copenlu/druid huggingface dataset:
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-09-07): This new variant, dubbed BA.2.86, has now been detected in at least 15 cases across six countries, including Israel, Denmark, South Africa, and the United States. This is a trickle of new cases, not a flood, which is somewhat reassuring. But with COVID surveillance no longer a priority, the world’s labs are also sequencing about 1 percent of what they were two years ago, says Thomas Peacock, a virologist at the Pirbright Institute. The less surveillance scientists are doing, the more places a variant could spread out of sight, and the longer it will take to understand BA.2.86’s potential. [...] A second and more likely possibility is that BA.2.86 ends up like the other post-Omicron variants: transmissible enough to edge out a previous variant, but not transmissible enough to cause a big new surge. Since the original Omicron variant, or BA.1, took over, the U.S. has successively cycled through BA.2, BA.2.12.1, BA.5, BQ.1, XBB.1.5—and if these jumbles of numbers and letters seem only faintly familiar, it’s because they never reached the same levels of notoriety as the original. Vaccine makers track them to keep COVID shots up to date, but the World Health Organization hasn’t deemed any worthy of a new Greek letter.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-09-06): The updated booster generated a strong antibody response against BA.2.86, according to Moderna. The variant has not yet gained widespread prevalence in the United States but has raised alarm among experts and health officials because of its high number of mutations. [...] The Centers for Disease Control and Prevention has indicated that BA.2.86, dubbed "Pirola" by some on social media, may be more capable of causing infection in people who have had Covid or were vaccinated, although the agency added there is no evidence to date that it can cause more severe illness. [...] The current increases in cases and hospitalizations in the U.S. are most likely being driven by infections with XBB lineage viruses, not the BA.2.86 variant, according to the CDC.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-12-06): The Omicron subvariant BA.2.86 is derived from the BA.2 subvariant but has over 30 mutations in spike relative to both BA.2 and recently circulating subvariants such as XBB.1.5 (Fig. 1A), making its emergence a major concern since many of the mutations are predicted to confer escape from neutralizing antibodies1. [...] The Omicron BA.2.86 subvariant started to be identified by global genomic surveillance samples collected from 24 July 2023 onwards, but because of the reduced rate of surveillance the exact time when it started to spread is unclear. Likewise, it is unclear when and where it arose. In this work, we use phylogenetic analysis to investigate the origin of BA.2.86 and neutralization and virological assays to measure escape from neutralizing antibodies and other viral properties to give an indication of how different this variant is likely to be from recently circulating subvariants descended from XBB. We find that BA.2.86 likely evolved in Southern Africa. Despite the extensive genomic changes relative to other circulating variants, our data supports the notion that BA.2.86 is not substantially different from recent variants in escape from neutralizing antibodies or cellular infection.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-09-03): "Two independent labs have basically shown that BA.2.86 essentially is not a further immune escape compared with current variants," Dr. Dan Barouch, director of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center and leader of one of the labs, told CNN. [...] So when BA.2.86 appeared on the scene in late July with eerie echoes of Omicron, variant hunters were spooked, and researchers leapt into action to learn more about the new lineage. It has spread to at least 11 countries, including the United States. [...] In an update posted Friday, the group concluded that BA.2.86 doesn’t meet its definition of a variant of concern because it doesn’t have any evidence that the profile represents a harmful change to its biological properties or a growth rate suggesting it would move at least as fast as or faster than currently circulating variants.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-23): Variant hunters flagged BA.2.86 this month after it was found in Israel. It has more than 30 gene changes from BA.2, its next closest ancestor, representing an evolutionary leap on par with the one the virus made from Delta to Omicron in 2021 or the leap between BA.2 and XBB.1.5, which circulated a year apart, the CDC said. [...] BA.2.86 appears to have emerged in humans only recently. The earliest known samples of the new variant were collected in late July. [...] It’s not clear whether BA.2.86 will be able to do that, the CDC says.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-30): Annex: UKHSA clinical advice on the emerging risk of BA.2.86 UKHSA conducts routine monitoring and surveillance of COVID-19 and the emergence and spread of new variants internationally. A new variant, BA.2.86 was identified due to its high number of mutations. The mutations, including many in spike protein, mean that the variant may be antigenically altered compared to previously circulating variants, and other changes in viral properties are also possible. There are a small number of cases identified globally but as genomic surveillance is now very limited internationally, there is a very high degree of uncertainty about the spread and growth of this variant at present and the situation is dynamic. It will take a period of several weeks to grow the virus and confirm its biological properties, and epidemiological studies cannot be conducted until there are a larger number of cases to include. Should this variant cause an increase in transmission, the earliest epidemiological signal may be from increasing hospital admissions in the UK or other countries. Waiting to respond until this data is available will mean that any interventions are unlikely to change the impact on health services.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-18): It's still unclear how transmissible BA.2.86 is, though experts said it seems capable of sidestepping vaccine protection to some degree. [...] So far, only a handful of cases of the new variant, BA.2.86, have been identified globally. In addition to one case in Michigan, the variant has also been spotted in Denmark, Israel, and the UK, according to sequences uploaded to GISAID, a global virus database. The World Health Organization labeled BA.2.86 a "variant under monitoring" on Thursday. The designation applies to variants with an unusually large number of mutations that warrant tracking of their global spread.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-11-21): The highly mutated SARS-CoV-2 variant BA.2.86 is still neutralized by antibodies in the blood The spike protein of BA.2.86 — a subvariant of Omicron — has a large number of mutations, and binds to its receptor in host cells with high affinity. Despite these characteristics, BA.2.86 is no more resistant to antibodies from vaccinated individuals than are the dominant variants that are currently in circulation. [...] Read the paper: Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2024-01-08): The BA.2.86 variant of omicron is the ancestor of the currently dominating JN.1 and has about 60 more spike protein mutations than the original, or parent, coronavirus, including over 30 more than its close omicron relatives – the early BA.2 variant and the recently dominant XBB.1.5 variant among them. These mutations led scientists to worry that so many changes would make the variant as tough to contain as the initial omicron outbreak in 2021-22. [...] "But BA.2.86 appears to have increased infectivity of human lung epithelial cells compared to all omicron variants, so that’s a little worrisome. And, consistent with infectivity, it also has increased fusion activity with human lung epithelial cells," said Liu, also a professor in the Department of Microbial Infection and Immunity. "That raises a potential concern about whether or not this virus is more pathogenic compared to recent omicron variants." [...] Additional experiments pointed to the potential for BA.2.86 to be more likely to cause severe disease than its omicron relatives. Researchers found BA.2.86 was more efficient at infecting a cell line derived from the human lower airway epithelium in the lung. Infection of these cells is greatly facilitated through a cell surface protein, known as TMPRSS2, to promote membrane fusion, and this protein is a known contributor to SARS-CoV-2 infection and disease symptoms in the respiratory tract.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-10-25): On August 17, 2023, genomic sequencing identified BA.2.86 in a pooled sample of swabs from 10 TGS participants collected on August 10 at Dulles International Airport near the District of Columbia. Testing and sequencing of the individual samples confirmed the presence of BA.2.86 in one individual sample on August 20. The sample was collected from a U.S. resident returning from a 15–30-day trip to Japan; health authorities in Japan were notified upon confirmation. The traveler reported no previous COVID-19 infection and had last received a COVID-19 vaccine dose in October 2022. This sequence was the second publicly reported BA.2.86 sequence in the United States and the seventh reported globally,¶ preceding the first BA.2.86 sequence submission reported from Japan by 17 days.** The TGS sample was sent to a CDC laboratory, but virus isolation was not successful. Phylogenetic analyses indicated that the TGS sample contained distinct genetic differences from other BA.2.86 sequences collected in August 2023 (Figure), consistent with BA.2.86 circulation and divergence from BA.2.86.1 viruses several months before detection (4,5). [...] As a component of comprehensive U.S. SARS-CoV-2 genomic surveillance, TGS detected the BA.2.86 variant within days of its first identification globally, highlighting its importance for the detection of variants entering the United States. This identification provided important context regarding BA.2.86 geographic spread and diversity. Although virus isolation was not successful in this case, continued surveillance and sample collection are important to enable rapid laboratory characterization of variant sensitivity to antibody neutralization and antiviral drugs. Early variant detection among travelers and laboratory characterization of new variants are essential components of CDC’s respiratory illness surveillance, especially as global sequencing volumes decline.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2024-09-26): Based on what CDC knows now, existing tests used to detect and medications used to treat COVID-19 appear to be effective with this variant. BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines. Scientists are evaluating the effectiveness of the forthcoming, updated COVID-19 vaccine. CDC’s current assessment is that this updated vaccine will be effective at reducing severe disease and hospitalization. At this point, there is no evidence that this variant is causing more severe illness. That assessment may change as additional scientific data are developed. CDC will share more as we know more. [...] 9/20/2023: Clarification on BA.2.86 risk assessment posted on 8/23/2023. The first risk assessment CDC released on BA.2.86 included the following sentence: "BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines." The intent of this sentence was to raise the possibility that BA.2.86 might be more capable of causing infection compared with other variants currently circulating, but this sentence has been misinterpreted by some. Vaccination remains the best available protection against the most severe outcomes of COVID-19, including hospitalization and death. COVID-19 vaccines also reduce the chance of having Long COVID. Since this webpage was originally posted, laboratory data have become available that suggest existing antibodies from previous COVID-19 vaccines and COVID-19 infection provide protection against this variant similar to other circulating variants and that updated COVID-19 vaccines are expected to provide similar protection as other circulating variants.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-11-27): - Since CDC's first post on BA.2.86 in August 2023, the proportion of infections caused by BA.2.86 has slowly increased. In the CDC Nowcast posted Nov. 27, 2023, BA.2.86 is projected to account for 5-15% of currently circulating variants. [...] - CDC contributed to and agrees with the World Health Organization's recent risk assessment about BA.2.86 suggesting that the public health risk posed by this variant is low compared with other circulating variants, based on available limited evidence. - Updated COVID-19 vaccines are expected to increase protection against BA.2.86, as they do for other variants.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-24): Covid-19: Scientists sound alarm over new BA.2.86 "Pirola" variant [...] Genetic sequencing has found BA.2.86 in six covid cases so far, the earliest being in Denmark on 24 July. The other cases were from Israel, the UK, and the US. None of the cases seem linked. The UK Health Security Agency said that the UK case was in a person with no recent travel history, suggesting a degree of community transmission within the UK. The genetic diversity suggests that BA.2.86 has been in circulation for months, said Balloux. "Interestingly, all 30-plus mutations on that long branch are found in the spike …
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-10-25): Each surveillance component provides distinct information, that, when considered together, enable robust situational awareness for early warning signals and support epidemiologic characterization if more widespread transmission is established. The SARS-CoV-2 variant BA.2.86, first detected in August 2023, has more than 30 mutations in the spike protein compared with other currently circulating variants. This sequence divergence of BA.2.86 suggested potentially reduced antibody protection from previous SARS-CoV-2 infection and vaccination, especially before early laboratory-based evaluations were conducted. Consequently, CDC is actively monitoring BA.2.86 to guide public health actions and surveillance efforts (1). Continued variant tracking and further evidence, such as real-word evaluations, are needed to understand the full public health impact of BA.2.86. This report highlights the use of a diverse, multicomponent surveillance system for early warning, and describes how this approach has informed the response to the SARS-CoV-2 BA.2.86 variant. [...] Other existing surveillance systems†††† might become critical to monitoring the impacts of BA.2.86. If circulation increases, epidemiologic data related to relative transmissibility, disease severity, and vaccine and therapeutic effectiveness will be important to understanding this variant’s impact on human health. If BA.2.86 exceeds 1% of circulating variants within the United States, it will be reported through CDC’s Nowcast estimates over time and by region. If BA.2.86 circulation expands to represent a significant proportion of circulating variants in the United States, other complementary COVID-19 surveillance systems that capture detailed laboratory- and patient-level data can be tracked in parallel to understand epidemiologic impacts. If new data become available that result in heightened concern, CDC can launch epidemiologic field studies on transmissibility and severity.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-09-12): Among the new mutations that BA.2.86 carries, 14 reside within an area of the spike protein called the receptor binding domain, which binds to the receptors on host cells. This suggests that BA.2.86 could have a greater capacity for infecting than its predecessor. In addition, the new sublineage, BA.2.86, is even more dissimilar when compared to the most recent sublineage, XBB.1.5, with 35 new mutations in the spike protein – including some unusual mutations – than to its precursor, BA.2. These alterations intrigue infectious disease specialists like me, and we are working to understand how they might affect this new variant’s behavior. [...] The emergence of BA.2.86 underscores the need for flexibility in current vaccine strategies to ensure continued effectiveness against these new variants. The newly FDA-approved fall 2023 COVID-19 booster shots are formulated to target XBB.1.5, which was dominant in early 2023 when public health officials made the reformulation decisions. The 2022 booster shot was designed to target both the original strain of SARS-CoV-2 as well as the BA.4 and BA.5 omicron lineages.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2024-09-18): BA.2.86 is an Omicron subvariant of SARS-CoV-2, the virus that causes COVID-19. BA.2.86 is notable for having more than thirty mutations on its spike protein relative to BA.2.[1] The subvariant, which was first detected in a sample from 24 July 2023,[2] is of concern due to it having made an evolutionary jump on par with the evolutionary jump that the original Omicron variant had made relative to Wuhan-Hu-1, the reference strain first sequenced in Wuhan in December 2019.[3][4][5][6] It is a mutation of BA.2, itself a very early mutation in the Omicron family.[4] BA.2.86 was designated as a variant under monitoring by the World Health Organization on 17 August 2023.[7] The variant was nicknamed Pirola by media, although no official sources use this name.[8] Its descendant JN.1 (BA.2.86.1.1) became the dominating Lineage in Winter 2023/2024.[9][10] [...] Nomenclature [edit]Some news media have used the colloquial name "pirola" to describe the BA.2.86 variant.[29][30] The name is reported to have been created by a social media user by combining the names of the Greek letters pi and rho, which follow the letter omicron in the Greek alphabet.[31]
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-21): Research is under way to determine whether the mutation-laden lineage BA.2.86 has the potential for global spread — or whether it is nothing to worry about.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-31): So far, only 26 cases of "Pirola," as the new variant is being called, have been identified: 10 in Denmark, four each in Sweden and the United States, three in South Africa, two in Portugal, and one each the United Kingdom, Israel, and Canada. BA 2.86 is a subvariant of Omicron, but according to reports from the CDC, the strain has many more mutations than the ones that came before it. [...] What is unique about the BA 2.86 variant? [...] "Vaccine coverage for the BA.2.86 is an area of uncertainty right now," said Mostafa.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-08-31): Will BA.2.86 ('Pirola'), the New Coronavirus Variant, Increase COVID-19 Cases? [...] BA.2.86 is a newly designated variant of Omicron, which itself is a variant of SARS-CoV-2, the virus that causes COVID-19. BA.2.86 has additional mutations compared to previously detected Omicron subvariants. More specifically, it is derived from BA.2, an Omicron subvariant that circulated more than a year ago, Dr. Roberts adds. [...] According to the Centers for Disease Control and Prevention (CDC), existing tests to detect and medications used to treat COVID-19 (such as Paxlovid, Veklury, and Lagevrio) appear to be effective with BA.2.86, but this variant may be more capable of causing infection in people who have had COVID-19 or have been vaccinated against it. There is currently no evidence that the strain is causing more severe illness.
Claim: With the new BA.2.86 variant, “We’re in a situation where vaccination, according to the CDC, increases the likelihood of infection” (John Campbell, 2023-08-29)
Evidence (2023-12-22): CDC has been tracking JN.1 for months, since it first split from its parent, BA.2.86. JN.1 is similar to BA.2.86 but has an additional mutation (L455S) in the spike protein. JN.1 continues to cause an increasing share of infections and is now the most widely circulating variant in the United States. For the two weeks ending on December 23, 2023, JN.1 is expected to account for 39-50% of all SARS-CoV-2 variants. That's an increase from the projected prevalence two weeks ago of 15-29%. We're also seeing an increasing share of infections caused by JN.1 in travelers, wastewater, and most regions around the globe. [...] It's important to know that existing vaccines, tests, and treatments still work well against JN.1, so this variant does not affect CDC's recommendations. Recent laboratory data (here and here) show that the updated 2023-2024 COVID-19 vaccines produce antibodies that protect against JN.1, further indicating that our vaccines work well against this variant. At this time, the spread of JN.1 does not appear to pose additional risks to public health beyond that of other recent variants. CDC is closely monitoring COVID-19 increases domestically and internationally and will communicate if the situation changes.