Oregon health officials have reported a dozen cases of coronaviruses involving more contagious variants – including a strain with an apparently homemade mutation producing a combination that has never been found in the United States.
The emergence of variants occurred when Oregon recorded sharp declines in the cases of identified coronaviruses, painting a picture that was sometimes confusing. If more communicable versions of the virus were in Oregon, why were the cases decreasing?
What do these variants mean for the spread of COVID-19 in Oregon? We talked to the geneticist who identified most cases in the state with variants. Here’s what you need to know.
In January, the Centers for Disease Control and Prevention predicted a strain of COVID-19 known as B.1.1.7, first identified in the UK, could become the dominant strain in the United States sometime in March. It is one of three variants of concern that the agency is tracking.
Oregon reported his first case among an employee at the University of Portland that same month. Eleven of these cases have already been identified.
But how bad is it in Oregon right now? The short answer is: we still don’t know, partly because the analysis is delayed by about a month.
Identifying a coronavirus strain from a known infection is a lengthy process that requires specialized analysis called genomic sequencing. For the United States, it currently takes an average of 30 days to sequence a sample when it arrives. Since not all cases are sequenced, public health officials and researchers collect samples from a subset of cases to determine the prevalence of variants.
Of 158,000 confirmed or suspected coronavirus cases in Oregon, nearly 3,500 samples since the beginning of the pandemic have been sequenced and sent to GISAID, a database used by scientists around the world to track the COVID-19 outbreak.
Dr. Brian O’Roak, a geneticist at Oregon Health & Science University, and his laboratory sequenced nearly 3,000 of them.
Based on data from its sample team mainly from the Portland metropolitan area, the prevalence of the UK strain in Oregon is currently estimated at 1% based on sequenced samples from January. But O’Roak said his team is only now beginning to sequence a large number of positive samples from February and March, when the variant may have been more easily circulated in Oregon.
“We only know now that B.1.1.7 levels are still relatively low in Oregon, but we saw in the UK and elsewhere that it can spread quickly,” said O’Roak.
Variant B.1.1.7 is worrisome because it has spread rapidly across the UK. Detected in December, the variant had a set of distinct mutations in its genetic code – tiny copy errors formed during reproduction – which were considered more lethal and contagious than previous strains of COVID-19.
There are more than 3,000 cases of the strain now detected in America, with the highest numbers in Florida and Michigan.
Some of Oregon’s current sequencing data for B.1.1.7 may also be distorted because of the samples that are sequenced, said O’Roak.
The spread of the variant was first discovered in the United States through the “abandonment of the S gene”, which refers to a part of the virus’s genetic code that was deleted in the S gene.
The test for this deleted gene was a way to distinguish variants from the United Kingdom and other countries from the original strains of the coronavirus. Then samples would be taken from this batch and sequenced to find out which cases were actually the B.1.1.7 strain in the United Kingdom.
This method “does not give the true prevalence” of B.1.1.7 in the United States, said O’Roak. This is because the abandonment pattern could be more easily detected, requesting more sequencing in search of B.1.1.7.
He said the objective of the OHSU laboratory is to speed up the sequencing of all available samples, regardless of whether the loss of the S gene has been detected, which should paint a more accurate picture of how prevalent variant B.1.1.7 is in the Oregon.
The actual prevalence is likely to be even lower than the current numbers, said O’Roak, when the February sample sequencing is complete.
“To really do that, I think that at the scale that we need to move forward and be able to closely monitor these variants of concern, we need more resources,” he said.
Meanwhile, Oregon last week also identified its first case of a variant of Brazil’s COVID-19. It was detected in Douglas County.
One of Oregon’s 11 cases of variant B.1.1.7 is a discrepant case. It has a distinct mutation, E484K, also known as “Eek”.
O’Roak said the mutation “occurred spontaneously” and was not carried anywhere else in the world.
It was discovered by O’Roak and his colleagues when they analyzed 13 test results from coronavirus samples collected by the Oregon State Public Health Laboratory. Ten of the samples were variant B.1.1.7, including one that had the “Eek” mutation.
They were able to determine that this mutation probably originated in Oregon and was not imported from elsewhere after finding genetic similarities with other virus samples. These other viruses may have been the “parents” of this coronavirus if someone were to map a family tree, said O’Roak.
The virus may have mutated in the following hypothetical scenario:
Person A contracts strain B.1.1.7 of COVID-19 and then infects person B. While the virus is inside person B, the Eek mutation forms. When person B infects person C, he passes a virus from the B.1.1.7 strain that includes the Eek mutation, and person C can continue to spread to other people.
In this scenario, O’Roak’s lab probably sequenced samples from people like Person A and Person C, based on the limited data they have, said O’Roak.
Mutations in viruses are common and generally small enough to not significantly impact the functioning of the virus. Mutations that are beneficial for the survival of a virus, however, can accumulate until a new strain is formed.
The Eek mutation was originally found in the B.1.351 strain first detected in South Africa in November and, subsequently, in the P.1 strain first detected in Brazil. Early data suggests that this mutation may make the virus less susceptible to human antibodies, or virus fighters, that are generated in your body when you receive the vaccine.
There is inconclusive evidence on how well existing vaccines developed to combat COVID-19 protect against these new strains. Much of the research done was published online as a “pre-printed” version, which means that it has not gone through the rigorous review process by other scientists.
The Oregon Health Authority said it was “too early to speculate” about how the spread of COVID-19 variants affects the effectiveness of vaccines currently approved in the United States by Johnson & Johnson, Moderna and Pfizer.
“Current vaccines are still expected to protect against serious infections, resulting in hospitalizations and deaths,” the agency said in a statement on Saturday. “The best vaccine is one that is immediately available.”
A report published on March 8 indicates that the Pfizer-BioNTech COVID-19 vaccine showed a high capacity to combat the coronavirus strains in the United Kingdom and Brazil with a slightly smaller, but still “robust” response to the South African variant , at least in a context laboratory.
However, a UK study that combined the B.1.1.7 strain with the Eek mutation in a laboratory setting found a “more substantial loss” in how effective the vaccine’s antibodies neutralized the coronavirus.
Research on the Modern vaccine found “reduced, but still significant” efficacy against the South African variant.
Viruses with the Eek mutation can also be more difficult to treat.
A study in late February tested bamlanivimab – a monoclonal antibody treatment authorized for high-risk patients with mild to moderate COVID-19 – against variants originating in the United Kingdom, South Africa and P.2. variant (another strain of the virus found for the first time in Brazil).
It was not effective against the P.2 variant or the one that originated in South Africa, which both have Eek. The study also tested antibodies induced by the Pfizer-BioNTech vaccine and found “slightly reduced” efficacy against all three strains included in the study.
As there is limited evidence in the real world, however, it is unclear how these variants “will behave outside the laboratory,” said O’Roak.
– Jaimie Ding
[email protected]; 503-221-4395; @j_dingdingding