Oregon health officials have reported a dozen cases of coronavirus involving more contagious variants – including one strain with an apparently homemade mutation that yields a combination never found in the United States.
The appearance of the variants occurred when Oregon recorded a sharp decrease in identified cases of coronavirus, and painted a sometimes confusing portrait. If there were more transmissible versions of the virus in Oregon, why would the cases go down?
What do these variants mean for the distribution of COVID-19 in Oregon? We spoke 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 that a strain COVID-19, known as B.1.1.7, first identified in the United Kingdom, would become the dominant strain in the United States in March. This is one of the three concerns that the agency is monitoring.
Oregon filed its first case under an employee at the University of Portland the same month. Eleven such cases have now been identified.
But how bad is it in Oregon now? The short answer is: we do not know yet, partly because the analysis is about a month behind.
Identifying a coronavirus strain of a known infection is a time-consuming process, requiring specialized analyzes, called genomic sequencing. For the United States, it currently takes an average of 30 days to follow a sample from arrival. Since not every case follows sequence, public health officials and researchers conduct a subset of cases to determine the occurrence of variants.
Of the 158,000 confirmed or suspected cases of coronavirus in Oregon, approximately 3,500 samples have been sequenced since the onset of the pandemic and submitted to GISAID, a database used by scientists around the world to detect the COVID-19 outbreak .
Dr. Brian O’Roak, a geneticist at Oregon Health & Science University, and his lab followed about 3,000 of them.
Based on his team’s data of mainly samples from the metropolitan areas in Portland, the prevalence of the British tribe in Oregon is currently estimated at 1% based on samples in sequence from January. But O’Roak said his team is only now beginning to track a large number of positive samples from February and March, when the variant may have spread more easily in Oregon.
“We only know now that levels of B.1.1.7 in Oregon are still relatively low, but we’ve seen in the UK and elsewhere that it can spread fairly quickly,” O’Roak said.
The B.1.1.7 variant is of concern because it has spread rapidly across the UK. The variant was detected in December and has a number of different mutations in its genetic code – small copying errors formed during reproduction – that are more deadly and contagious than the previous strains of COVID-19.
There are more than 3,000 cases of the strain now being detected in America, with the highest numbers in Florida and Michigan.
Some of Oregon’s current sequence data for B.1.1.7 could also be skewed, thereby sequencing samples, O’Roak said.
The spread of the variant was first discovered in the United States by means of ‘S-failure of genes’, which refers to a part of the virus’ genetic code that was removed from the S-gene.
Testing for this deleted gene was a way to distinguish variants of the UK and other countries from the original strains of the coronavirus. Samples will then be taken from this batch and followed to determine which cases were actually the B.1.1.7 strain from the United Kingdom
This method “does not give you the true look” of B.1.1.7 in the United States, O’Roak said. This is because the dropout pattern is easier to spot, which will result in more sequence in search of B.1.1.7.
He said the goal at OHSU’s laboratory is to accelerate all available samples, regardless of whether the S gene failure was detected, which should give a more accurate picture of how common the B.1.1.7 variant is in Oregon. .
The actual prevalence could probably be even lower than current numbers, O’Roak said when the order for February samples was completed.
“To really do that, I think on the scale 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 COVID-19 variant from Brazil. It was found in Douglas County.
One of Oregon’s 11 cases of the B.1.1.7 variant is an outlier. It has a distinct mutation, E484K, also known as ‘Eek’.
O’Roak said the mutation occurred spontaneously and was not transported from 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 the B.1.1.7 variant, 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. The other viruses could have been the “parents” of this coronavirus if one were to map a pedigree, O’Roak said.
The virus may have mutated in the following hypothetical scenario:
Person A pulls up the B.1.1.7 strain of COVID-19 and then infects Person B. While the virus is inside Person B, the Eek mutation forms. When Person B then infects Person C, they transmit a virus from strain B.1.1.7 which includes the Eek mutation and can propagate Person C to others.
In this scenario, O’Roak’s lab will likely track samples of people like Person A and Person C, based on the limited data they have, O’Roak said.
Mutations in viruses are common and usually small enough not to affect the functioning of the virus. However, mutations that are beneficial for the survival of a virus can accumulate until a new strain is formed.
The Eek mutation was originally found in the B.1.351 strain that was first detected in South Africa in November and later the P.1 strain that was first detected in Brazil. Early data suggest that this mutation may make the virus less susceptible to human antibodies, or virus fighters, that are generated in your body when you get a vaccine.
There is unconvincing evidence on how well existing vaccines developed to combat COVID-19 are protected against these new strains. Much of the research done was published online as a ‘pre-print’ version, meaning that it did not go through the rigorous process of review by other scientists.
The Oregon Health Authority said it was ‘too early to speculate’ on how the distribution of COVID-19 variants would affect the effectiveness of the currently approved vaccines in the United States by Johnson & Johnson, Moderna and Pfizer.
“The current vaccines are likely to still protect against serious infections leading to hospitalizations and deaths,” the agency said in a statement Saturday. “The best vaccine is the one that is immediately available.”
A report released on March 8 indicates that the Pfizer-BioNTech COVID-19 vaccine has a high capacity to control coronavirus strains from the UK and Brazil, with a slightly lower but still ‘robust’ reaction to the variant from South Africa, at least in a laboratory. institution.
However, a UK study combining the B.1.1.7 strain with the Eek mutation in a laboratory found a “greater loss” in how effective vaccine antibodies neutralized the coronavirus.
Research on the Moderna vaccine has found that the effectiveness of the variant from South Africa has a reduced, but still significant ‘effectiveness.
Viruses with the Eek mutation can also be more difficult to treat.
A study in late February tested bamlanivimab – a monoclonal antibody treatment allowed for high-risk patients with mild to moderate COVID-19 – against the UK, South Africa and P.2 variant variants (more). a virus strain first found in Brazil).
It was not effective against the P.2 variant or the origin in South Africa, which both have Eek. The study also tested antibodies induced by the Pfizer-BioNTech vaccine and found that its effectiveness was ‘slightly reduced’ compared to all three strains included in the study.
However, because there is limited evidence from the real world, it is unclear how these variants will ‘behave outside the laboratory’, O’Roak said.
– Jaimie Ding
[email protected]; 503-221-4395; @j_dingdingding