Virus World

Continued evolution of SARS-CoV-2 has led to the emergence of several new Omicron subvariants, including BQ.1, BQ. 1.1, BA.4.6, BF.7 and BA.2.75.2. Here we examine the neutralization resistance of these subvariants, as well as their ancestral BA.4/5, BA.2.75 and D614G variants, against sera from 3-dose vaccinated health care workers, hospitalized BA.1-wave patients, and BA.5-wave patients. We found enhanced neutralization resistance in all new subvariants, especially the BQ.1 and BQ.1.1 subvariants driven by a key N460K mutation, and to a lesser extent, R346T and K444T mutations, as well as the BA.2.75.2 subvariant driven largely by its F486S mutation.

The BQ.1 and BQ.1.1 subvariants also exhibited enhanced fusogenicity and S processing dictated by the N460K mutation. Interestingly, the BA.2.75.2 subvariant saw an enhancement by the F486S mutation and a reduction by the D1199N mutation to its fusogenicity and S processing, resulting in minimal overall change. Molecular modelling revealed the mechanisms of receptor-binding and non-receptor binding monoclonal antibody-mediated immune evasion by R346T, K444T, F486S and D1199N mutations. Altogether, these findings shed light on the concerning evolution of newly emerging SARS-CoV-2 Omicron subvariants.

Preprint available in bioRxiv (October 20, 2022):

https://doi.org/10.1101/2022.10.19.512891 

NEW YORK: Pfizer and BioNTech's COVID-19 vaccine appeared to only lose a small bit of effectiveness against an engineered virus with three key mutations from the new variant found in South Africa, according to a laboratory study conducted by the US drugmaker. The study by Pfizer and scientists from the University of Texas Medical Branch (UTMB), which has not yet been peer-reviewed, showed a less than two-fold reduction in antibody titer levels, indicating the vaccine would likely still be effective in neutralising a virus with the so-called E484K and N501Y mutations found in the South African variant. The study was conducted on blood taken from people who had been given the vaccine. Its findings are limited, because it does not look at the full set of mutations found in the new South African variant. The scientists are currently engineering a virus with the full set of mutations and expect to have results from that in about two weeks, according to Pei-Yong Shi, an author of the study and a professor at UTMB.

The results are more encouraging than another non-peer reviewed study from scientists at Columbia University earlier on Wednesday which used a slightly different method and showed antibodies generated by the shots were significantly less effective against the South Africa variant. One possible reason for the difference could be that the Pfizer findings are based on an engineered coronavirus, and the Columbia study used a pseudovirus based on the vesicular stomatitis virus, a different type of virus, UTMB's Shi said.  He said he believes that finding in pseudoviruses should be validated using the real virus. The study also showed even better results against several key mutations from the highly transmissible UK variant of the virus. Shi said they were also working on an engineered virus with the full set of mutations from that variant as well.

Research cited available in bioRxiv (Jan. 27, 2021):

https://doi.org/10.1101/2021.01.27.427998

Now, a new study published in the preprint server bioRxiv in August 2020 shows that under conditions resembling those in vivo, IFNs may promote efficient viral invasion instead. The virus behind the current COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is known to spread more efficiently than the earlier pathogenic coronaviruses, SARS-CoV, and MERS-CoV. However, the case fatality rate so far has been much lower, at 2% to 5%, compared to 10% in SARS and ~ 40% in MERS. Scientists think the virus is inhibited by interferons (IFNs), even more than the earlier viruses. In fact, IFNs are currently being used to reduce the severity of COVID-19. Now, a new study published in the preprint server bioRxiv* in August 2020 shows that under conditions resembling those in vivo, IFNs may promote efficient viral invasion instead.

What are IFITMs?

Interferon-induced transmembrane proteins (IFITMs 1, 2, and 3) are proteins that are considered to be inhibitory of a variety of viruses, including the SARS-CoVs. Most of the evidence for this has come from studies that used cells that overexpress these proteins and are infected by pseudoviruses. The investigators looked at innate immune effectors directed against SARS-CoV-2 entry into the target cells. Viral entry involves spike-mediated recognition of the host receptor, angiotensin-converting enzyme (ACE) 2, triggering an irreversible conformational change of the spike protein to its fusion form by proteolytic cleavage into S1 and S2 subunits. The cleaved protein fuses to the plasma membrane and gains entry to the cell. IFITMs are a family of IFN stimulated genes (ISGs) is known to prevent this fusion, in the case of influenza A viruses, rhabdoviruses, and HIV.

IFITM Overexpression Inhibits Pseudovirus S Binding

Previous work has shown that when these proteins are expressed at excessively high levels, pseudoparticles expressing the spike protein of SARS and MERS are unable to enter the host cell. The mechanism of inhibition might reduce the rigidity and curvature of the plasma membrane such that fusion cannot happen. While IFITM1 is only the plasma membrane, IFITM2 and 3 are localized on lysosomal membranes within the cell. Many scientists think that such viruses cannot replicate in cells where these proteins are expressed. However, some studies have shown that IFITMs can actually increase the intensity of infection with some human coronaviruses. At the same time, mutant IFITMs could enhance infection with many viruses from this family, including SARS. The current study shows that the overexpression of IFITMs specifically reduces the entry of SARS-CoV-2 spike-mediated pseudoparticles, by two orders of magnitude for IFITM2 and IFITM3 in particular, and less potently by IFITM1. Infectivity of these pseudoviruses was not reduced, however, and in fact, it was slightly increased in one case, since it may increase the rate at which the spike protein is built into the pseudovirus. The initial tests showed that both SARS-CoV and SARS-CoV-2 spike proteins expressed in pseudoviruses are inhibited efficiently by IFITMs, the first even more than the second. The mechanism of such inhibition appears to be via ubiquitination and palmitoylation. In all cases, they found that IFITMs reduce cell-to-cell fusion mediated by the spike-ACE2 binding. The depletion of these proteins led to a 3- to 7-fold increase in spike-mediated infection by all pseudoviral particles. Further testing in a cell line lacking IFITM expression showed that the number of S-ACE2 binding foci leaped upward by four- to ten-fold. These findings strongly imply that IFITM proteins are efficient inhibitors of SARS-CoV-2 S-mediated viral entry....

Study available as preprint at bioRxiv (August 18, 2020):

https://doi.org/10.1101/2020.08.18.255935

A study of people in Sierra Leone suggests that the virus can lie in hiding from the immune system before re-emerging later and sparking a new response—although researchers didn't examine whether this could make people infectious again. A substantial proportion of people who survive Ebola may produce a spike in antibody levels more than six months after they’ve recovered from the disease, according to a study published today (January 27) in Nature.   Analyzing multiple plasma samples from 51 survivors of the West African outbreak of 2013–2016, researchers found that the levels of virus-neutralizing antibodies declined, as expected, in the days and weeks following recovery. But these levels shot up again in some survivors around the 200- to 300-day mark before declining again—evidence that Ebola virus may be lingering inside their bodies and re-emerging to trigger immune defenses, the researchers conclude in their paper.  “The idea that there can be a source of virus that could restimulate the immune system isn’t surprising” in itself, says Carl Davis, an immunologist at Emory University who was not involved in the work. “But the fact that they were seeing this so frequently and to such a big magnitude is really pretty shocking Since the West African epidemic, which claimed the lives of more than 11,000 people, there have been multiple reports of viral persistence in survivors. One 2016 study, for example, reported that 24 of 429 men in Liberia who had been infected with Ebola tested positive for viral RNA in their semen more than 12 months after they’d recovered from the disease, with one testing positive more than a year and a half after completing treatment. Viral RNA isn’t necessarily evidence of infectious virus, but based on genomic and epidemiological data, researchers suspect that Ebola can be transmitted sexually by men several months after infection. 

Taking a different approach, University of Liverpool virologists Georgios Pollakis, Bill Paxton, and colleagues focused in the current study on measuring survivors’ immune responses to Ebola virus. Specifically, they analyzed the levels of virus-neutralizing antibodies in 115 healthy people in Sierra Leone who had recovered from prior infections and had volunteered to provide convalescent plasma to be used as an experimental therapy for other patients.   Using a combination of immunological assays, including treating some of the plasma samples with synthetic viral particles bearing specific Ebola virus proteins, the researchers monitored antibody levels between 30 and 500 days after participants were discharged from Ebola treatment units. Among the 51 participants who provided more than one sample, the researchers found that, on the whole, antibody levels seemed to decline following a person’s recovery, as expected. However, in more than half of those participants, the team detected an increase in antibody levels between about six months and a year post-recovery.  Such an antibody spike is unlikely to be the result of people receiving Ebola vaccinations during the study, Pollakis says. Plasma donors reported to clinicians that they hadn’t received vaccines. If they had been immunized, the researchers would have expected to see increased levels of antibodies only against the proteins used in the vaccine; instead, their assays revealed increased levels of antibodies against various viral proteins. Nor is the observation likely to be due to survivors being reinfected by other people, Pollakis adds. The samples were negative for viral RNA, and some of the observed antibody increases occurred after Sierra Leone had stopped reporting new Ebola cases, he explains.

Instead, the researchers hypothesize that the spike is the result of the immune system re-encountering viral antigens already within the body. This could happen if Ebola virus hides in so-called immune-privileged sites such as the eye, the reproductive tract, or the central nervous system—those regions typically better shielded from the immune system than other areas of the body—and then reappears once antibody levels have fallen below a certain threshold.  The findings suggest “that actually, a much larger proportion of individuals than were previously thought carry some form of viral antigens, if not the whole virus,” Pollakis says, “and that as the antibodies decline and reach a nadir around two hundred, two hundred and fifty days, the antigen gets the chance to come back in some form and stimulate the immune system again.” Nathalie MacDermott, an academic clinical lecturer at King’s College London who participated in the medical response to Ebola in West Africa and was not involved in the study, says that the findings seem to confirm something that has long been suggested by other investigations of Ebola survivors, although “the sample size is relatively small.” She adds that it will be important to understand what makes some people more susceptible to a recurrence of the virus than others, and to gather more detailed data on how long recurrent virus may stick around in survivors once it’s reappeared. Davis, who coauthored a 2019 study of B cell responses to Ebola in four survivors treated in the US, notes that it would be interesting to see if the same antibody patterns are present in a more diverse patient population. People selected as potential plasma donors might not be representative of all Ebola survivors—for instance, the authors speculate in their paper that donors are less likely to have viral recurrence, because they have to be healthy to take part in the study and therefore should be better at suppressing Ebola virus than the general population of survivors. But Davis notes that this relationship hasn't been demonstrated. He adds that further work could investigate immune-cell responses in addition to the antibody levels measurable in plasma samples......

Findings published in Nature  (Jan.27,  2021):

https://doi.org/10.1038/s41586-020-03146-y

Commentary in Nature (Jan. 27, 2021):

https://doi.org/10.1038/d41586-020-03044-3

All COVID-19 vaccine developers can use the network of five laboratories working together as part of centralised network to reliably assess and compare immunological responses generated by COVID-19 vaccine candidates.   Five laboratories initially selected to work together as part of centralised network to reliably assess and compare immunological responses generated by COVID-19 vaccine candidate. Global group will minimise variation between individual lab analyses to enable uniform way of evaluating and identifying the most successful candidates. All COVID-19 vaccine developers (both CEPI-funded and non-CEPI funded) can use the network. In order to monitor interest and adjust the testing capacity, we are requesting that all COVID-19 vaccine developers interested in using CEPI’s centralised laboratory network complete this short survey. For any COVID-19 vaccine developer ready to submit their samples to the network, please complete our Sample Analysis Request Form. 

2 October 2020, Oslo, Norway –The Coalition for Epidemic Preparedness Innovations (CEPI) has today announced partnerships with five clinical sample testing laboratories to create a centralised global network to reliably assess and compare the immunological responses generated by COVID-19 vaccine candidates. Located across multiple regions globally, the laboratories initially selected for this vaccine-assessment network are: Nexelis (Canada) and Public Health England (PHE, UK), VisMederi Srl (Italy), Viroclinics-DDL (The Netherlands), icddr,b (formerly International Centre for Diarrhoeal Disease Research, Bangladesh), and Translational Health Sciences and Technological Institute (THSTI, India). The network will use the same testing reagents—originating in the labs of Nexelis and PHE—and follow common protocols to measure the immunogenicity of multiple COVID-19 vaccine candidates (both CEPI-funded and non-CEPI funded developers). This approach will ensure uniformity in assessment and informed identification of the most promising vaccine candidates. CEPI is actively negotiating with additional laboratories to participate in this network.

Advantages of centralising immunological response assessment

Typically, the immunogenicity of potential candidate vaccines is assessed through individual laboratory analyses, aiming to determine whether biomarkers of immune response—such as antibodies and T-cell responses—are produced after clinical trial volunteers receive a dose(s) of a vaccine candidate. However, withover 320 vaccine candidates against COVID-19 currently in development, there are likely to be numerous differences in data collection and evaluation methods. This includes potential variation in the range of correlates of immunity being measured by laboratories. Technical differences in how and where samples are collected, transported and stored can also occur, impacting the quality and usefulness of the data produced and making comparisons between measurements in individual laboratories difficult. In addition, with the wide range of COVID-19 vaccine approaches and technologies currently being deployed (e.g., recombinant viral vectors, live attenuated vaccines, recombinant proteins and nucleic acids), standard evaluation of the true potential of these vaccine formulations becomes very complex.

Through centralising the analysis of samples obtained from trials of COVID-19 vaccine candidates, the new clinical-sample-testing network will minimise variation in results obtained, which could otherwise arise due to such technical differences when carrying out independent analysis. The samples from participating vaccine developers will instead be tested in the same group of laboratories using the same methods, therefore, removing much of the inter-laboratory variability and allowing for head-to-head comparisons of immune responses induced by multiple vaccine candidates.

Supporting global COVID-19 vaccine development

Through this new network, up to the limit of programme funding, eligible COVID-19 vaccine developers (both CEPI-funded and non-CEPI funded developers) can use the laboratories, without per sample charges, to analyse the immune response elicited by their COVID-19 vaccine candidates in preclinical, Phase I and Phase IIa studies. Data obtained on the immunogenicity of CEPI-funded vaccine candidates will be used to inform and advance CEPI’s COVID-19 vaccine portfolio by providing quick and accurate evaluation of its candidate vaccines. By opening the sample testing network to other COVID-19 vaccine programmes, CEPI also aims to ensure that all eligible developers—regardless of their size—can benefit from this analysis. Certain commitments may be required for eligibility, such as making timely publication of sample testing results and sharing data that will be produced on the immunogenicity of COVID-19 vaccine candidates to facilitate future regulatory decisions. The number of samples available for testing per developer may be limited depending on response...