drugs to target and treat those diseases.

Projects funded by the program will use versions of genes that do not make functional proteins, called null alleles. In the absence of making its functional protein, a given genes function can be more readily deduced by studying the resulting biological characteristics, or phenotype. The researchers expect this process to make it easier to interpret the results.

Currently, over 6,000 out of the estimated 19,000 protein-coding genes have not been well-studied. Among the genes that have been studied, only a subset of their functions is well-characterized.

Creating a catalog of what all human genes do is no easy feat. Most genes are likely to have more than one function and behave differently depending on the type of cell in which they are expressed. In addition, genes may turn on or off depending on the cells relationship to surrounding cells, environment and age.

Research funded by the MorPhiC program will use cell culture models such as organoids, which are miniature, three-dimensional models composed of multiple cell types that mimic the function of real tissues and organs. Research that works with cells in culture has a major advantage: it can more robustly study human cells, and therefore, human genes. All data will be made available to the broader research community. If Phase 1 is successful, NIH will activate a second phase to characterize a larger set of human genes.

MorPhiC is meant to add another layer of functional information between the gene knock-out at the DNA level and the organism-level effects. We want to catalog the effects of knocking out each gene within cells and together with information from other studies use that to understand how genes function to produce an organism, said Adam Felsenfeld, Ph.D., NHGRI program director in the Division of Genome Sciences.

The MorPhiC program offers a new approach to understanding gene function when compared to other programs at NIH and NHGRI. For example, a well-established NIH effort to probe gene function has been investigating the consequences of knocking out genes in mice at the level of tissues and organs as part of the Knockout Mouse Program. Another effort is applying new technologies, genome-sequencing strategies and analytical approaches to significantly increase the proportion of human genetic diseases with an identified genetic cause, as part of the Genomics Research to Elucidate the Genetics of Rare Diseases Consortium. Research into understanding how genomic variation affects genome function and phenotype is also an area of ongoing NHGRI investment through the Impact of Genomic Variation on Function Consortium.

MorPhiC complements these other efforts by examining the impact of human gene knock outs at the molecular and cellular level, said Carolyn Hutter, Ph.D., director in the Division of Genome Science. Ultimately, catalytic advances will come when we are able to collaborate across these different programs.

Funding for Phase 1 of the MorPhiC program will be awarded to support the following investigators:

The National Human Genome Research Institute (NHGRI) is one of the 27 institutes and centers at the NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Intramural Research develops and implements technology to understand, diagnose and treat genomic and genetic diseases. Additional information about NHGRI can be found at: http://www.genome.gov.

About the National Institutes of Health (NIH):NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov.

NIHTurning Discovery Into Health

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NIH initiative to systematically investigate and establish function of every human gene - National Institutes of Health (.gov)

BALTIMORE Researchers led by a team at Harvard Medical School have taken a step toward whole-genome recoding in human cells, demonstrating that the human amber stop codon TAG can be simultaneously edited in dozens of genes in a single experiment.

In a proof-of-concept study published last month in Nature Communications, the researchers, led by Harvard Medical School geneticist George Church, converted the TAG stop codon in 33 essential genes in a human cell line via a single transfection, marking the first large-scale recoding of the human genome.

This paper "pushed the limit" of how many different loci can be targeted at once for base editing in the human genome, said Eriona Hysolli, one of the study's corresponding authors and a former postdoctoral researcher in Church's lab.

According to Hysolli, the study, which was more than half a decade in the making and was conducted in collaboration with researchers from the Chinese Academy of Sciences, was built upon the Church group's previous accomplishment that replaced all UAG stop codons with UAA across the entire Escherichia coli genome. Hysolli, now head of biological sciences at Colossal Biosciences, said the team had to overcome a multitude of technical obstacles in order to extend recoding to the human genome.

For one, she said, compared with the relatively compact bacterial genomes, mammalian genomes are generally much larger and more complex. Besides having a greater number of genes, they also tend to harbor numerous intergenic regions that separate genes far apart from each other. Additionally, because many genome editing tools are adapted to work in prokaryotes, they often cannot function efficiently or are not yet available for mammalian cells.

There are also hurdles associated with multiplex base editing to tackle several genes at once. These include making the different targeted loci in the genome accessible, delivering a larger payload with multiple guide RNAs (gRNAs) into a cell efficiently, and curtailing the off-target promiscuity of the editing tools.

To explore the feasibility of genome-wide recoding in human cells, the researchers looked to the TAG stop codon, which represents fewer targets, given it is the least commonly used human codon, and can be theoretically edited to TAA by cytosine base editors.

To cope with the scale of the human genome, the team developed a python-based software, named Genome Recoding Informatics Toolbox (GRIT), that can automate the process of part design for recoding.

Based on the human genome reference GRCh38.p13 and the Online Gene Essentiality (OGEE) Database, GRIT identified a total of 6,700 TAG codons within the HEK293T cell line that was used in the study, of which 6,648 are editable across the human haploid genome by base editors. Moreover, the software discovered 1,947 TAG codons that are located in essential genes, of which 1,937 are editable.

Because multiplex TAG to TAA editing requires multiple gRNAs and base editors protein to be simultaneously delivered into a single mammalian cell, the researchers designed and synthesized artificial DNA fragments, or so-called gBlocks, that can each carry five individual gRNA cassettes and remain stable when introduced into mammalian cells.

After optimizing a strategy for multiplexed base editing, the researchers showed they were able to successfully convert up to 33 TAG codons to TAA at once out of 47 target sites via a single transfection.

To evaluate the on- and off-target efficiencies of the recoding, the team performed whole-genome sequencing on highly modified clones and compared the results with the negative control. While the off-target effects in this study were "definitely significant," most of them were found outside of the coding regions, Hysolli said.

Calling the study "very impressive," Magomet Aushev, a genome editing expert at the Wellcome Centre for Mitochondrial Research at Newcastle University in the UK, said this paper laid a foundation for other researchers who hope to achieve multiplex gene editing.

"One of the cool things that CRISPR brought to the genome editing table was multiplexing," he said, adding that unlike previous efforts, which mostly deployed CRISPR to modify repetitive sequences in the genome, this study targeted different genes using different guide RNAs, which is "really cool."

With all UAG stop codons replaced with UAA, the Church group previously engineered E. coli to be resistant to certain bacteriophages by depleting release factor 1 (RF1), which is responsible for terminating translation for UAG and UAA.

Similarly, the Harvard researchers and their collaborators envisaged that by converting the TAG stop codon to TAA genome wide and replacing the endogenous eukaryotic release factor 1 (eRF1) with engineered eRF1 variants, they might be able to generate virus-resistant human cell lines a goal for the Genome Projectwrite (GP-write)project, an initiative of the Human Genome Project jointly spearheaded by Church and a handful of other researchers.

Aushev said that while the recent publication is "a really good initial study" that tested the waters of how far scientists can go with the current technology for human genome recoding, there is still a vast knowledge gap to fill when it comes to achieving virus-resistant human cell lines via whole-genome recoding.

"Base editing is like fixing a tire, while genome engineering is like building a whole car," he said. "Maybe a technology that is meant to fix tires is not the best way to go. Maybe there needs to be some innovation on the genome engineering side to develop some newer technologies [that are] more ambitious."

Beyond the technical challenges, scientists also do not know the possible side effects of whole-genome recoding in humans, Aushev pointed out. "It could be that maybe nothing happens, or maybe something bad happens. It's just difficult to say because this has never been done."

Mirroring Aushev's point, Hysolli also thinks there is still a long way to go before scientists can harness human genome recoding for applications such as manufacturing of cell therapies or virus-proof therapeutics production.

Meanwhile, Hysolli said there are several potential strategies that scientists can work on to help improve the efficiency and multiplex capability of the TAG conversion. These include continuing to develop new base editors to boost editing efficiency while minimizing off-target effects, improving guide RNA delivery capability, and designing new delivery mechanisms to achieve more efficient transfections.

"It's always a little bit more challenging to work on the mammalian genome side," Hysolli said. "We have just laid the foundation for how we can potentially achieve this work."

More here:
Researchers Demonstrate Multiplex Codon Editing in the Human Genome - GenomeWeb

image:Status of COVID-19 during the Tokyo 2020 Olympic and Paralympic Games view more

Credit: The Instutite of Medical Science, The University of Tokyo

In the middle of the COVID-19 pandemic, the Tokyo 2020 Olympic and Paralympic Games were held in the summer of 2021. Participants from over 200 countries or regions gathered in Japan. Scientifically understanding how the new coronavirus transmitted through such mass gatherings can be utilized for future events in similar situations.Just before the games, the Alpha variant (B.1.1.7) was being replaced with the more contagious Delta substrain AY.29, which harbors two additional characteristic mutations compared with its parent AY.4. It emerged in Japan and became dominant in Tokyo. Through genome analysis, we identified 118 AY.29 samples in 20 countries, and among these, at least 55 independent strains. While there are strains unrelated to the events such as a strain transmitted to the USA from Okinawa, there remains the possibility that 41 strains were associated with the Olympic and Paralympic participants. This study was published on August 3rd, 2022 in Frontiers in Microbiology.The research was organized by IMSUT (Prof. Seiya Imoto, Human Genome Center) and IBM Research (Takahiko Koyama, Research Staff Member, TJ Watson Research Center and Michiharu Kudo, Senior Technical Staff Member, IBM Research - Tokyo) groups. The article was published in Frontiers in Microbiology at 5:00 AM BST on August 3rd 2022.

Background /ChallengeThe new coronavirus has been rapidly evolving by accumulating mutations during the pandemic. Emergence of new variants have been dramatically affecting our lives. Nevertheless, mutations can be utilized to trace transmission routes. IMSUT and IBM developed the SARS-CoV-2 Variant Browser, which provides surveillance and tracing tools to researchers and public health officials*3,*4.In the summer of 2021, the Tokyo 2020 Olympic and Paralympic Games were finally held after a year of postponement. Participants from over 200 countries or regions visited Japan. Scientifically understanding how the new coronavirus propagated through a series of international mass gathering events can be utilized for future events not limited to COVID-19. In this study, we have analyzed the SARS-CoV-2 strains transmitted overseas during the time of the Olympic and Paralympic Games.

ResultJust before the games, the Alpha variant (B.1.1.7) was being replaced with the more contagious Delta variant AY.29, which harbors two additional characteristic mutations 5239C > T (NSP3 Y840Y) and 5514T > C (NSP3 V932A), compared with its parent AY.4. It emerged in Japan and became dominant in Tokyo (Figure1A, B). During the events, a total of 863 positive cases were reported (Figure 1C). Out of 863 positive cases, 174 cases occurred in Olympic visitors from abroad, and 80 cases occurred in Paralympic visitors from abroad.

By analyzing over 6 million genomes from the international genome database in GISAID and NCBI, we uncovered 118 samples of the Delta substrain AY.29 in 20 countries such as the USA, the UK, Canada, Germany, South Korea, Hong Kong, Thailand, and the Philippines (Figure2). At least 55 independent strains were propagated to overseas from Japan. Out of the exported 55 strains, 41 of them were collected after August 1st and with their ancestral strains collected in Greater Tokyo While there are strains unrelated to the events such as a strain transmitted to the USA from Okinawa via US military stationed in Okinawa, the possibility remains that 41 strains are associated with the returning Olympic and Paralympic participants.

The identified AY.29 samples appear to be the tip of the iceberg. In particular, it is difficult to grasp the whole picture in the countries and areas with low rates of genome surveillance. Among the 20 countries, most European and North American countries had vaccination rates over 50%, and sufficient genomic surveillance was conducted; transmissions seem contained. However, propagation to unvaccinated regions might have caused damage we cannot assess. Since samples in those unvaccinated countries are also undersampled with a longer lead time for data sharing, it will take longer to grasp the whole picture.Regarding the novel exogenous strains introduced into the Japanese population by the participants from abroad, we identified 61 novel exogenous strains in 900 unusual samples that dont have prefectural information. As we expect more international mass gathering events, it becomes more important to share the data and disclose information regarding SARS-CoV-2 in a timely manner. IMSUT will keep providing the information to researchers and public health officials.IMSUT has been conducting research in SARS-CoV-2 genomes to find new treatment methods and preventive measures by leveraging expertise obtained through genome and data science research to date. In the Tokyo 2020 Olympic and Paralympic Games, IMSUT played a role in analyzing SARS-CoV-2 genomes obtained in wastewater samples in the Tokyo 2020 Olympic and Paralympic village*5,*6. To accelerate socio-economic recovery from the COVID-19 pandemic, IMSUT will make efforts to contribute to proposing concrete measures.

Publication

Takahiko Koyama*, Reitaro Tokumasu, Kotoe Katayama, Ayumu Saito, Michiharu Kudo and Seiya Imoto "Cross-border transmissions of the Delta substrain AY.29 during Tokyo Olympic and Paralympic Games" Frontiers in Microbiology Aug. 2022*Corresponding AuthorDOI: 10.3389/fmicb.2022.883849URL: https://www.frontiersin.org/articles/10.3389/fmicb.2022.883849

Research contact:Human Genome Center, The Institute of Medical Science, The University of TokyoSeiya Imoto, Director/ProfessorURL: https://www.ims.u-tokyo.ac.jp/imsut/en/lab/hgclink/page_00073.htmlMedia Contact:International Affairs Office, The Institute of Medical Science, The University of TokyoURLhttps://www.ims.u-tokyo.ac.jp/imsut/en/index.htmlReference:(*1) GISAID : https://www.gisaid.org/(*2) NCBIhttps://www.ncbi.nlm.nih.gov/sars-cov-2/(*3) Koyama T., Platt D., Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ. 2020;98:495-504.(*4) IBM and the Institute of Medical Science, the University of Tokyo develop a system for rapid analysis and visualization of viral genome mutations to reduce the risk of COVID-19 infection spreading in Japan: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00095.html(*5) Tracking SARS-CoV-2 during Tokyo 2020 via wastewater~Wastewater-based epidemiological tracking of COVID-19 in the Tokyo 2020 Olympic and Paralympic village showed that SARS-CoV-2 was present in areas without diagnosed individuals~: https://www.ims.u-tokyo.ac.jp/imsut/jp/about/press/page_00151.html(*6) Kitajima M., Murakami M., Iwamoto R., Katayama H., Imoto S. COVID-19 wastewater surveillance implemented in the Tokyo 2020 Olympic and Paralympic Village Journal of Travel Medicine Volume 29, Issue 3, April 2022.

Frontiers in Microbiology

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Cross-border transmissions of the Delta substrain AY.29 during Tokyo Olympic and Paralympic Games

3-Aug-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Cross-border transmissions of the Delta substrain AY.29 from Japan to the world during the Tokyo Olympic and Paralympic Games - EurekAlert

Washington, DC, 28 September 2022 (PAHO) - Health authorities of the Region of the Americas agreed today to take a series of actions to expand and strengthen genomic surveillance of pathogens with pandemic and epidemic potential in the Region.

The Strategy on Regional Genomic Surveillance for Epidemic and Pandemic Preparedness and Response, approved in the framework of the 30th Pan American Sanitary Conference of the Pan American Health Organization (PAHO), highlights the imperative need for the Region to equip itself with advanced tools for early detection and monitoring of viruses that pose a serious threat to health.

"Emerging and re-emerging pathogens with epidemic and pandemic potential present a significant risk in the Region," said Ciro Ugarte, Director of PAHO's Health Emergencies Department. "For that reason, it is essential to increase our ability to use genomic sequencing to quickly identify and characterize changes in viruses that can cause them to spread faster or cause more severe disease," he said.

Climate change, unplanned urbanization, the establishment of human settlements in jungle areas, and increased travel are additional risk factors for the emergence and spread of pathogens. As of May 2022, around 30% of all cases of COVID-19 and 44% of deaths worldwide occurred in the Americas, making the Region's vulnerability clear.

The new strategy will help countries and PAHO consolidate and expand the advances made in genomic surveillance to date. These include the COVID-19 Genomic Surveillance Regional Network (COVIGEN), created in March 2020, more than a year before variants of concern required a change of strategy to combat the spread of SARS-CoV-2.

The main impact of COVIGEN has been to strengthen and expand national SARS-CoV-2 genomic sequencing and surveillance capacities. Currently, more than 30 countries and territories in the Region actively participate as members of the network.

With a horizon of 2028, the lines of action of the strategy on genomic surveillance include:

PAHO will provide technical cooperation to its Member States for implementation of the strategy. It will also promote the consolidation of a regional genomic surveillance network for epidemic and pandemic preparedness and response beyond SARS-CoV-2, including influenza, arboviral diseases, and bacterial pathogens.

Originally posted here:
Countries of the Americas Agree to Increase Genomic Sequencing to Detect Potentially Pandemic Pathogens - Pan American Health Organization

Los Angeles, USA: A recent report published by Verified Market Research, titled [Global Whole Genome Sequencing (Wgs) Market, History and Forecasts for 2022-2029, data broken down by manufacturers, key regions, types and applications], contains an in-depth analysis of the Global Whole Genome Sequencing (Wgs) Market. The research report is divided in such a way as to highlight the key areas of the market and give the reader a complete picture. The report examines various aspects of the Whole Genome Sequencing (Wgs) market, such as its opportunities to explore its driving forces and limitations, market size, market segment analysis, regional prospects, key players and the competitive environment. Market Research Report Whole Genome Sequencing (Wgs) uses the methodology of primary and secondary research to provide accurate data to its readers. To fully assess the market and key players. Analysts also used SWOT analysis and analysis of Porters five strengths.

In the Global Whole Genome Sequencing (Wgs) Market, analysts provided historical and forecast data on the market, as well as the expected growth of average annual indicators. This will help the reader to evaluate the market in terms of its growth.

Whole Genome Sequencing (Wgs) Market is growing at a moderate pace with substantial growth rates over the last few years and is estimated that the market will grow significantly in the forecasted period i.e. 2020 to 2027.

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Global Whole Genome Sequencing (Wgs) Market : Drivers and Restraints

In this chapter, the report provides a full explanation of the driving forces of the market. It highlights the main driving forces of the market, which are expected to make a significant contribution to the growth of the market. It covers various industries that are developing in the same field, identifies the main areas of application and determines which of them will play an important role. The report also examines some of the new technologies and developments presented by manufacturers that are expected to become notable engines for the global Whole Genome Sequencing (Wgs) market.

This chapter also gives the reader important information regarding restrictions that may hinder the growth of the Whole Genome Sequencing (Wgs) market in the future. This research report discussed factors such as changes in land prices, labor and production costs, environmental issues, new government policies and business standards. In addition, the analysts also gave an idea of the potential opportunities existing in the global market of Whole Genome Sequencing (Wgs). It offers a new perspective of turning threats into viable options to give the company a chance to win.

Global Whole Genome Sequencing (Wgs) Market : Competitive rivalry

The research report includes an analysis of the competitive environment present in the Global Whole Genome Sequencing (Wgs) Market. It includes an assessment of current and future trends in which players can invest. In addition, it also includes an assessment of the financial prospects of the players and explains the nature of the competition.

Key Players mentioned in the Global Market Research Report Whole Genome Sequencing (Wgs) Market:

Market segmentation of Whole Genome Sequencing (Wgs) market:

Whole Genome Sequencing (Wgs) market is divided by type and application. For the period 2021-2028, cross-segment growth provides accurate calculations and forecasts of sales by Type and Application in terms of volume and value. This analysis can help you grow your business by targeting qualified niche markets.

Whole Genome Sequencing (WGS) Market, By Product Type

Large Whole-Genome Sequencing Small Genome Sequencing

Whole Genome Sequencing (WGS) Market, By Industry

Humanity Plant Animal Microorganism Virus

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Whole Genome Sequencing (Wgs) Market Report Scope

Global Whole Genome Sequencing (Wgs) Market: Regional segmentation

For further understanding, the research report includes a geographical segmentation of the Global Whole Genome Sequencing (Wgs) Market. It provides an assessment of the volatility of political scenarios and changes that may be made to regulatory structures. This estimate provides an accurate analysis of the regional growth of the Global Whole Genome Sequencing (Wgs) Market.

Middle East and Africa (GCC countries and Egypt)North America (USA, Mexico and Canada)South America (Brazil, etc.)Europe (Turkey, Germany, Russia, Great Britain, Italy, France, etc.)Asia-Pacific region (Vietnam, China, Malaysia, Japan, Philippines, Korea, Thailand, India, Indonesia and Australia)

Global Whole Genome Sequencing (Wgs) Market: Research methodology

The research methodologies used by analysts play a crucial role in how the publication was compiled. Analysts used primary and secondary research methodologies to create a comprehensive analysis. For an accurate and accurate analysis of the Global Whole Genome Sequencing (Wgs) Market, analysts use ascending and descending approaches.

Table of Contents

Report Overview:It includes major players of the global Whole Genome Sequencing (Wgs) Market covered in the research study, research scope, and Market segments by type, market segments by application, years considered for the research study, and objectives of the report.

Global Growth Trends:This section focuses on industry trends where market drivers and top market trends are shed light upon. It also provides growth rates of key producers operating in the global Whole Genome Sequencing (Wgs) Market. Furthermore, it offers production and capacity analysis where marketing pricing trends, capacity, production, and production value of the global Whole Genome Sequencing (Wgs) Market are discussed.

Market Share by Manufacturers:Here, the report provides details about revenue by manufacturers, production and capacity by manufacturers, price by manufacturers, expansion plans, mergers and acquisitions, and products, market entry dates, distribution, and market areas of key manufacturers.

Market Size by Type:This section concentrates on product type segments where production value market share, price, and production market share by product type are discussed.

Market Size by Application:Besides an overview of the global Whole Genome Sequencing (Wgs) Market by application, it gives a study on the consumption in the global Whole Genome Sequencing (Wgs) Market by application.

Production by Region:Here, the production value growth rate, production growth rate, import and export, and key players of each regional market are provided.

Consumption by Region:This section provides information on the consumption in each regional market studied in the report. The consumption is discussed on the basis of country, application, and product type.

Company Profiles:Almost all leading players of the global Whole Genome Sequencing (Wgs) Market are profiled in this section. The analysts have provided information about their recent developments in the global Whole Genome Sequencing (Wgs) Market, products, revenue, production, business, and company.

Market Forecast by Production:The production and production value forecasts included in this section are for the global Whole Genome Sequencing (Wgs) Market as well as for key regional markets.

Market Forecast by Consumption:The consumption and consumption value forecasts included in this section are for the global Whole Genome Sequencing (Wgs) Market as well as for key regional markets.

Value Chain and Sales Analysis:It deeply analyzes customers, distributors, sales channels, and value chain of the global Whole Genome Sequencing (Wgs) Market.

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Read more from the original source:
Whole Genome Sequencing (Wgs) Market Size And Forecast To 2022 |Illumina, Thermo Fisher, BGI, Agilent Technologies, 10x Genomics The Colby Echo News...

Genomic testing has been used for years on a case-by-case basis in clinical care, but is now increasingly seen as an important contributor to advancing population health.

During a September Becker's Hospital Review webinar sponsored by Helix a population genomics and viral surveillance company Feby Abraham, PhD, chief strategy officer of Houston-based Memorial Hermann Health System, and James Lu, MD, PhD, co-founder and CEO of Helix, discussed the role of genomics programs in supporting health systems' population and precision health objectives.

Three key takeaways were:

The strategic goals of the program, which will embed the Helix end-to-end platform, are to:

"We are going to innovate care delivery to inspire patients to [engage in] more proactive upfront interventions," Dr. Abraham said. He emphasized that higher patient engagement would be accomplished by intensifying patient education efforts as part of the genomic screening program. That, in turn, will improve patient retention, which is a key benefit for providers delivering care both under a fee-for-service and a value-based model.

As organizations embrace using genomic screening and data more broadly, integrated solutions that power large-scale clinical and research programs such as Memorial Hermann's will be central to implementing enterprise-wide genomics initiatives.

To view the full webinar,click here.

To register for upcoming webinars, click here.

Originally posted here:
Innovation in practice: using genomic testing in routine care to boost population health - Becker's Hospital Review