The new highly contagious strain of COVID-19 that is spreading acrossOut the UK may now be touring the USA
The challenge is to find.
Unlike the United Kingdom, America has not yet fully harnessed the power of genomics to quickly detect major changes in the virus that could alter the trajectory of the country ‘s pandemic.
“We are working blind,” with insufficient screening to know the prevalence of the strain, said Dr. Charles Chiu, from UC San Francisco, whose laboratory is collaborating with the state’s Department of Public Health to pursue the new variant, called B.1.1 .7., On viral samples among recent UK travelers in many California counties.
On Friday, Chiu’s laboratory discovered two new cases of the variant virus in samples collected from members of a family in the Big Bear area on December 20. A member of the household had contact with a traveler who returned from the UK on December 11. The discovery follows news of two cases in San Diego and two cases in Denver, all confirmed on Wednesday. As of Saturday, the variant has been reported in 33 other countries.
Since none of the people involved in the US cases reported travel, experts fear not detected Community propagation.
Like all viruses, the pathogen COVID-19 makes minor changes to its genome as it reproduces. Understanding this evolution – and especially what mutations can change its behavior – is essential to estimate the threat of new strains.
The genetic makeup of the virus, stored on a single strand of RNA, determines whether it can suddenly become resistant to drugs or whether a vaccine is protective or futile.
But of the more than 19 million COVID-19 cases officially reported in the United States, only 58,500, or 0.3 percent, have been genetically analyzed for variants, according to the latest data from a centralized database.
And most of these analyzes are taking old cases. The average time between sample collection and sequence sharing in the USA is 96.6 days – compared to 38.5 days in the United Kingdom. While more than half of the samples in that country are sequenced in one month, only 14.7% of the samples in the USA are.
It is no accident that the country’s first case was found in Colorado. Unlike California and most other states, the Colorado state laboratory sequences all COVID-19 samples for the UK variant, according to health officials. This laboratory also sequences all suspicious samples sent by commercial laboratories.
California is sequencing samples of people who meet at least one of the following criteria: Recent trip to the UK or Europe; exposure to people with recent trips to the UK or Europe; or a diagnostic test with mutations indicating that it may be related to the UK strain. These samples are sent to a network of laboratories – including the California Department of Public Health and local public health laboratories, diagnostic laboratories, Chan Zuckerberg Biohub, Invitae Corporation, UCSF and Scripps Institute – collectively called “COVIDNet”.
The discovery of the variant by the state is a warning sign, said Stacia Wyman, a scientist at the Innovative Genomics Institute in Berkeley, whose team sequenced the genomes of 700 samples of the East Bay COVID-19 virus.
“I deeply suspect it is in many other places,” she said. With more universal sequencing, “we would know that”.
So far, California has largely focused its sequencing efforts on specific incidents, such as outbreaks in nursing homes, correctional institutions, hospitals and other group settings. Whenever an event called “super-spreading” occurs, academic and public health laboratories rush to inspect viral genomes to track transmission patterns.
This strategy revealed, for example, that one person infected 52 others at a fraternity party at UC Berkeley last July. Three specific mutations defined this cluster, said Wyman, whose team led the investigation. His team looked for this pattern in the genetic sequences of many samples – and, to his relief, found no evidence that the virus had spread to the wider community.
“It was just closed,” she said. “The whole strain that defined that cluster just disappeared, because the university had a very good response to it.”
The two San Diego cases were discovered due to that county’s close relationship with Scripps Research, which has a renowned genome sequencing program. The initial disease was detected during UCSD’s mandatory testing program, and in just 17 hours, Scripps had a response.
It is not clear how and where this new worrying variant came about.
Although this virus is usually quite stable, accumulating only one or two mutations per month, there were several notable changes during the course of the pandemic, according to the World Health Organization.
One of the first variants, a mutation called D614G that increases infectivity and transmission, appeared in China last winter; in June, this was the dominant form of the virus. Another new strain, which potentially decreases immune protection, was detected in Denmark in August; fortunately, it does not appear to have spread widely.
The new UK variant of concern has 23 distinct differences compared to what is currently circulating. One of these changes seems to make it more easily transferable. Although this virus is no more deadly than the existing strain, it can be more difficult to contain.
Another variant, announced by South Africa on December 18, also appears to increase transmissibility and has since spread from two provinces to four other nations.
A powerful computer browser at UC Santa Cruz is helping scientists compare hundreds of viral sequences at once, revealing where these new mutations are located and how common they are. The so-called SARS-CoV-2 Genome Browser also shows which parts of the genome are being studied by various teams and provides information about the mutations. Based on computer code written by postdoctoral scholar Yatish Turakhia, the browser is much faster than the existing tools.
“We absolutely need to increase our vigilance over what the virus is doing and how it is being transmitted,” said David Haussler, professor of biomolecular engineering at UCSC, who leads the effort. “We must control how the virus is taking advantage of us.”
The two largest sequencing centers in California are Chan Zuckerberg Biohub of San Francisco, which sequenced and published 2,817 genomes of the COVID-19 virus, and Anderson Lab of Scripps Research, based in La Jolla, which sequenced and published 2,374 genomes.
A federal infrastructure of “sequencing centers” would create more consistent, representative and weighted analyzes, said Wyman of IGI. “At the moment, each state does its own thing.”
Here’s the challenge: sequencing is expensive. Requires labor. Takes time. And it distracts attention from the most urgent public health needs.
Unlike the United Kingdom, whose national strategy called “genomic surveillance” is administered by a handful of large laboratories, the American effort falls on the tired shoulders of many state and local health departments, which are already stressed by the pandemic. There is no federal funding for a coordinated, real-time effort. And because our healthcare system is fragmented, there is no single channel that provides all positive samples for sequencing.
There is a new federal initiative called SPHERES (Sequencing for Response to Public Health Emergencies, Epidemiology and Surveillance), but it serves mainly as a central data repository. You don’t pay for actual lab work.
“We can’t even do enough diagnostic tests. So, how would you have the resources needed for sequencing? ”Said Dr. Omai Garner, associate director of clinical microbiology for the UCLA Health System. “It is prohibitively expensive and very, very challenging, technically.”
With the number of current cases, it is understandable that the country is focused on testing, vaccines and reducing the burden on hospitals, agree the experts.
But the arrival of the UK strain warns us of what else could happen, they said. Even after everyone is vaccinated, the nation must be vigilant for the surprise emergence of new dangerous strains.
“The idea is to identify local outbreaks of these new variants before they have a chance to spread, so that they are contained,” said Chiu.
“A really robust surveillance system will help not only control the pandemic now,” he said, “but also in the future.”
How COVID-19 “complete genome sequencing” is done:
- Scientists take infected cells and treat them with chemicals that break them down, releasing viral RNA. The RNA is then purified.
- The RNA is cut into short fragments of known length, using enzymes.
- Scientists make many copies of each fragment of RNA using a process called polymerase chain
reaction (PCR). The pool of fragments generated in a PCR machine is called an “RNA library”. - The RNA library is loaded into a sequencer. The combination of nucleotides (A, U, C and G) that make up each individual RNA fragment is determined, and each result is called an “RNA reading”.
- The sequencer produces millions of RNA readings and specialized computer programs are used to put them together in the correct order, like pieces of a puzzle.
- When completed, the genome sequence containing millions of nucleotides – including any surprising changes in the usual sequence, called mutations – is ready for further analysis.