Daily Archives: December 7, 2021

What is the current newborn screening?

All babies in the UK are offered the heel prick or blood spot test at around five days old to screen for nine serious health conditions, including cystic fibrosis, sickle cell disease and various metabolic diseases. These conditions, if identified, can be treated or managed. Genetic testing is only offered in certain cases, such as if there is a concern that the baby might be at risk of an inherited disorder.

What is whole-genome sequencing?

Whole-genome sequencing (WGS) reads out the entire DNA code. It is already being used in the NHS to diagnose rare diseases and could be used to screen for mutations that are linked to a wider range of treatable serious diseases that affect babies. Genomics England says that using WGS could allow the current nine conditions screened for to be expanded to more than 200. Genetic data can also be used to predict a persons risk of adulthood diseases, such as Alzheimers and heart disease.

Do other countries offer whole-genome sequencing?

No. There have been pilot studies for whole-genome sequencing for newborn screening, including a trial at Boston Childrens hospital, in which about 7% of families took up the offer. There are also countries that screen for a larger number of childhood diseases using an expanded panel of biochemical and targeted gene tests.

Is this the only approach?

Geneticists are in agreement that the UKs newborn screening should be upgraded. Whole-genome sequencing is one way of achieving this. Another option would be to enhance the existing screening using a panel of genetic tests designed to detect mutations on specific genes. Some argue that these tests would be cheaper, and potentially more accurate for certain conditions.

Are there advantages to WGS?

A key advantage is flexibility: new conditions could be added to the screening list relatively easily since data for the entire genome is already being collected. Such a large dataset of genomic and linked health records would also allow scientists to learn more about genetic predictors of health and disease and potentially help develop new treatments. Some say that genomics will inevitably play an increasingly important role in healthcare and argue that it will be an advantage for participants, and the UK, to be at the forefront of this development.

What are the downsides?

Whole-genome sequencing can be less efficient at predicting some conditions than biochemical tests. This means that WGS would need to be combined with the existing screening process, rather than replacing it. There are also some conditions that are not currently screened for, such as spinal muscular atrophy, which may be detected more readily using a targeted gene test, optimised to pick up certain mutations.

WGS allows scientists to screen for mutations in an almost unlimited number of genes, but screening genes that are less well understood can create a risk of false positives. When genetic mutations of unknown significance are discovered, it can create a diagnostic grey zone. Whole-genome sequencing is also expensive roughly 1,000 per genome once analysis and data storage is accounted for. Based on this estimate, it would cost around 700m to sequence all newborns annually.

There are also significant ethical questions about the consent process for collecting whole-genome data, which can be used to predict health outcomes in adulthood, and questions about who owns this data and how access to it is determined.

The rest is here:
What are pros and cons of whole-genome sequencing for every UK baby? - The Guardian

PUNE With six people tested for the Omicron Covid-19 variant in the Pimpri Chinchwad municipal corporation limits, authorities have shifted their focus to increase the percentage of vaccinations and ensuring Covid appropriate behaviour, which will be monitored on priority.

Around 48% of the population in Pimpri-Chinchwad have completed both doses of the vaccination. Currently, we are not issuing any new orders for Covid regulations, but the focus is on covering more people with both doses of the vaccine, said Rajesh Patil, commissioner, PCMC.

In the last few months, we returned to a normal routine and Covid norms like wearing a mask, and maintaining social distance are not being followed seriously. Now again, it will be monitored strictly. If the situation demands, new orders will be issued in the coming days, added Patil.

In PCMC limits, 138 people have come kin from high-risk countries since Saturday. There have been 86 people subjected to RTPCR tests, of which six were detected with Omicron, while the genome sequencing report of 10 is still awaited.

Five of the six tested for the Omicron variant are asymptomatic, while only one was symptomatic. For those coming from high -risk countries a 14-day quarantine is compulsory, said Patil.

PCMC is currently not considering a sero survey.

The sero survey will be decided on the basis of the booster dose, at this stage we have not thought about it. Discussion about the sero survey is going on, said Patil.

New order on mass gatherings soon

Amid the Omicron threat, PCMC officials are considering a new order on mass gatherings.

We will be coming out with a new order on mass gatherings which will be restricted to reduce the risk of the Omicron variant, said Patil.

Covid vaccination in Pimpri-Chinchwad

48%: Both doses

88%: First dose

Follow this link:
Genome sequencing of 10 cases awaited in PCMC - Hindustan Times

The genome sequencing reports of the five merchant navy crew are expected to arrive by Wednesday or Thursday.

Five people, including two Russian nationals, who arrived in Goa on board a merchant navy ship were isolated after they tested positive for Covid-19 and their samples have been sent for genome sequencing to detect the presence of the Omicron variant, an official said on Monday.

State Epidemiologist Utkarsh Betodkar said the five are being treated as Omicron suspects and the genome sequencing reports are expected to arrive from Pune in neighbouring Maharashtra on Wednesday or Thursday.

"The ship had arrived in Goa on November 18 after leaving Cape Town in South Africa on October 31, and the two Russians had boarded it en route. The testing of crew first revealed one Covid-19 case and then five, he said.

The five have been isolated at the community health centre in Cansaulim as per Central government guidelines for such cases, he added.

Click here for IndiaToday.ins complete coverage of the coronavirus pandemic.

Continue reading here:
Omicron: 5 merchant navy ship crew isolated in Goa awaiting genome test report - India Today

Amid growing concerns of new Covid-19 variant Omicron, the BMC has decided to conduct genome sequencing on all samples taken from those who have been infected with coronavirus in the last one week.

The civic body has already started tracing international travelers who have been landing at the Mumbai airport since November 11. If found positive, their samples are being sent for genome sequencing to check for Omicron.

Officials from BMCs public health department said that besides international travelers, samples of infected patients from the past week are also being sent for genome sequencing as a precautionary measure.

According to a list received from the airport, more than 1,000 international passengers from countries at risk have arrived in Mumbai since November 11. Many of them have already completed 15 days and there is very little chance that they may test positive for the virus. However, they could have come in contact with other people. So, samples of daily cases will be sent for genome sequencing, said an official.

Among the international passengers who have arrived at Mumbai airport since November 11, around 100 are from the city. They have been traced and tested, said BMC officials. So far, six international passengers from countries at risk have been found positive and their samples sent for genome sequencing. They are from Mumbai, Mumbai Metropolitan Region, Pimpri-Chinchwad and Pune.

From November 11 till Thursday, 2,868 passengers from 40 countries have arrived at the airport.The BMCs genome sequencing lab in Kasturba Hospital takes about four to five days to test a sample. Also, the machine requires a minimum of 350 samples at a time to conduct tests.

Mumbai on Wednesday reported 108 Covid-19 cases, lowest in 19 months. In all, 37,877 samples were tested. In the last one month, the number of daily cases has seen a gradual decrease.

The BMC is also increasing daily testing in the wards. We are doubling the number of daily tests. Contact tracing of all international passengers who have come to Mumbai in the last couple of weeks has also been done, said Dr Avinash Vaydande, Medical Officer of Health (MOH) of R North ward (Dahisar).A few administrative wards have recorded zero daily cases in recent past. In the last few days, the daily cases in our ward have gone down to one or two, said Dr Jitendra Jadhav, MOH of L ward (Kurla).

Visit link:
Omicron Alert: Infected samples from past week to be sent for genome sequence - The Indian Express

Last Friday, just a day after South African scientists first announced the discovery of the Omicron variant, Europe reported its first case: The new coronavirus variant was in Belgium. Before the weekend was out, Australia, Britain, Canada, Denmark, Germany, Israel, Italy and other countries had all found cases.

But in the United States, scientists kept searching.

If we start seeing a variant popping up in multiple countries across the world, usually my intuition is that its already here, said Taj Azarian, a genomic epidemiologist at the University of Central Florida.

On Wednesday, American officials announced that scientists had found it in a California patient who had recently returned from South Africa. By then, Canada had already identified six cases; Britain had found more than a dozen.

On Thursday, additional cases were identified in Minnesota, Colorado, New York and Hawaii, and a second case was found in California, indicating that more are almost certainly lurking, scientists said. Why wasnt the variant detected sooner?

There are various potential explanations, including travel patterns and stringent entrance requirements that may have delayed the variants introduction to the United States. But there are also blind spots and delays in the countrys genomic surveillance system. With many labs now conducting a targeted search for the variant, the pace of detection could quickly pick up.

Since the beginning of the pandemic, scientists have been sequencing the genetic material from samples of the virus, a process that allows them to spot new mutations and identify specific variants. When done routinely and on a large scale, sequencing also allows researchers and officials to keep tabs on how the virus is evolving and spreading.

In the United States, this kind of broad genomic surveillance got off to a very slow start. While Britain quickly harnessed its national health care system to launch an intensive sequencing program, early sequencing efforts in the United States, based primarily out of university laboratories, were more limited and ad hoc.

Even after the C.D.C. launched a sequencing consortium in May 2020, sequencing efforts were stymied by a fragmented health care system, a lack of funding and other challenges.

In January, when cases were surging, the United States was sequencing fewer than 3,000 samples a week, according to the C.D.C.s dashboard, far less than 1 percent of reported cases. (Experts recommend sequencing at least 5 percent of cases.)

But in recent months, the situation has improved dramatically, thanks to a combination of new federal leadership, an infusion of funding and an increasing concern about the emergence and spread of new variants, experts said.

Genomic surveillance really has caught up in the U.S., and it is very good, said Dana Crawford, a genetic epidemiologist at Case Western Reserve University.

The country is now sequencing approximately 80,000 virus samples a week and 14 percent of all positive P.C.R. tests, which are conducted in labs and considered the gold standard for detecting the virus, Dr. Rochelle P. Walensky, the director of the Centers for Disease Control and Prevention, said at a White House briefing on Tuesday.

The problem is that the process takes time, especially when done in volume. The C.D.C.s own sequencing process typically takes about 10 days to complete after it receives a specimen.

We have really good surveillance in terms of quantity, said Trevor Bedford, an expert on viral evolution and surveillance at the Fred Hutchinson Cancer Research Center in Seattle. He added, But by nature, it lags compared to your case reporting. And so well have good eyes on things from two weeks ago.

This kind of delay is not uncommon in countries that have a lot of samples to sequence, Dr. Bedford said.

In some states, the timeline is even longer. The Ohio Department of Health notes that, from start to finish, the process of collecting the sample, testing it, sequencing it and reporting it can take a minimum of 3-4 weeks.

But now that scientists know what they are looking for, they should be able to expedite the process by prioritizing samples that seem most likely to be Omicron, scientists said.

Dec. 6, 2021, 9:04 p.m. ET

In one small bit of luck, Omicron generates a different genetic signal on P.C.R. tests than the Delta variant, which currently accounts for essentially all coronavirus cases in the United States. (In short, mutations in the new variants spike gene mean that Omicron samples test negative for the gene, while testing positive for a different telltale gene.)

Many labs are now expediting these samples, as well as samples from people who recently returned from abroad, for sequencing.

All of the agencies that are involved with genomic surveillance are prioritizing those recent travel-associated cases, Dr. Azarian said.

That may have been how the first California case was flagged so quickly. The patient returned from South Africa on Nov. 22 and began feeling sick on Nov. 25. The person tested positive for the virus on Monday and scientists then sequenced the virus, announcing that they had detected Omicron two days later.

The quick turnaround by the U.S. genomic surveillance system is another example of how much better our system has become over the past few months, Dr. Crawford said.

As much as surveillance has improved, there are still gaps that could slow the detection of more cases in the United States, including enormous geographic variation.

Some states are lagging behind, said Massimo Caputi, a molecular virologist at the Florida Atlantic University School of Medicine.

Over the last 90 days, for instance, Vermont has sequenced and shared about 30 percent of its virus cases and Massachusetts has sequenced about 20 percent, according to GISAID, an international database of viral genomes. Six states, on the other hand Kentucky, Pennsylvania, Ohio, South Carolina, Alabama and Oklahoma have each sequenced and reported fewer than 3 percent of their cases, according to GISAID.

Moreover, scientists can only sequence samples from cases that are detected, and the United States has often struggled to perform enough testing.

Testing is the weakest part of our pandemic response, said Dr. Eric Topol, the founder and director of Scripps Research Translational Institute in La Jolla, Calif. It has been from day one.

Although testing, like genomic surveillance, has vastly improved since the early days of the pandemic, it is still highly uneven. And while rapid, at-home tests have many advantages, the shift of some testing from the lab to the home may present new challenges for surveillance.

With increasing at-home rapid diagnostic tests, if that isnt followed up with, like, a P.C.R. test, those cases wont get sequenced, said Joseph Fauver, a genomic epidemiologist at the University of Nebraska Medical Center. The problem is not insurmountable, he added, but maybe theres a little blind spot there.

There are other, more optimistic reasons that scientists have not detected more cases, although they remain theoretical.

Perhaps infected patients have mild symptoms, and hence are not getting tested and are not subject to genomic surveillance, said Janet Robishaw, the senior associate dean for research at the Florida Atlantic University College of Medicine.

(It is still far too early to know whether Omicron causes disease that is any more or less severe than other variants, scientists stress. Even if the cases are disproportionately mild, which is not yet clear, that could be because the variant has mostly infected young or vaccinated people so far, who are less likely to develop severe disease.)

It is also possible that there was not much community spread of the variant in the United States until recently. When the cases are mostly isolated, and tied to foreign travel, they can fly under the surveillance radar.

Were kind of looking for a needle in the haystack if were looking for just single cases that are unrelated, Dr. Azarian said.

Although it is not yet clear where Omicron emerged, the first outbreaks were detected in South Africa, where the variant is now widespread.

There are fewer flights between southern Africa and the United States than between that region and Europe, where other early Omicron cases were detected, Dr. Caputi said.

And until early November, the United States had banned international travelers from the European Union and South Africa, he noted. Even when officials lifted the ban, travelers from those locations were still required to provide proof of both vaccination and a recent negative Covid test. These measures may have postponed Omicrons arrival.

It is conceivable that Omicron spread is lagging behind in the U.S., Dr. Caputi said in an email.

Either way, he added, he expected scientists to find more cases soon.

See more here:
Why Didnt the U.S. Detect Omicron Cases Sooner? - The New York Times

Govind SharmaJAMMU, Dec 6: Two Genome Sequencing laboratories which were planned to be set up in Jammu as well as in Srinagar during 2nd wave of COVID-19, are nowhere in sight and the health authorities in both the regions are still bound to send the samples of Coronavirus positive patients for Genome Sequencing in National Centre for Disease Control (NCDC) Delhi.As the Omnicron variant of Coronavirus has started spreading its tentacles in India, it has become necessary for the Health authorities to do genome sequencing of every Coronavirus positive patient so that this new variant may be stopped from spreading by detecting it timely as according to the experts across the globe, Omnicron variant spreads two times faster than the Delta variant.In view of Omnicron threat, the Government of India, in its latest guidelines, has asked the States and Union Territories to send samples of every COVID positive patient for genomic testing at the INSACOG laboratory network. Following the guidelines of the Government of India, Health authorities in both Jammu and Kashmir Divisions are sending the samples of the COVID positive patients to NCDC Delhi, which is unable to provide the genome testing reports timely, thereby defeating the objective of the genome sequencing.Official sources told Excelsior that during peak of 2nd COVID wave, Health authorities of the UT had decided to setup one Genome Sequencing lab each in Jammu division as well as in Kashmir region as the NCDC Delhi was taking weeks of time to send reports of genome sequencing. They said at that time it was decided that in Jammu region, the Genome Sequencing lab will be established in Government Medical College Jammu while in Kashmir, it was planned to set up either in SKIMS Soura or GMC Srinagar.Accordingly, the technical specifications for the machine used in Genome Sequencing were shared with Jammu and Kashmir Medical Supplies Corporation Limited (JKMSCL) for procurement of two such machines worth Rs 2 crore (approximately) each, sources said, but lamented that even after a lapse of over six months time, the requisite machines could not be procured and the labs for Genome Sequencing were not established.Sources informed that there are only a few genome sequencing labs in the country and all the States are dependent on these labs for Genome testing of samples of COVID positive patients. Had the genome sequencing labs established timely in the UT as was planned, it would have been very helpful for the Health authorities of the UT to timely detect and check spread of Omnicron variant, they said.When contacted, Dr Yashpal Sharma, Managing Director, JKMSCL said that the tenders for the procurement of the genome testing machines were floated thrice by them but every time only a single bid was received. He said now, the concerned authorities in Jammu as well as in Kashmir are evaluating the technical specifications of received bid and if their specifications match, the financial bid will be opened and the machines will be procured. The whole process will take at least 40-60 days, he added.

The Leading Daily of Jammu and Kashmir , India

See original here:
Planned to setup in Jammu & Srinagar during 2nd COVID wave, two Genome Sequencing labs nowhere in sight - Jammu Kashmir Latest News | Tourism |...

Meanwhile, an official in the Health department said, We have directions to send all samples of foreign returnees (international travellers) for genome sampling to the lab in Delhi.

He, however, said that they sent 5 percent of the total COVID positive cases in general for their genome sampling in Delhi.

They take around one and half months and the period is too long which needs to be reduced to one week time so that the infected patients can be treated timely, he said. The official said that they had a review meeting yesterday in which they requested their higher ups to ensure that the genome testing report should come within a week's time. During second wave, we had sent samples for genome sequencing and it came too late when the infected person had recovered from COVID19. In such cases the chances of infection to other persons can be more, the official cited an example.

Link:
Surveillance officers asked to ensure expedited genomic analysis through IGSLs - Greater Kashmir