- The new strain, known as SARS-CoV-2 VUI 202012/01, has been first identified in the UK
- Infectious disease experts are still piecing together what they know about the new strain
- It is theoretically more infectious, which means it may transmit more easily
- Is it deadlier than earlier COVID? No. There is “no evidence” this variant causes more severe illness or increased risk of death
- Fresh fears that the pandemic may continue to accelerate may be unfounded
As health authorities around the world start administering the first COVID-19 shots, a “new strain” of the SARS-CoV-2 has emerged. It has been dubbed as "more infectious", according to the World Health Organisation (WHO).
The British media described the new variant of SARS-CoV-2, first detected in Kent in September, as one that “appears to spread more quickly”. This has sparked fears that COVID-19 cases may spike, further accelerating the pandemic.
Now, there's a need for more clarity -- and lesser misunderstanding -- on this new variant. Here’s a Q&A of what we know so far:
What happened? What's the rough timeline? How many were infected with the new strain?
On December 14, 2020, UK health authorities identified a new SARS-CoV-2 variant through genomic sequencing. A WHO report on December 21, 2020 bears this out.
The update came after a total of 1,108 cases infected with the new SARS-CoV-2 strain have been detected in the UK (as of 13 December 2020).
What’s the result of the discovery of this new strain?
Dozens of countries have suspended transport links with the UK. Some countries have banned travel from other countries with known cases of the new strain, too.
Discovery of the “new strain” has triggered a new global panic, and fresh shutdowns. It's a knee-jerk reaction from fear of the unknown. But experts said this may not be necessary, as viruses mutate all the time, as all biological creatures do.
What’s the new strain called?
It is called SARS-CoV-2 VUI 202012/01, short for the first “variant under investigation” in December 2020, according to the Centers for Disease Control and Prevention (US CDC).
How was the variant picked up?
The variant was detected as part of an epidemiological and virological probe initiated earlier in December 2020. Scientists conduct a constant surveillance of minute mutations in viruses, particularly SARS-CoV-2, the pathogen behind the current pandemic. An unexpected rise in COVID-19 cases in South East England triggered suspicion, in part due to a three-fold spike in the 14-day case notification rate from epidemiological week 41 to week 50 (5 October to 13 December 2020). The variant was identified in people with PCR-confirmed coronavirus cases under 60 years of age.
Does the variant spread at a higher rate than the previously known ones?
Yes. Initial analyses indicate that the variant may spread more readily between people.
What do scientists know about this variant?
Virologists are still piecing together what they know about the new strain. Experts said the variant was traced back to Kent in southeast England, where it was found as early as September 20, 2020.
By October, the variant began spreading rapidly throughout the region, the WHO stated. Then cases continued to spike at an unexpected pace through November. This prompted an investigation and discovery of the mutation earlier in December 2020. Between October 5 and December 13, more than 50% of the viral samples from southeast England that were sequenced were found to be the VUI 202012/01 strain.
Cases of the new variant have been reported worldwide, in the following countries:
• The Netherlands
• US (Florida, California)
[This list will be updated as new information comes]
The CDC stated it could already be circulating across the US mainland unnoticed.
How infectious is the virus?
UK health authorities said the variant could be “up to 70% more transmissible" than the original strain of the virus.
How deadly is this new strain?
There is “no evidence” the new variant makes people sicker, according to initial reports. The US CDC stated that the new virus strain doesn’t increase the risk of death. Many of the cases are asymptomatic and self-isolating.
What is the reproduction rate of the new strain?
Maria Van Kerkhove, head of the WHO’s emerging diseases and zoonosis unit, has estimated that the new virus has seen an increase in the reproductive rate of the virus from 1.1 to 1.5.
In short, each person infected with the VUI 202012/01 strain is estimated to infect another 1.5 people, while the original strain only infected an average of 1.1.
Is the faster spread (reproductive rate) due to the mutation?
Dr. Mike Ryan, executive director of the WHO’s health emergencies program, said it was unclear if the increase in spread in the UK is because of the mutation or human behavior.
“We’ve seen an estimate of a small increase in the reproductive number by the UK,” he said.
Is the weather (winter) helping this new strain?
Dr Ryan said while current data indicate the virus is spreading faster, it could also mean it is more contagious or spreads more easily in colder months.
It could also mean people are getting lax about following social distancing protocols. “It remains to be seen how much of that is due to the specific genetic change in the new variant. I suspect some,” said Dr Ryan.
Is there anything unusual in this mutation?
No. Viruses mutate all the time. SARS-CoV-2, the virus behind COVID-19 “mutates regularly,” the CDC noted. The overwhelming majority of mutations are insignificant.
Investigations are on to establish to establish the following:
• whether the variant is more infectious;
• whether it causes people to become more sick;
• whether it can re-infect people who previously had COVID-19; and
• what kind of antibody response the new variant prompts.
The U.K. is also conducting genomic surveillance. This will help scientists understand the scope of spread of the new variant. The UK has also placed affected areas under tier 4 restrictions, the strongest lockdown measures in the country.
In the U.S., “viruses have only been sequenced from about 51,000 of the 17 million US cases,” so the new strain could have slipped notice, according to the CDC.
What’s the current status of viral surveillance?
To sequence more virus samples, the US CDC launched in November a new initiative, the National SARS-CoV-2 Strain Surveillance program. It’s supposed to be fully running this month (January 2021). Under the scheme, each US state will send the CDC at least 10 samples every other week for sequencing and further study.
What does this mean for vaccines?
Lab studies had been heightened and are ongoing to help epidemiology experts know whether the new virus has different biological properties or could alter vaccine efficacy. There’s no verdict on this question yet.
Initial results show that the mutations include changes to the “spike protein" the virus uses to infect human cells. Both Pfizer’s and Moderna’s vaccines, authorized for use in many countries today, use messenger RNA, or mRNA, technology.
It’s a new, revolutionary way to produce vaccines that uses genetic material to generate a “fake” virus – in this case, a harmless piece of spike protein – to induce an immune response against the virus.
What about the reported loss of PCR assay tests that target the Spike protein?
It’s early days. WHO drew attention to the concern about the reported loss of performance of PCR assays that target the spike (S) gene of the virus. It advised labs that use commercial PCR kits for which the targeted viral genes are not clearly identified in the manufacturer’s instructions to contact the manufacturer for more information.
“Laboratories using in-house PCR assays that target the S gene of the virus should also be aware of this potential issue. In order to limit the impact on the detection capacities in the countries, an approach using different assays in parallel or multiplex assays targeting different viral genes is also recommended to allow the detection of potential arising variants,” the WHO stated.
How confident are experts that new vaccines will help protect against new strain?
BioNTech CEO Ugur Sahin said recently that the company’s coronavirus vaccine with Pfizer will work against the new strain. There’s a caveat: To be completely sure, he added further studies are needed.
Dr. Moncef Slaoui, the US coronavirus czar, also expressed confidence that Pfizer’s and Moderna’s Covid-19 shots will be effective against the new mutation. Both shots induce an immune response against several structures found around the spike protein. The chances one set of mutations would completely alter those structures “are extremely low,” Dr Slaoui added.
The variant is defined by the presence of a range of 14 mutations resulting in amino acid changes and three deletions. Some of these mutations may influence the transmissibility of the virus in humans:
• One of the mutations identified (N501Y) is altering an amino acid within the six key residues in the receptor binding domain (RBD).
• According to the Global Initiative on Sharing Avian Influenza Data (GISAID) database, this same receptor binding domain mutation (N501Y) has been independently reported in several countries including South Africa (n=45) and Australia (n=37).
• Sequence analysis revealed that N501Y mutation of the virus reported in the United Kingdom and South Africa originated separately.
• Another mutation of biological significance, P681H, has been found in the RBD.
• Finally, the deletion at position 69/70 has been found to affect the performance of some diagnostic PCR assays that use an S gene target.
• Most PCR assays worldwide use multiple targets and therefore the impact of the variant on diagnostics is not anticipated to be significant.
Risk assessment: What the WHO says
“All viruses, including SARS-CoV-2, change over time, but most of these mutations or changes do not have a direct benefit to the virus or may even be detrimental to its propagation. Further laboratory investigations are required to more fully understand the impact of specific mutation on viral properties and the effectiveness of diagnostics, therapeutics and vaccines. These investigations are complex and require time and collaboration amongst different research groups.”
What is the best way to deal with it? What are scientists doing?
Open science, which leads to global knowledge sharing is key. The sharing of full genome sequences is facilitating detailed analyses.
The WHO SARS-CoV-2 Virus Evolution Working Group is working with colleagues from the UK and around the world to better understand the available results and support further studies.
The new strain underscores the importance of prompt, accurate and open sharing of epidemiological, virological and full genome sequence information among research teams in different countries, including through open-source platforms such as GISAID and others.
To understand the specific mutations described by the United Kingdom and other countries, further studies are needed and must continue to pinpoint any minute changes in the function of the virus in terms of infectivity and pathogenicity.
WHO advises all countries to increase the routine sequencing of SARS-CoV-2 viruses where possible, and sharing of sequence data internationally, in particular, to report if the same mutations of concern are found.
— With Associated Press, WHO inputs