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COVID appears to be in retreat in the U.S. and other nations that have widespread access to vaccines. But some developing countries with high infection rates have become hotspots for viral variants that may be more transmissible or resistant to vaccinesand these variants can quickly cross national borders. For example, the B.1.167.2 variant (now dubbed Delta) that was first detected in India has spread to more than 70 countries and regions, including the U.S.

Much of the developing world lacks the capacity for viral surveillanceefforts to monitor the spread and evolution of new variants. This process requires expensive genomic-sequencing technology and trained workforces that many nations do not have. Nepal, for instance, has sequenced just 0.01 percent of the more than 600,000 cases reported in the country so far. New variants could undo hard-won progress in curbing the pandemic, according to Alina Chan, a postdoctoral fellow specializing in gene therapy and cell engineering at the Broad Institute of the Massachusetts Institute of Technology and Harvard University. Variants that evolve to be able to reinfect previously infected people are likely to also reduce the efficacy of vaccines, she says.

Scientists and organizations around the world are now working to build capacity to hunt for variants in developing countries. They are mobilizing to deliver funds, training and equipment to where these resources are needed most, with aspirations of creating a lasting viral surveillance infrastructure. COVID is the catalyst, says Jairo Mendez-Rico, a microbiologist and adviser on viral diseases at the Pan American Health Organization (PAHO), headquartered in Washington, D.C. But we also need to survey for other pathogens that for sure will come in the future.

In India, 27 laboratories have now banded together to create the Indian SARS-CoV-2 Genomics Consortium (INSACOG). The group plans to sequence 5 percent of all positive COVID cases in the country (the current rate is only 0.09 percent). Shahid Jameel, a virologist and director of the Trivedi School of Biosciences at Indias Ashoka University, says that bringing existing surveillance capacity under a single umbrella could, in principle, make that a feasible goal. But there are not enough trained field-workers, he says, and the laboratories have acute shortages of chemical reagents needed for genomic analyses.

International experts are now stepping in to help. Recently, a nonprofit volunteer group called INDIA COVID SOS formed to assist with the pandemic response in the country. It aims to scale genomic surveillance across India, as well among neighboring South Asian nations. Aditi Hazra, an epidemiologist at Harvard Medical School, co-leads the groups sequencing team, which meets regularly on video conference calls with the directors of Indias sequencing consortium. She says a key objective is to extend viral surveillance to more people in rural areas, where much of the population lives.

Rural surveillance is a priority in Africa as well. Millions of people on the continent live in remote areas that are also hot spots for disease outbreaks, says Akaninyene Otu, a medical doctor and a senior lecturer at the University of Calabar in Nigeria. Several new partnerships aim to boost sequencing in African countries. Otu highlights the Africa Pathogen Genomics Initiative (Africa PGI), which launched last year with support from international donor organizations and private companies. Most of the sequencing capacity in Africa is concentrated in South Africa, Kenya, Nigeria, Morocco and Egypt. The Africa PGI, which is headed by the Africa Centers for Disease Control and Prevention, is setting out to create a pan-African network of sequencing centers to serve the continents 54 countries.

In Latin American countrieswhich are currently reporting some of the highest COVID infection rates in the worldPAHO is spearheading the COVID-19 Genomic Surveillance Regional Network. Some countries in the region already have fairly strong sequencing capabilities, but the network is leading efforts to build surveillance capacity where it does not exist at all, which is the case throughout much of Central America. In the interim, two large reference labsone in Brazil and one in Chileare sequencing samples sent by other countries at PAHO's expense, Mendez-Rico says.

In addition to building partnerships and networks, scientists are also exploring low-cost sequencing technologies that could be deployed easily in the field. Nearly all of the SARS-CoV-2 cases sequenced so far have relied on large, expensive instruments housed in climate-controlled lab facilities. As an alternative, INDIA COVID SOS is encouraging wider use of a handheld sequencing device made by Oxford Nanopore Technologies in England. The device, called the MinION, can run on a battery pack, processes 96 samples at a time and uses software to generate whole genome sequences that can be stored on a laptop. We're looking for technologies that are cheap, efficient, scalable and portable, and this is an example, Hazra says.

Keith Robison, a computational biologist at Ginkgo Bioworks, a Boston-based biotechnology company, agrees that the MinION is a practical option for developing nationsespecially in rural settings. The portable technology was widely used during the recent Ebola outbreaks in the Democratic Republic of the Congo and other West African countries. You can generate sequences with it from anywhere, he says. The MinION has its drawbacks: the quality of the data is not as good as what the lab-based instruments provide, Robison notes. However, that can also be computationally corrected if you have many copies of the same sequence, he says.

Tue Sparholt Jrgensen, a postdoctoral researcher in microbiology at the Technical University of Denmark, argues that whole-genome sequences may not always be needed. All the important SARS-CoV-2 mutations identified so far, he says, sit on the same stretch of genome encoding the microbes well-known spike protein. Jrgensen says scientists can simply target this piece of the viral geome with an alternative method called Sanger sequencing. This method, which was used as part of the effort that led to the sequencing of the complete human genome back in 2003, is still employed by labs all over the world. Unlike whole-genome methods that sequence millions of genetic fragments simultaneously, the Sanger method sequences one fragment at a time. Sanger can't replace whole-genome sequencing, but you can use it for targeted analyses at a fraction of the cost, Jrgensen says. People have been using it in small labs for decades. Id use it to monitor for known variants, [to] qualify samples for whole genome sequencing and for contact tracing [of infected people] in hospitals.

Jrgensen and his colleagues are now working with health officials in Rwanda on plans to expand Sanger-based COVID surveillance in the country. If a new variant emerges in Rwanda and starts spreading [elsewhere] in Africa, then we want to know about it, he says.

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New Coronavirus Variants Are Urgently Being Tracked around the World - Scientific American

JAKARTA - A weak zonal lockdown system and a lack of whole-genome-sequencing equipment to detect more transmissible new Covid-19 variants are the two main challenges Indonesia is facing, experts say.

They called for a quick fix as the world's largest archipelagic nation of 17,500 sprawling islands saw Covid-19 cases surging past the two-million mark on Monday (June 21).

Instead of a large-scale lockdown, Indonesia has so far imposed only localised ones based on a colour-coded regime. Badly hit regions are labelled red zones and subject to tougher restrictions. Those with fewer Covid-19 cases are labelled either orange or yellow.

The country has 34 provinces that are made up of more than 500 cities and regencies.

The zoning system covers even small neighbourhoods, each having between 10 and50 households. A neighbourhood is labelled a red zone if there are cases in at least 10 households in the past seven days. Green is for areas with no detected infection.

Cities and regencies are labelled based on factors such as hospital bed occupancy ratios (BOR), positivity rate and mortality rate.

Those with an average of above 80 per cent BOR are red zones, while those with 60 per cent to 80 per cent rate are labelled orange or yellow - depending on other parameters such as their total hospital bed capacity relative to the total suspected and confirmed cases.

A green zone is one with BOR of below 60 per cent.

There are 29 red zones currently, including Bandung (West Java province), Bangkalan (East Java) and Pekanbaru (Riau).

But many believe the system and the "micro lockdowns" are not working well.

Dr Aman Bhakti Pulungan, chairman of Indonesian Paediatric Society, said: "We do not acknowledge those green, red zones because there are no borders."

For example, it is not a standard measure to set up a checkpoint between regions labelled red and green that filters the number of people going in and out to contain the spread of the virus. The government does it only in certain emergency situations.

For instance, the local authorities set up a temporary checkpoint on the causeway between Madura island and the main Java island earlier this month to screen people coming from Bangkalan regency in Madura. This was after a surge in Covid-19 cases in Bangkalan, where many patients died within 48 hours of being hospitalised.

Dr Pandu Riono, from the University of Indonesia's medical school, said another shortcoming of the colour-coded system is that no one knows how to label a region with a low testing rate.

In addition, the government has not monitored the implementation of measures or punished breaches adequately, Dr Pandu told The Straits Times.

"Whatever form of social restrictions we take, what is most important are implementation, evaluation and punishment," he said. "We can use the ubiquitous CCTV to monitor. Next, we can take action to ensure there are penalties and incentives."

The government encourages regions to punish residents who flout the mask-wearing rule. Those in Jakarta, for example, pay a fine of 250,000 rupiah (S$23) or do an hour of community work such as sweeping pavements.

Experts are also concerned with the lack of whole-genome-sequencing equipment to detect new variants of the virus, and the non-disclosure of test results.

"Not every province has it In some cases, it is equivalent to walking in the dark and blind-folded. We want to wage a war but we cannot see the enemy," Dr Pulungan said.

Health Minister Budi Gunadi Sadikin has confirmed that based on genome sequencing tests, cases in Jakarta, Kudus in Central Java province, and Bangkalanare dominated by the Delta variant.

Dr Siti Nadia Tarmizi, a health ministry spokesman, told The Straits Times that there are 17 laboratories across Indonesia that have genome-sequencing equipment.

"We are planning to add between three and five, " she said.

Dr Pulungan also said there needs to be a system where hospitals or health departments of provinces and cities do sampling, regularly collect genome-sequencingdata and share it with the public.

"This is what the WHO (World Health Organisation) wants," he added.

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Indonesia's Covid-19 fight hindered by weak lockdown, lack of genome-sequencing data - The Straits Times

Express News Service

BENGALURU: The Genomic Surveillance Committee, formed by the State Government recently, has come up with an action plan to scale up genomic sequencing by training laboratory staff through online and on-ground training.

The plan follows a recent announcement by Health Minister Dr K Sudhakar that seven genome sequencing labs would be set up at five government medical colleges, Wenlock Hospital in Mangaluru and Vijaypura district hospital.

The Centre for Cellular and Molecular Platforms(C-Camp), IBAB and IT-BT Department, with the support of Strand-HCG Hospital, IISc and NCBS, will train the laboratory staff online on and on the ground as to how to carry out genomic surveillance, said Dr Vishal Rao, a member of the States Genomic Surveillance Committee and Regional Director -- Head and Neck Surgical Oncology, HCG Cancer Centre.

Genomic sequencingof positive samples started in the State this yearafter the UK variant was found and a total of 127 tested positive. Later, the South African variant surfaced with six infections. Now, theDelta and Kappa Indian variants have infected 318 and 112 people in the State.

Committee officials said the technology and staff are needed to be ramped up to carry out better genomic surveillance.

We have so far conducted genome sequencing of 350-400 samples in the past few months in the State. Ideally, we should have done at least double that. We need to scale up technology and conduct at least 1,000 sample tests a week. This is the only way we can keep a clinical track of the variants, Dr Rao added.

One of the committee members pointed out that it will take at least three to four months for medical colleges to start genomic surveillance. Merging of existing capabilities of IISc and Strand Life Sciences Pvt Ltd will play a key role, he added.

The committee is also planning to follow the Chan Zuckerberg Initiative (CZI), which has set up a Covid tracker dashboard, to make genome sequencing and analyses freely available to all primary healthcare centres.

Dr Rao said that it is imperative to rely on machine learning models and AI algorithms to execute genomic surveillance efficiently.

Dr Vijay Chandru, Lancet Commissioner and a member of Genomic Surveillance Committee, said, It is time for us to bring the best-in-class capabilities in the country to drive better genomic surveillance. The public effort driven by INSACOG has laid a foundation, but we now need to scale it up and have real-time dashboards to enable early warning signals to manage the next wave.

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Lab staff in Karnataka to be trained for genome surveillance ahead of third COVID wave - The New Indian Express

New York, June 22, 2021 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Agrigenomics Market by Application, Sequencer Type, Objectives And Region - Forecast year 2026" - https://www.reportlinker.com/p04147669/?utm_source=GNW The large-scale genetic characterization in some of the commercially relevant crops has provided a framework that is applicable to other crops as well. With the mounting dual challenges of population growth and climate change, new strategies, including genetic advancements, must be available to producers to address concerns of yield optimization and food security.

The market for livestock is projected to grow at the highest CAGR between 2021 and 2026.The livestock segment is projected to gain further growth traction during the forecast period owing to rapid adoption and commercialization of the novel genotyping platforms and related techniques such as marker-based selection (MAS) and marker-based breeding (MAB) to identify complex inheritance traits.The global demand for animal-based food products is expected to increase by 70% by 2050.

The implementation of advanced genetic technologies in livestock production will ensure minimal environmental impact with optimized animal health & fertility.A shift from traditional animal breeding to genomic selection is estimated with the introduction of genome analysis tools. The presence of next-generation sequencers has enabled researchers to quickly and effectively determine the single nucleotide polymorphisms associated with commercially important phenotypic traits and estimate the breeding value (EBV) at an earlier stage of young animals.

The Marker-assisted selection by objective is projected to grow at the highest CAGR between 2021 and 2026.The Marker-assisted selection is expected to grow at the highest rate during the forecast period as it is cheaper and faster than any conventional phenotypic assays, depending on the trait. Marker-assisted selection or marker-aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (morphological, biochemical, or DNA/RNA variation) linked to a trait of interest (e.g., productivity, disease resistance, abiotic stress tolerance, and quality), rather than on the trait itself. This process has been extensively researched and proposed for plant and animal breeding. It uses conventional breeding approaches and does not involve transgenic approaches. Marker-assisted breeding uses DNA markers associated with desirable traits to select a plant or animal for inclusion in a breeding program early in its development. This approach dramatically reduces the time required to identify varieties or breeds which express the desired trait in a breeding program. The marker may be the sequence of the gene that determines the trait, but in most cases, it is a DNA sequence which is located very close to the gene of interest and is therefore always inherited with the trait. Desirable traits include disease resistance, salt tolerance, and high yield. Hence, DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection.

Illumina HiSeq Family by sequencer type is projected to grow at the highest CAGR between 2021 and 2026.The Illumina Hi Seq Family held the largest share in 2020 and is also expected to grow at the highest rate as it is an efficient ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Based on sequencer type, Illumina Hi Seq Family led the agrigenomics market, exhibiting a significant share of in 2020, registering a value of USD 1,393.2 million. It is also the most widely utilized next-generation sequencing (NGS) technology owing to its high throughput and exceptional operational performance. It also exhibits greater sensitivity to detect low-frequency gene variants. PacBio and solid sequencers are also expected to exhibit decent growth rates during the forecast period. Sequencing by ligation (SOLiD) utilizes DNA ligase, an enzyme widely used in biotechnology for its ability to ligate double-stranded DNA strands owing to its two-base sequencing method, it is the most accurate and economical second-generation sequencing platform.

The agrigenomics market in the Asia Pacific region is projected to grow at the highest CAGR during the forecast period. The Asia Pacific region is projected to be the fastest-growing in the global agrigenomics market at a CAGR of 10.6%. The growth in the region is projected due to the progress in research and development activities in India, China, and Japan. The availability of high-quality reference genome sequences for a majority of crops has strengthened the foundation of functional genomics in the region. Asia Pacific is the most populous continent with growing concerns for food and nutritional security. The region also produces important food crops such as rice, wheat, barley, chickpea, and pigeon pea. The agrigenomics solutions adopted in a full-fledged manner across the key markets of the region can emerge as a strong tool in the attainment of zero hunger as a sustainable development goal.

In the process of determining and verifying the market size for several segments and sub-segments gathered through secondary research, extensive primary interviews have been conducted with the key experts.

The breakup of the profiles of primary participants is as follows: By Manufacturers: Tier 1 20%, Tier 2 50%, and Tier 3 30% By Designation: CXOs 31%, Managers 24%, Executives 45% By Geography: Europe 29%, Asia Pacific 32%, North America 24%, South America 12%, and RoW 3%The key players in this market include Thermo Fisher Scientific, Inc. (US), Agilent Technologies, Inc. (US), Illumina, Inc. (US), Eurofins Scientific SE (Luxembourg), and LGC Limited (UK). Some of these playersThermo Fisher Scientific, Inc. (US) and Illumina, Inc. (US)are both, technology and service providers who have streamlined their supply chain in providing agrigenomics services.

Research CoverageThe report segments the agrigenomics market based on type, species, application, and region. In terms of insights, this report has focused on various levels of analysescompetitive landscape, end-use analysis, and company profileswhich together comprise and discuss views on the emerging & high-growth segments of the agrigenomics , high-growth regions, countries, government initiatives, drivers, restraints, opportunities, and challenges.

Reasons to Buy the Report: Illustrative segmentation, analysis, and forecast pertaining to the agrigenomics market based on type, species, application, and geography have been conducted to provide an overall view of the agrigenomics market Major drivers, restraints, and opportunities for the agrigenomics market have been detailed in this report.Read the full report: https://www.reportlinker.com/p04147669/?utm_source=GNW

About ReportlinkerReportLinker is an award-winning market research solution. Reportlinker finds and organizes the latest industry data so you get all the market research you need - instantly, in one place.

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The global agrigenomics market is estimated to be USD 3.3 billion in 2021 and is projected - GlobeNewswire

The report on theGlobal CRISPR Genome Editing Market Research Report Covers, Future Trends, Size, Share, Past, Present Data and Deep Analysis, And Forecast, 2021-2027market documented by Zion Market Research (ZMR) means to offer a coordinated and orderly methodology for the major aspects that have influenced the market in the past and the forthcoming market prospects on which the organizations can depend upon before investing. It furnishes with a reasonable examination of the market for better decision-making and assessment to put resources into it. The report analyses the elements and a complete detailed outlook of the main players that are probably going to add to the demand in the global CRISPR Genome Editing market in the upcoming years.

The top Major Competitive Players are :Editas Medicine, CRISPR Therapeutics AG, Horizon Discovery PLC., Sigma-Aldrich, Genscript, Sangamo BiosciencesInc., Lonza Group AG, Integrated DNA Technologies, New England Biolabs Inc, Origene Technologies Inc., Transposagen Biopharmaceuticals, Thermo Fisher Scientific, Caribou BiosciencesInc., Precision Biosciences, Cellectis, Intellia TherapeuticsInc., Novartis among others.

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Global CRISPR Genome EditingMarket: Regional Analysis

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Global CRISPR Genome Editing Market Precise Outlook and Study of Top Players 2021 : Editas Medicine, CRISPR Therapeutics AG, Horizon Discovery PLC.,...

TheWhole Genome Synthesis Market Likely To Expand Splendidly During The Forecast Period 2020-2026report covers all of the aspects required to gain a complete understanding of the pre-market conditions, current conditions as well as a well-measured forecast.This report also researches and evaluates the impact of Covid-19 outbreak on theWhole Genome Synthesis Market, involving potential opportunity and challenges, drivers and risks.

A comprehensive evaluation of theWhole Genome Synthesis Markethas been presented in the report for the forecasted period 2020 to 2025. In order to get a deep insight into the market, a wide range of segments have been covered in the report along with the thorough analysis of the key trends and the factors that impact the market. The main highlight of the report includes the key factors that impact theWhole Genome Synthesis Market, the market dynamics, major drivers, restraining factors, and the opportunities and threats that arise in the market. The intrinsic factors that have been identified are restraints and drivers. The identified threats and opportunities are the extrinsic factors that exist in the market setting. The thorough study provides an insight into the market development in terms of the revenue generation capacity during the forecasted period.

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Whole Genome Synthesis Marketresearch methodologies comprise primary research, secondary and expert panel reviews. Secondary research consists of the following sources: company annual report, research papers, and press releases, as documented in the industry. For further understanding, the following have been considered: Industry magazines, trade journals, government websites, and associations since they also contain vital information that can be useful during the study period. If all these sources are efficiently used to gather information about the industry, then theWhole Genome Synthesis Marketachieves its goals in the study, which is most likely to expand its territory in the market.

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Whole Genome Synthesis Market Likely To Expand Splendidly During The Forecast Period 2020-2026 The Manomet Current - The Manomet Current