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27th January 2022
The Omicron Covid variant is environmentally stable and can survive for at least 21 hours on human skin and 193 hours on plastic surfaces. This was the finding by a team from the Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan.
The Omicron variant has numerous mutations which have likely led to enhanced transmissibility. One potential factor associated with greater transmissibility is the spread from contact with human skin. The stability of the original COVID-19 variant on human skin has been found to be 9 hours which is considerably longer than the human influenza A virus. While some evidence has revealed how both the B.1.1.7 and B.1.351 covid variants had similar levels of surface stability, there is a lack of comparative data for all of the currently identified variants.
For the present study, the Japanese team examined the environmental stability of several circulating variants of concern, including the Omicron variant and compared this to the original Wuhan strain. They also sought to determine the disinfectant efficacy against the different strains. The stability was tested on human skin samples collected from forensic autopsy specimens approximately one day after death. The stability of the variants was also evaluated on plastic (polystyrene plates).
In all experiments, samples were applied to the surface of either skin or plastic and incubated and the amount of remaining viable virus determined. They defined the survival time as the time until virus could no longer be detected and each experiment was conducted three times.
Omicron covid variant survival
When tested on plastic surfaces, the Wuhan strain survived for 56 hours (95% CI 39 – 76.7 hours) whereas the omicron variant survived for 193.5 hours (95% CI 153.1 – 236.2 hours). For comparative purposes, the delta variant survived a similar length of time (114 hours).
When tested on human skin, the Wuhan strain survived for 8.6 hours (95% CI 6.5 – 10.9 hours) whereas the omicron variant lasted 21.1 hours (95% CI 15.8 – 27.6 hours). The Delta variant also survived longer than the Wuhan strain, lasting 16.8 hours (95% CI 13.1 – 21.1 hours).
In the presence of a 40% ethanol solution, the omicron covid variant was completely inactivated within 15 seconds. Furthermore, on human skin, all strains were completely inactivated after 15 seconds with exposure to 35% ethanol.
Discussing their findings, the authors noted how the Omicron variant appeared to survive on plastic surfaces for much longer than the Wuhan strain and that this enhanced environmental stability could be an important factor with the increased level of transmissibility of the variant. They added that since the variant is completely inactivated after 15 seconds, this highlighted the importance of continued infection control measures such as hand hygiene.
Hirose R et al. Differences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability BioRxiv 2022
5th January 2022
A third COVID-19 vaccine dose appears in practice to be unlikely to offer much protection against the Omicron compared to Delta variant. This was the finding of a preprint from a large Canadian study by a team led by Public Health Ontario, Toronto, Canada.
The Omicron COVID-19 variant was first reported to the World Health Organisation (WHO) from South Africa on 24 November 2021 and WHO has since designed it as a variant of concern due to an increased transmissible nature and the potential for immune evasion. Moreover, early data suggests that while a third COVID-19 vaccine dose offers higher protection against Omicron, the authors added that ‘even with three vaccine doses, neutralisation against the omicron variant was lower (by a factor of 4) than that against the delta variant.’
In trying to provide some much needed data on the real-world effectiveness of vaccine effectiveness (VE) against the Omicron or Delta variant, the Canadian team examined individuals 18 years and over, with a positive PCR test result between November 2021 and December 2021, excluding long-term residents and those who had received only a single COVID-19 vaccine dose or a second dose less than 7 days prior to testing.
The researchers identified confirmed cases of infection, irrespective of symptoms or severity using provincial reportable data. Any positive samples with an S-gene Target failure (SGTF), were considered to be due to infection with Omicron since this failure is absent in those with the Delta variant. They compared infection rates (compared to those who were unvaccinated and which served as the reference group) for individuals with either two or a third COVID-19 vaccine dose.
The team identified 3,442 Omicron positive, 9,201 Delta positive and 471,545 negative controls. Omicron infected individuals were generally younger, mean age 34.8 years (49.2% male) compared to 43.7 years (same gender proportion) for Delta infections.
After two doses of a COVID-19 vaccine, VE efficacy against Delta was 71% (95% CI 66 – 75%) > 240 days after the second dose but this figure increased to 93% (95% CI 92 – 94%) > 7 days after a third dose. In contrast, two vaccine doses was not protective against Omicron at any point in time and the VE was – 38% (95% CI – 61 to – 18%) after the second dose. However, VE against Omicron was 37% (95% CI 19 – 50%) > 7 days after a third COVID-19 vaccine and these findings were consistent for all combinations of the vaccines used.
The authors discussed how their findings have potentially important implications in so far as proof of vaccination (defined by at least two doses) should no longer be considered as fully vaccinated. They concluded that protection from three vaccine doses offers some protection against the variant but the effectiveness against severe disease remains uncertain.
Buchan SA et al. Effectiveness of COVID-19 vaccines against Omicron or Delta infection MedRxiv 2021.
24th December 2021
According to a preprint study by researchers from the Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa, Omicron infections appear to be associated with reduced risk of hospitalisation and after admission, less severe disease than the Delta variant.
While the Omicron COVID-19 variant was only identified in November 2021, there has been a flurry of research activity directed at trying to understand its transmissibility, the level of disease severity and effect on healthcare services. While initial laboratory studies have indicated that the variant can escape neutralisation by antibodies generated in fully vaccinated and boosted sera samples, these studies cannot foretell the clinical impact of the variant.
The South African researchers undertook a data linkage study of COVID-19 infections, case data and genomic information to establish whether an Omicron infection was associated with higher rates of hospitalisation and more severe disease among those who were hospitalised in comparison to the Delta COVID-19 variant. Although whole genome sequencing was not used, they utilised the presence of a S Gene Target Failure (SGTF), which serves as a proxy for Omicron and samples were examined between 1st October 2021 and 6th December 2021. Positive infections were therefore classified as either an SGTF or non-SGTF. The severity of an Omicron infection was assessed by comparison of SGTF and non-SGTF infections and to infections known to be caused by the Delta variant and regression models created and adjusted for several factors known to be associated with hospitalisation (e.g., age, sex, co-morbidities).
During the period of study there were 161,328 COVID-19 cases recorded and the proportion of SGTFs increased from 3% (early October 2021) to 98% (early December).
A total of 11,495 hospital admissions occurred with 2.5% due to an SGTF compared to 12.8% with a non-SGTF (p < 0.001). Multivariate analysis revealed that individuals with a SGTF had a lower odds of hospitalisation (adjusted odds ratio, aOR = 0.2, 95% CI 0.1 – 0.3, p < 0.001). In addition, once hospitalised, the odds of having severe disease were also reduced in those with SGTF although there was uncertainty over this estimate given the wide confidence intervals (aOR = 0.70, 95% CI 0.30 – 1.40).
Finally, the researchers found that compared to infection with the Delta variant, those with an SGTF had a significantly lower risk of severe disease (aOR = 0.30, 95% CI 0.20 – 0.50, p < 0.001).
The authors suggested that these data suggested that an Omicron infection was probably less severe than other variants such as Delta but recognised that this reduced severity might be accounted for by the higher levels of population immunity due to either natural infection and/or vaccination.
These results are broadly similar to those of a second recently published preprint from Scotland which found a nearly 70% reduced risk of hospitalisation (expected ratio = 0.32, 95% CI 0.19 – 0.52) for those with an Omicron infection. The study also found that giving a third or booster dose was associated with a 57% reduced risk of symptomatic infection.
Although both studies are preliminary, they do suggest the possibility that infection with the new variant is potentially less severe than other forms.
Wolter N et al. Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa. MedRxiv 2021
22nd December 2021
In a laboratory-based study, third booster sera samples from patients have been shown to produce a four to six-fold reduction in neutralisation against the Omicron COVID-19 variant. This was the finding of a preprint study by researchers from the Aaron Diamond AIDS Research Center, New York, US.
The Omicron COVID-19 variant (B.1.1.529) was first identified in southern Africa and appears to have a high level of transmissibility and will likely cause outbreaks across the globe. A concern with this particular variant is that it contains more than 30 mutations,15 of which are present in the receptor-binding domain region which is the target for neutralising antibodies produced in response to vaccination. It is therefore possible that the Omicron might lead to an increased level of infection despite vaccination although current opinion is that this could be mitigated by a third booster sera sample.
In the absence of clinical data, the US team sought to better understand the extent to which the Omicron variant is able to evade antibody neutralisation, by testing the activity of serum collected from a number of different patient samples. Initially the team created an Omicron pseudovirus and tested this against 10 sera samples collected from the Spring of 2020, which were likely to have been infected with the wild-type (original) COVID-19 virus. While there was a robust response to the wild-type, there was a greater than 32-fold reduction against Omicron and only two samples produced antibody titres above the limit of detection.
The team then turned their attention to both fully vaccinated and third booster sera (TBS) samples. For the two mRNA-based vaccines, BNT162b2 and mRNA-1273, there was a >21-fold decrease in ID50 and > 8.6-fold decrease in boosted sera samples. For the other vaccines, Ad26.COV2.S and ChAdOx1, all samples produced antibody titres below the limit of detection apart from two samples for which the individual had a history of a prior infection.
Using 15 third booster sera samples obtained from BNT162b2 (13) and mRNA-1273, the researchers discovered that although each of these third booster sera produced antibody titres above the limit, there was a mean 6.5-fold drop compared to the wild-type.
Using authenticated Omicron isolates and samples from BNT162b2 and mRNA-1273, there was a greater than 6-fold drop in titres for fully vaccinated and a greater than 4.1-fold drop for boosted samples.
Finally, testing sera with monoclonal antibodies, the researchers found that all four combinations of monoclonal antibodies in clinical use lost substantial activity against Omicron.
Although this was a laboratory-based study and might not be replicated in clinical practice, the authors believed that COVID-19 is potentially only a mutation or two away from being resistant to current antibodies and that it was important to devise strategies that anticipate the evolutional direction of the virus and that future work should focus on the development of agents targeting conserved parts of the virus.
16th December 2021
Discovery Health, a private health insurance administrator from South Africa, has released real-world data on the Omicron outbreak in South Africa, indicating that among those with at least two doses of BNT162b2, there was a 70% reduced risk of severe complications of COVID-19 that required hospitalisation.
Although a press release rather than a full, peer-reviewed study, the available data offers some insight of the first three weeks of the Omicron-driven wave in South Africa, and, as the release emphasises, the results should be considered preliminary and could change as the wave develops further.
The analysis provided in the press release includes more than 211,000 COVID-19 test results, 41% from adults who had already received two doses of BNT162b2. Among these 211,000 test results, approximately 78,000 were attributed to the Omicron variant and in those who were fully vaccinated with BNT162b2, the vaccine offered only 33% protection against infection (compared to unvaccinated individuals). However, the Discovery Health data showed that fully vaccinated individuals had a 70% protection against hospital admission during the initial wave of the Omicron variant and this protection was consistent across a range of chronic illnesses including hypertension, hypercholesterolaemia and other cardiovascular diseases. In addition, protection was maintained across all ages but was slightly lower among older patients. For example, in patients aged between 60 to 69, protection reduced to 67% and 60% for those aged 70 to 79 years.
A more worrying concern from the Discovery Health analysis was how overall, the Omicron variant appeared to be much more transmissible, with a 40% higher risk of re-infection. In those who had been infected during the second South African wave (with the beta variant), the risk was 60% higher and higher still at 73%, in those infected during the initial COVID-19 wave in the country.
With respect to children, the press release states that children under 18 years of age had a 20% higher risk of admission to hospital for COVID-19-related complications if infected with Omicron although overall, children were 51% less likely to test positive for the virus during the Omicron period.
On a more positive note, the Discovery Health analysis does indicate that COVID-19 infection caused by the Omicron variant is generally mild disease adding that ‘this lesser severity could, however, be confounded by the high seroprevalence levels of SARS CoV-2 antibodies in the general South African population, especially following an extensive Delta wave of infections.’
The current press release is both encouraging and worrying and until further data becomes available, the impact of the Omicron variant remains to be seen.
13th December 2021
In a press release, Pfizer and BioNTech have announced that serum antibodies induced after three doses of their COVID-19 vaccine (BNT162b2) are able to neutralise the Omicron variant.
The company’s laboratory study involved testing human sera obtained from the blood of individuals who had received two or three 30-µg doses of the BNT162B2 using a pseudovirus neutralisation test, which used to study the effect of antibodies to neutralise the capability of viruses to enter cells and thus prevent infection. The sera were collected from subjects 3 weeks after receiving the second dose or one month after receiving the third dose of their vaccine
In the study, each sample of serum was simultaneously tested for its neutralising antibody titre against the original (or wild-type) COVID-19 spike protein as well as the Omicron spike variant. The researchers found that after a third vaccine dose, there was a significant, 25-fold increased level of neutralising antibody titres against the Omicron strain spike protein. In fact, antibody titre levels against the Omicron variant were comparable to the neutralisation against the wild-type strain observed in sera from individuals who received two doses of the companies’ COVID-19 vaccine. However, data on the persistence of these neutralising antibodies over time is uncertain and will be determined over time.
At the present time, there is still much to learn about the Omicron variant although a preliminary study from South Africa in 12 people has provided some answers. The study included 12 individuals with a mean age of 57 years (66% male), 6 of whom had been vaccinated with the remaining 6 having been both vaccinated and previously infected. The purpose of the study was to examine whether the Omicron variant still required the ACE2 receptor to gain entry to cells and if plasma from those vaccinated with BNT162b2 were able to neutralise the variant. The results showed that the ACE2 receptor was still required to gain entry to cells but also that there was a 41-fold reduction in antibody neutralisation against Omicron compared with the original wild-type. However, on the plus side, escape was much less in those who had been previously infected the COVID-19.
There is still much to learn about the Omicron variant, in particular its transmissibility and whether it results in more severe infections and hospitalisations.
However, one point reassuring point mentioned in Pfizer-BioNTech press release was how 80% of the regions of the spike protein that are recognised by cytotoxic (killer) T (CD8 +) cells are unchanged in the variant. It is possible therefore, that three doses, i.e., full vaccination and a booster, will hopefully provide an enhanced immune response and which may be sufficient to prevent the variant from causing more severe disease.
3rd December 2021
The Omicron variant (OV) of COVID-19 is potentially associated with a nearly three-fold increased risk of re-infection according to a study by South African researchers from the South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, South Africa.
Although the latest variant was only recently identified in South African where infection rates began to climb, genomic sequencing of the variant indicates that it has between 26 and 32 mutations in the spike protein, many of which are present in the receptor binding domain. However, of more concern is how many of the mutations present are associated with escape from neutralising antibodies and, as a consequence, the currently available vaccines might not be as effective.
B.1.1.529 has been deemed a variant of concern by the World Health Organization although at the present time, a good deal of information about its transmissibility, the level of disease severity and effectiveness of current vaccines remains unknown. With the appearance of an increasing number of COVID-19 variants, one key question is whether these can lead to re-infection either after natural or acquired immunity from vaccination.
For the present study, the South African team set out to determine whether the risk of re-infection had changed over time by examining rates of re-infection and whether the OV might had impacted on these rates. They used epidemiological data from the National Institute for Communicable Diseases and the line list of repeated COVID-19 tests and all positive tests are recorded in the combined data sets. Although these data are recorded as de-identified cases, the presence of repeat cases were used to calculate the time between consecutive positive tests for these individuals. Using the dates of reported infection, the researchers were able to calculate the time between successive infections for each person and the period of analysis was from the start of the pandemic in March 2020 and to the end of November 2021.
A total of 35,670 individuals with at least two suspected infections were identified, although 332 had three infections and one individual at least four. Re-infections showed a bimodal distribution, peaking near 180 and 360 days, representing the first and second waves of the pandemic.
However, for the more recent second infections (after October 2021), there were a higher number of re-infections among individuals whose primary infection had occurred during the third wave. In addition, since mid-November, re-infections were occurring in those whose primary infection had been during the first and second waves. Among those who had more than one infection, 47 experienced the third infection in November 2021 and which the authors suggested could be associated with the omicron variant.
Using regression modelling, the team determined the relative hazard ratio for re-infection to be 0.75 (95% CI 0.59 – 0.97) for wave 2 versus wave 1 and for wave 3 versus wave 1 it was 0.71. However, the hazard ratio for the period from 1 November 2021 to 27 November versus wave 1 was 2.39 (95% CI 1.88 – 3.11), i.e., the risk of re-infection was almost three times higher during November 2021.
Commenting on these findings, the authors suggested that risk of re-infection compared to a primary infection had reduced over the three waves and which was to be expected as the population gained greater immunity, even in the presence of the beta and delta variants. However, the increased rate of re-infection during November 2021 suggested that the rise was driven by the OV, although they couldn’t be certain because not all of the samples had been sequenced.
They concluded that there was evidence of a substantial increase in the risk of re-infection that has coincided with the emergence of the OV in South Africa which seemed to have a greater ability to re-infect previously infected individuals.