Virus World

Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.

Published (April 18, 2024):

https://doi.org/10.1016/j.chembiol.2024.03.008

Immunocompromised people get a new drug to protect against Covid-19 for the first time since the Omicron variants forced another drug off the market. The Food and Drug Administration on Friday authorized a new antibody to protect immunocompromised individuals against Covid-19. The drug, known as Pemgarda and marketed by the biotech Invivyd, is the first such drug to become available since the agency pulled AstraZeneca’s Evusheld off the market in January 2023. New Omicron variants had rendered Evusheld ineffective. Some immunocompromised patients — a group that includes certain cancer patients, patients with some autoimmune or genetic disorders, and organ transplant recipients — have been eagerly awaiting the new prophylactic. Because their condition or drugs they take for it weaken their immune systems, they don’t always get adequate protection from vaccination. Antibody treatments can add additional protection.  There remains a need for additional Covid protections. Last week, over 10,000 patients with Covid-19 were admitted to U.S. hospitals. 

Still, it’s not clear how many patients will avail themselves of the new treatment. Invivyd, the drug’s developer, estimated there are 9 million immunocompromised people in the U.S., but its initial focus will be on the 485,000 with the most acute need: Stem cell transplant recipients, organ transplant recipients, and blood cancer patients. Evusheld itself had gone vastly underused when it was available, prompting the federal government to launch efforts to educate the public about its existence. And the need is probably less acute now for some: Although immunocompromised patients have a reduced response to vaccination, many may still gain some protection from multiple rounds of vaccination and exposure to the virus. Uptake for other measures to mitigate Covid risk, such as boosters and Paxlovid upon infection, has also declined precipitously, despite public health efforts. 

“We will explore having it available at our institution, so that our very compromised patients and the services and specialities that take care of those patients know that it’s an option,” said Priya Nori, an infectious disease specialist at Albert Einstein College of Medicine. “But we’re not expecting gangbusters in terms of interest.” Invivyd has not yet disclosed a price.  The company was originally founded in 2020 by antibody expert Tillman Gerngross, under the name Adagio, and raised $309 million in an IPO a year later. But the company’s original antibody — which had been designed to be all but variant-proof — was soon rendered ineffective by the advent of Omicron, eventually leading to Gerngross’s resignation and a series of high-level changes at the company. Pemgarda is a re-engineered version of the original antibody, designed to cover Omicron variants. That gave Invivyd a faster path to getting a new preventative on the market than competitors who started from scratch.

FDA EUA letter (March 22, 2024):

https://www.fda.gov/media/177068/download 

Invivyd Press release: 

https://investors.invivyd.com/news-releases/news-release-details/invivyd-announces-fda-authorization-emergency-use-pemgardatm 

SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1−/− transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1−/− transgenic mice, and a longer-term in HLA-B*0702 Ifnar1−/− transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1−/− transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines. The origin of SARS-CoV-2 cross-reactive T cells in unexposed humans is unclear. Here, the authors use HLA transgenic mouse models of sequential infections with human coronavirus OC43 and SARSCoV-2 and show that OC43 elicits cross-protective immunity against SARS-CoV-2, which partially depends on CD4 + T cells.

Published in Nature Communications (Jan. 26, 2024):

https://doi.org/10.1038/s41467-024-45043-2 

Scientists identified a new class of antibodies in human blood that are able to target multiple strains of influenza A virus in the lab. A newly discovered class of antibodies in human blood can neutralize different types of the flu virus and could be key to the development of broadly protective vaccines against the seasonal viruses, scientists say.  Circulating flu viruses constantly mutate, so "we need annual influenza virus vaccines to keep pace with continuing viral evolution," the researchers behind the discovery said in a statement. "Our work suggests that the barriers to eliciting more broadly protective immunity may be surprisingly low," they said.  There are four types of flu virus, known as influenza A, B, C and D, with A and B being responsible for the seasonal flu epidemics in the U.S. every year. Influenza A comes in many subtypes whose differences lie in two proteins that the virus uses to infect our cells: hemagglutinin (H) and neuraminidase (N). For example, H1N1 and H3N2 are subtypes of influenza A that routinely infect people. Within each subtype are different "strains" that constantly tweak their genetic code. For example, a strain of H1N1 is currently the dominant virus causing flu in the U.S. Influenza B, meanwhile, is divided into two lineages — Yamagata and Victoria — and is typically responsible for a much smaller proportion of flu cases.

Making effective flu shots relies on harnessing the protective power of antibodies — immune proteins that attack invading pathogens — but the virus' ability to quickly mutate makes this challenging. Flu vaccines prime the immune system to produce specific antibodies that latch onto a flu virus and prevent it from infecting cells after it invades the body. However, these vaccines are formulated to target specific strains, and because those strains mutate year over year, people then need a new flu shot each year to keep up. In the new study, published Thursday (Dec. 21) in the journal PLOS Biology, scientists described a newfound class of antibodies in human blood samples that target multiple forms of the influenza A virus.  The research was conducted only in the lab, so the scientists aren't sure exactly how these antibodies contribute to the body's flu shot response. However, one day, these antibodies could be used to develop vaccines that are more effective at protecting people from multiple strains of flu at the same time.  To guard against influenza A, conventional flu vaccines usually prompt the immune system to produce antibodies against the H protein on the surface of the virus. Antibodies have previously been discovered that target two main types of hemagglutinin, called H1 and H3, at the same time. However, they can only do this if there is a specific mutation in H1, namely the insertion of an amino acid in the outer edge of the protein that binds to a receptor on the outside of our cells. This consequently limits the antibodies' efficacy against different flavors of flu virus. 

Through lab experiments, the study authors identified antibodies that are abundant in human blood and can bind to certain H1 and H3 strains of influenza A, whether or not this hemagglutinin mutation is present. This means that they'd theoretically be able to provide broad protection against both subtypes of virus, potentially even as circulating strains mutate over time.  The authors also looked at how well these antibodies targeted strains of H1 and H3 that have circulated in the past. The antibodies reacted with H3 strains from the late 1980s to late 1990s and H1 strains from the early 2000s through to 2015.  This suggests the patients whose blood was sampled originally made the antibodies in response to H3 strains of the virus. Then, after a later exposure to H1 strains at a later date through either infection or vaccination, the antibodies became primed to target H1 as well. These findings may have important applications for future vaccine design.  "Given the right series of influenza virus exposures/vaccinations, it is possible for humans to mount robust antibody responses that neutralize divergent H1N1 and H3N2 viruses, opening new avenues to design improved vaccines," the authors said in the statement.  In other words, there may be a way to ensure vaccines trigger the production of these broad-acting antibodies, to ensure the shots guard against both subtypes of the virus equally well.

Michael Dahl walked into a UCSF clinic in San Francisco the other day, as he has done many times since the brain-sapping symptoms of long COVID changed his life nearly two years ago.

But this time, he and his doctors hoped it would be Dahl who will change long COVID. On Aug. 22, Dahl became the first person to receive an infusion of monoclonal antibodies aimed at treating the confounding condition that has impaired millions of people around the world. The clinical trial is one of only a small number testing a treatment or cure for the post-COVID condition, which is bafflingly complex, often robbing people of the ability to think clearly, wake up refreshed from sleep, exercise, or even breathe deeply. Yet, the repair that Dahl is testing is surprisingly simple. It rests on evidence that pieces of the coronavirus that causes COVID can linger in the body for years after infection. UCSF scientists want to see if annihilating those bits can improve or even erase the debilitating symptoms. “This is just hypothetical, but that is why we’re doing the study,” said Dr. Michael Peluso, principal investigator of the trial dubbed outSMART-LC. “We’re going to take the virus out of commission — we think — and see if people feel better.”

Published August 14, 2023 in CMAJ

Highlights

Summary

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been responsible for a global pandemic. Monoclonal antibodies (mAbs) have been used as antiviral therapeutics; however, these therapeutics have been limited in efficacy by viral sequence variability in emerging variants of concern (VOCs) and in deployment by the need for high doses. In this study, we leveraged the multi-specific, multi-affinity antibody (Multabody, MB) platform, derived from the human apoferritin protomer, to enable the multimerization of antibody fragments. MBs were shown to be highly potent, neutralizing SARS-CoV-2 at lower concentrations than their corresponding mAb counterparts.

In mice infected with SARS-CoV-2, a tri-specific MB targeting three regions within the SARS-CoV-2 receptor binding domain was protective at a 30-fold lower dose than a cocktail of the corresponding mAbs. Furthermore, we showed in vitro that mono-specific MBs potently neutralize SARS-CoV-2 VOCs by leveraging augmented avidity, even when corresponding mAbs lose their ability to neutralize potently, and that tri-specific MBs expanded the neutralization breadth beyond SARS-CoV-2 to other sarbecoviruses. Our work demonstrates how avidity and multi-specificity combined can be leveraged to confer protection and resilience against viral diversity that exceeds that of traditional monoclonal antibody therapies.

Published in ScienceTranslational Medicine (May 24, 2023):

https://doi.org/10.1126/scitranslmed.adf4549 

Covid-19 antibody drug developers have had a rough time. One by one, antibody medicines that reached the market under emergency use saw their authorized indications narrowed and then revoked by the FDA due to ineffectiveness against newer strains of the virus. By the end of last year, no Covid-19 antibody drugs remained authorized for use in the U.S. InflaRx is showing that Covid-19 antibody drug research is still alive. The FDA this week authorized the biotech’s antibody, vilobelimab, as a treatment for Covid-19 in hospitalized adults. The drug is meant for severe cases. The authorization specifies treatment must start within 48 hours of the patient receiving mechanical ventilation or artificial life support. Jena, Germany-based InflaRx will market its new product under the name “Gohibic.” The antibody drugs whose authorizations were revoked all targeted some part of SARS-CoV-2 in order to prevent it from infecting cells. InflaRx’s target isn’t on the virus. The biotech’s antibody addresses a part of the immune response believed to play a role in the inflammation that leads to Covid-19 progression. The drug targets C5a, a protein of the complement system, which is a part of the immune system.

Authorization of InflaRx’s drug provides an alternative to Olumiant, an Eli Lilly drug. Like Gohibic, Olumiant is also authorized for treating hospitalized patients within 48 hours of starting mechanical ventilation or artificial life support. This Lilly drug works by blocking JAK proteins associated with inflammation. But Olumiant is a small molecule made into a pill—a challenging formulation for patients receiving breathing assistance. Olumiant can be dissolved in water and swallowed or administered via a gastrointestinal tube. But InflaRx’s Gohibic provides yet another dosing option, as that drug is administered as an intravenous infusion. InflaRx initially developed its antibody as a treatment for hidradenitis suppurativa, a rare inflammatory skin disorder. In 2019, the antibody drug failed a Phase 2b test in that indication. With the onset of the pandemic the following year, InflaRx began a clinical trial testing the antibody in Covid-19 patients. The Gohibic EUA request was based on data from a placebo-controlled Phase 3 study that enrolled 369 mechanically ventilated patients in intensive care units. According to study results, after 28 days, the treatment group showed a 23.9% reduction in death from all causes compared to the placebo arm. The most common adverse reactions reported in the study included pneumonia, sepsis, delirium, and pulmonary embolism. The FDA also said serious infections have been reported in Covid-19 patients who received Gohibic. Now that InflaRx has emergency authorization for Gohibic, the company said it is communicating with the FDA about the next steps for a biologics license application seeking full regulatory approval. The company is having similar discussions with regulators in Europe.

FDA Press Release (April 4, 2023):

https://www.fda.gov/drugs/drug-safety-and-availability/fda-authorizes-gohibic-vilobelimab-injection-treatment-covid-19 

More than half had antibodies showing they had been infected at some point during the pandemic, equivalent to 16.4 million Canadian adults. A large-scale survey of Canadian adults selected at random across all 10 provinces found that virtually the entire population had antibodies against the virus that causes COVID-19 by summer 2022. Some 98.1 per cent had detectable antibodies against SARS-CoV-2, the virus that causes COVID, either through vaccination, a past infection, or both, according to the survey from Statistics Canada and partners. Over half, 53.9 per cent, had antibodies indicating they had been infected at some point during the pandemic — which translates to 16.4 million adults having caught COVID, whether they realized it or not. And that number might actually be higher because antibodies usually wane over time and can become undetectable through blood testing. StatCan, the Public Health Agency of Canada and Canada’s COVID-19 Immunity Task Force partnered on the surveys, in which participants complete an online questionnaire and send a blood sample that is analyzed for antibodies against SARS-CoV-2. The survey conducted between April and August 2022 yielded information showing that antibodies against SARS-CoV-2 have become widespread across the country. Other revealing data include:

• While nearly half (47.9 per cent) of those who had a past infection had tested positive at some point, more than two-in-five Canadians (41.7 per cent) who had caught COVID were unaware they had ever been infected.

• Over one-in-10 (10.3 per cent) who suspected they had been infected had antibodies but had never tested positive, either through a rapid antigen or polymerase chain reaction (PCR) test.

It’s more than 20 times the rate of infection indicated by a similar survey conducted between late 2020 and April 2021. At that point, just 2.6 per cent of Canadian adults had a past infection.

• Over a third (36.9 per cent) of those who never tested positive nor suspected they had been infected showed the presence of infection-acquired antibodies.

• Nearly nine-in-10 (88.3 per cent) who had had a past infection still had antibodies in summer 2022. And 56.4 per cent who had never tested positive but thought they might have caught COVID had detectable antibodies from a past infection.

• By early 2022, rapid tests were more common than PCR tests: 59.8 per cent of those who had a past infection used the self-administered rapid test, while 40.2 per cent were given a PCR test.

• Younger Canadians were more likely than older adults to have antibodies against COVID, likely due to taking fewer precautions against contracting the virus than seniors and those with underlying conditions. 

• Antibodies against a SARS-CoV-2 infection were highest from 14 to 90 days after an infection (89.9 per cent) and this percentage gradually decreased over time. However, more than two-thirds (67.7 per cent) still had detectable antibodies more than 180 days later.

• Though rates were still fairly high (roughly 50 per cent), fewer people with a disability or chronic condition had antibodies indicating an infection than those who didn’t report any conditions (57.7 per cent).

• Seroprevalence of antibodies from infection differed somewhat from province to province. B.C. was in the middle of the pack (51.5 per cent), while Alberta and Saskatchewan (both 57.4 per cent) had the highest infection rates, and Nova Scotia the lowest (46.5 per cent).

• Racialized, non-Indigenous Canadians (60.1 per cent) had higher rates of infection than non-racialized Canadians (51.8 per cent). Infection rates varied widely among different population groups: 53.2 per cent who identified as Chinese had a past infection, while those who are Black (80.7 per cent), Arab (78.1 per cent), Filipino (69.8 per cent) or Latin American (64.6 per cent) had significantly higher rates. (Data on Indigenous Canadians wasn’t collected among those who live on a reserve or First Nation settlement for this survey.)

• Rates of past infection were virtually identical among men and women, 54.3 per cent and 53.4 per cent, respectively.

• Despite the fact they’re generally at higher risk of severe outcomes, over half of Canadians 65-and-older who had antibodies from past infection were unaware they had been exposed to the SARS-CoV-2 virus.

The data on SARS-CoV-2 antibodies is from dried blood spot (DBS) samples collected from a self-administered finger prick. The survey was conduacted from April to August 2022 and was sent out to 105,998 Canadian adults. (About half responded to the questionnaire and roughly 30 per cent sent blood samples for analysis.)

More about how the data was collected and analyzed can be found at the StatCan detailed information page.

jruttle@postmedia.com

The Food and Drug Administration has approved Tocilizumab for use against moderate to severe Covid-19 symptoms. The FDA has approved an early gift for those suffering from Covid-19 this holiday season. Tocilizumab, branded Actemra by pharmaceutical company Genentech, is a monoclonal antibody now approved for treating Covid-19 in hospitalized adult patients in moderate to severe conditions. All treatments to this point of the pandemic were only temporarily approved via emergency use authorization, speaking to the value of Tocilizumab. Here we discuss how the antibody was discovered and how it works. Unlike many monoclonal antibody treatments we discuss, Tocilizumab has a long history dating back 25 years. Clinical development of the antibody began in 1997 by Chugai Pharmaceuticals in Japan to treat rheumatoid arthritis. Chugai Pharmaceuticals and Genentech are now under the Roche Group umbrella, a Swiss multinational healthcare company. The researchers at Chugai Pharmaceuticals found that specific mouse antibodies contained anti-human IL-6 receptors. Interleukin-6, or IL-6, is a secreted cytokine protein expressed by white blood cells. In terms of disease, IL-6 stimulates inflammatory processes when the body is exposed to various pathogens and clinical conditions such as diabetes, multiple sclerosis, and rheumatoid arthritis.

Upon identifying the anti-human IL-6 receptors in mice, the researchers grafted the receptor onto a human IgG constant Fc region using recombinant DNA technology, effectively humanizing the receptor. Later research by Kishimoto et al. confirmed that the engineered mouse antibody receptor grafted to the human IgG constant Fc exclusively blocked IL-6 trans-signaling without affecting other significant pathways. IL-6 inhibition sufficiently blocks inflammation without inhibiting other immune defenses against infection. Contrary to popular belief, many of the classic symptoms we experience when we are sick are not directly caused by an invading pathogen but rather consequences of our immune system fighting off the pathogen. Inflammation is one of the most prominent causes of body pain, fatigue, fever, rash, and other significant symptoms most endure during sickness. In severe cases, inflammation may cause severe pain, lack of appetite, and severe headaches and chills. To produce the drug en masse, Chugai Pharmaceutical used genetic manipulation of host cells. They encoded the genes that code for tocilizumab production onto a human host T-cell. The encoded T-cell is then transfected into Chinese hamster ovary cells. These cells are then manipulated to express countless tocilizumab genes, creating a master that can be copied several times.

Vaccination represents the key strategy to control the COVID-19 pandemic through induction of neutralising antibody responses and T cell-associated immunity that substantially decrease the risk of developing severe disease.  However, individuals who are immunocompromised (eg, because of comorbidities, high age, or immunosuppressive treatment) might not mount a full adaptive immune response and thus remain susceptible. For individuals at high risk, individual monoclonal antibodies (mAbs) or cocktails of mAbs are administered as prophylaxis or therapy.  All mAbs currently approved by the US Food and Drug Administration (FDA) or European Medicines Agency (EMA) target the spike (S) protein.  During the course of the COVID-19 pandemic, several SARS-CoV-2 lineages evolved mutations that confer partial or full resistance against some mAbs. Consequently, only few mAbs remain suitable for treatment of individuals at high risk, and only bebtelovimab shows high efficacy against multiple omicron sublineages. However, novel omicron sublineages have been detected, harbouring additional S protein mutations within the epitopes of bebtelovimab and other mAbs. Novel sublineages include BA.4.6 (with increasing incidence in several countries worldwide), BA.2.75.2 (with increasing incidence in India), BJ.1 (mainly observed in India and Bangladesh; notably BJ.1 is one parental lineage of the currently increasing XBB recombinant), and BQ.1.1 (with increasing incidence in the USA and Europe).

The emergence of the highly divergent SARS-CoV-2 Omicron variant has jeopardized the efficacy of vaccines based on the ancestral spike. The bivalent COVID-19 mRNA booster vaccine within the United States is comprised of the ancestral and the Omicron BA.5 spike. Since its approval and distribution, additional Omicron subvariants have been identified with key mutations within the spike protein receptor binding domain that are predicted to escape vaccine sera. Of particular concern is the R346T mutation which has arisen in multiple subvariants, including BA.2.75.2 and BQ.1.1.

Using a live virus neutralization assay, we evaluated serum samples from individuals who had received either one or two monovalent boosters or the bivalent booster to determine neutralizing activity against wild-type (WA1/2020) virus and Omicron subvariants BA.1, BA.5, BA.2.75.2, and BQ.1.1. In the one monovalent booster cohort, relative to WA1/2020, we observed a reduction in neutralization titers of 9-15-fold against BA.1 and BA.5 and 28-39-fold against BA.2.75.2 and BQ.1.1. In the BA.5-containing bivalent booster cohort, the neutralizing activity improved against all the Omicron subvariants. Relative to WA1/2020, we observed a reduction in neutralization titers of 3.7- and 4-fold against BA.1 and BA.5, respectively, and 11.5- and 21-fold against BA.2.75.2 and BQ.1.1, respectively. These data suggest that the bivalent mRNA booster vaccine broadens humoral immunity against the Omicron subvariants.

Preprint in bioRxiv (Nov. 1, 2022):

 https://doi.org/10.1101/2022.10.31.514636 

The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies.

The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.

Published March 30, 2024:

https://doi.org/10.1007/s15010-024-02223-y 

NIH researchers explore hidden, vulnerable region of influenza neuraminidase.

Researchers at the National Institutes of Health have identified antibodies targeting a hard-to-spot region of the influenza virus, shedding light on the relatively unexplored “dark side” of the neuraminidase (NA) protein head. The antibodies target a region of the NA protein that is common among many influenza viruses, including H3N2 subtype viruses, and could be a new target for countermeasures. The research, led by scientists at the National Institute of Allergy and Infectious Diseases’ Vaccine Research Center, part of NIH, was published today in Immunity. Influenza, or flu, sickens millions of people across the globe each year and can lead to severe illness and death. While vaccination against influenza reduces the burden of the disease, updated vaccines are needed each season to provide protection against the many strains and subtypes of the rapidly evolving virus. Vaccines that provide protection against a broad range of influenza viruses could prevent outbreaks of new and reemerging flu viruses without the need for yearly vaccine reformulation or vaccinations. One way to improve influenza vaccines and other countermeasures is to identify new targets on the virus’s surface proteins in “conserved” regions—portions that tend to be relatively unchanged between different strains of the virus. Influenza NA is a surface protein containing a globular head portion and a narrow stalk portion. The underside of the NA head contains a highly conserved region with targets for antibodies—known as epitopes—that make it vulnerable to antibody binding and inhibition of the virus, as well as not being impacted by mutations common in drug-resistant strains. This region is termed the “dark side” due to its partially hidden location and relatively unexplored characteristics.

The researchers isolated human antibodies that target the NA dark side from the blood of two people who had recovered from influenza type A subtype H3N2, a major subtype of seasonal flu viruses. In lab tests, the antibodies inhibited propagation of viruses from subtype H2N2, the subtype that caused pandemic influenza in 1957-58, and H3N2 viruses from humans, swine, and birds. The antibodies also protected mice from lethal infection by a subtype H3N2 virus when given to the animals either one day before or two days after infection, showing that the antibody may treat and prevent influenza in this model. The scientists analyzed the structure of two of the antibodies while bound to NA using advanced microscopy techniques known as cryogenic electron microscopy. Each antibody targeted different, nonoverlapping regions of the dark side, demonstrating that this region has multiple areas that may be useful to explore for countermeasure development. These findings show that the NA dark side has unique, previously untapped epitopes that could be applied to the development of new vaccine and therapeutic strategies. They suggest that antibodies targeting the NA dark side could be useful in combination with antivirals or other types of antibodies for interventions against influenza, as they are effective against influenza viruses with drug-resistant mutations. The researchers also note that NA dark side targets could be included in the next generation of broadly protective vaccines against influenza.

Study published in Immunity (March 24, 2024):

https://doi.org/10.1016/j.immuni.2024.02.003 

Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses.

Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Pre-print in bioRxiv (Jan. 16, 2024): 

https://doi.org/10.1101/2024.01.15.575741 

IMPORTANCE

We analyzed the kinetics and durability of the humoral responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination using >8,000 longitudinal samples collected over a three-year period (April 2020 to April 2023) in the New York City metropolitan area. Upon primary immunization, participants with pre-existing immunity mounted higher antibody responses faster and achieved higher steady-state levels compared to naive individuals. Antibody durability was characterized by two phases: an initial rapid decay, followed by a phase of stabilization with very slow decay resulting in an individual spike binding antibody steady state.

Booster vaccination equalized the differences in antibody levels between participants with and without hybrid immunity, but the antibody titers reached decreased with each successive antigen exposure. Break-through infections increased antibody titers to similar levels as an additional vaccine dose in naive individuals. Our study provides strong evidence for the fact that SARS-CoV-2 antibody responses are long lasting, with an initial waning phase followed by a stabilization phase.

Preprint available at medRxiv (August 28, 2023):

https://doi.org/10.1101/2023.08.26.23294679 

The Orthocoronaviridae subfamily is large comprising four highly divergent genera. Four seasonal coronaviruses were circulating in humans prior to the coronavirus disease 2019 (COVID-19) pandemic. Infection with these viruses induced antibody responses that are relatively narrow with little cross-reactivity to spike proteins of other coronaviruses. Here, we report that infection with and vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces broadly crossreactive binding antibodies to spikes from a wide range of coronaviruses including members of the sarbecovirus subgenus, betacoronaviruses including Middle Eastern respiratory syndrome coronavirus (MERS CoV), and extending to alpha-, gamma- and delta-coronavirus spikes. These data show that the coronavirus spike antibody landscape in humans has profoundly been changed and broadened as a result of the SARS-CoV-2 pandemic. While we do not understand the functionality of these crossreactive antibodies, they may lead to enhanced resistance of the population to infection with newly emerging coronaviruses with pandemic potential.

Preprunt in medRxiv (August 6, 2023):

https://doi.org/10.1101/2023.08.01.23293522 

This fall, parents and pediatricians will have a new option to protect babies from a lung-attacking virus that is the leading cause of hospitalization in infants under a year old in the United States every year. The US Food and Drug Administration approved nirsevimab to protect newborns from respiratory syncytial virus, or RSV, on Monday. Nirsevimab, which will be sold under the brand name Beyfortus, is not a vaccine. Vaccines prompt the body to make antibodies to defend against pathogens. Instead, nirsevimab is a form of passive immunity. It’s a ready-made antibody that can bind to the virus and block it from infecting healthy cells. The immune system doesn’t have to make anything. It’s given as a single injection to an infant before RSV season, which usually peaks in the fall and winter months. The FDA approval also allows a second injection for infants up to 24 months of age who remain vulnerable through their second RSV season. “RSV can cause serious disease in infants and some children and results in a large number of emergency department and physician office visits each year,” said Dr. John Farley, director of the Office of Infectious Diseases in the FDA’s Center for Drug Evaluation and Research. “Today’s approval addresses the great need for products to help reduce the impact of RSV disease on children, families and the health care system,” Farley said in a news release.

The group of experts who advise the US Centers for Disease Control and Prevention on its vaccine recommendations will next weigh in. The Advisory Committee on Immunization Practices, or ACIP, has issued draft recommendations and clinical considerations for nirsevimab’s use, but the group is expected to formalize those with a vote at its next meeting. After the CDC signs off, nirsevimab will become the second antibody available to protect young children against RSV. The other, called palivizumab or Synagis, has been used only to protect the most vulnerable babies: those born prematurely who are younger than 6 months. It lasts only a short time in the body, so doctors give it once a month, starting just before RSV season, until the risk has passed. It has been a help, but it’s only partially effective. It keeps vulnerable babies out of the hospital about 50% of the time. The antibody in nirsevimab has been stabilized so it lasts longer in the body — four to six months — and it seems to be more potent. It’s approved for use in all infants, even healthy infants born full-term. “This virus can affect all babies, so not just babies with certain health conditions but even healthy babies. So as a pediatrician, I’m very excited about the idea of having an immunization to prevent serious illness from RSV,” said Dr. Rachel Dawkins, medical director of the pediatric and adolescent medical clinics at Johns Hopkins All Children’s Hospital in St. Petersburg, Florida.

Nirsevimab may not be the only option for preventing the infection this fall. The FDA is weighing whether to approve Pfizer’s vaccine for pregnant women that would also protect babies. In that case, the mom makes the antibodies, which cross the placenta to safeguard the fetus and are expected to last through an infant’s first few months of life. That vaccine would protect babies from the moment they are born, a benefit if the infection shows up out of season. Vaccines also prompt the mom’s body to make more than one kind of antibody, which would provide broader-spectrum protection. “I would say any strategy that we can use to help prevent RSV and infants is a great one,” Dawkins said. “So if moms are able to be vaccinated to hopefully protect their newborns, that’s great. Or if the babies are able to be given this antibody, also great, and I think there is some evidence that they work together.” In a presentation at their June meeting, the ACIP committee thinking through the potential use of the antibody said that it may make sense to give both types of protection in certain circumstances but that most healthy babies will need only one or the other. “Obviously, they need to consider how both of those preventive products for RSV infection will coexist,“ said Dr. Michael Greenberg, a pediatrician who is North American medical head of vaccines for Sanofi, the company that is marketing the antibody. “Nirsevimab is really the first that’s going to be able to offer the protection for all infants, sort of irrespective of when they’re born, because there’s the flexibility in the timing of the administration,” Greenberg told CNN. In the clinical trials that led to its approval, nirsevimab was about 70% effective at cutting the risk that a baby would need a doctor’s visit for RSV, and it was about 78% effective at preventing hospitalizations due to RSV compared with a placebo, according to an FDA analysis.

That means nirsevimab would prevent 1 RSV hospitalization for every 56 infants treated. So even though antibodies like this tend one to be pricey, doctors say that if it keeps babies out of the hospital, that will probably make it worth the cost. In studies, the therapy was generally safe and well-tolerated. A few infants — less than 1% — had skin reactions after their shots, but these went away with treatment. “We run this gauntlet every year — RSV season,” said Dr. Frank Esper, a pediatric infectious disease specialist at the Cleveland Clinic in Ohio. “We see a lot of these infants. They come in; they can’t breathe. That’s the problem. That’s what RSV does. It causes so much swelling and secretions in their breathing tubes, called the bronchioles, that they just can’t get enough oxygen.” RSV is the leading cause of hospitalization in infants up to 1 year old. Most babies with RSV need extra oxygen; doctors help support their breathing for two or three days, and then they get better. “Babies are small, and because babies are small, their airways are small, and so it takes just a little amount of inflammation to clog them all up, and that’s what RSV does,” Esper said. In rare cases, RSV can be deadly. According to the CDC, it kills between 100 and 300 infants each year. And it’s not just a threat to young children; RSV sickens and kills elderly adults each year, too. Vaccines geared toward seniors have just been approved. “So anything that we have that can fight that problem, then the better,” Esper said. Eight years ago, Cheryl Meany enrolled in an early study testing nirsevimab when she was pregnant with twin girls. The babies were born a little early, at 33 weeks, as twins often are, and their early arrival meant they were more vulnerable to infections. She said she felt cautious about enrolling in the study, but her doctor told her he would absolutely do it if they were his own kids. Her newborns were given injections shortly after birth, but she didn’t find out that they’d gotten the active antibodies until almost five years later. “I kind of had an inkling,” Meany said. “They were born in December, and we live in upstate New York, where cold and flu season is rampant around here. And I’m a teacher, and my husband at the time was working in the hospital as a respiratory therapist, our older daughter was in school, so … just germs everywhere.” She says her twins were in day care at the time, “and they never got sick.” “This was just the best start for them and being preemies and all of the things that could have happened,” Meany said. “I really do believe that this kept them healthy in order to grow and thrive.”

FDA press release (July 17, 2023):

https://www.fda.gov/news-events/press-announcements/fda-approves-new-drug-prevent-rsv-babies-and-toddlers 

Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7–100 ng ml−1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future. A suite of human monoclonal antibodies block infection by all human ACE2 binding sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 variants, at subnanomolar concentrations in cell culture and protect mice against severe acute respiratory syndrome coronavirus 2 infection.

Published in Nature Microbiology (May 15, 2023):

https://doi.org/10.1038/s41564-023-01389-9 

A study by UPMC and the University of Pittsburgh School of Medicine found that monoclonal antibody treatments significantly reduced the risk of hospitalization or death from COVID-19. The research underscores the importance of investing in infrastructure and healthcare professional skills to efficiently deliver these treatments, particularly in case of more lethal virus variants emerging in the future. The COVID-19 pandemic created a real-life experiment that demanded health care providers nationwide rapidly stand up clinics to administer an evolving offering of monoclonal antibody treatments that — while initially proven safe and effective in clinical trials and approved under federal emergency use authorization — had never been tested at such a scale. The task was massive and the real-world benefit was uncertain, particularly for monoclonals approved later in the pandemic based only on laboratory data. An analysis published today (April 3, 2023) in the Annals of Internal Medicine by UPMC and University of Pittsburgh School of Medicine clinicians and scientists shows that it was worth it. “The virus was a moving target, and, for two years, monoclonal antibodies were approved, revoked, sometimes reauthorized, and sometimes scarce,” said lead author Kevin Kip, Ph.D., vice president of clinical analytics at UPMC. “Using UPMC’s database of patients treated with monoclonal antibodies —one of the largest in the U.S. — we are finally able to conclude that pushing through all these challenges unequivocally saved lives and prevented hospitalizations.” Monoclonal antibodies are human-made antibodies specifically designed to prevent a pathogen — in this case, the virus that causes COVID-19 — from entering human cells, replicating, and causing serious illness. The U.S. Food and Drug Administration granted emergency use authorization to five different COVID-19 monoclonal antibody treatments at various times between 2020 and 2022. All were restricted to people aged 12 and older with risk factors that made them more susceptible to bad outcomes from COVID-19. The treatments had to be administered intravenously or through injection by a healthcare professional. As the virus evolved, new monoclonal antibodies were introduced and older ones, which were no longer effective, were removed.

Starting with the first authorization at the end of 2020, UPMC opened dozens of clinics, set up emergency department infrastructure, and arranged home visits to maximize its ability to provide monoclonal antibodies to patients in Pennsylvania, New York, and Maryland. After the emergency use authorization was revoked for the last monoclonal antibody on November 30, 2022, and no new monoclonal antibodies were introduced, UPMC pulled anonymous clinical data on 2,571 patients treated with monoclonal antibodies and matched them with data from 5,135 patients with COVID-19 who were eligible for monoclonal antibodies but did not receive them. On average, people who received monoclonal antibodies within two days of a positive COVID-19 test reduced their risk of hospitalization or death by 39% compared to their peers who did not receive the treatment. Patients with immunocompromising conditions, regardless of their age, had an even greater reduced risk. Patients treated when the alpha and delta variants of the virus were circulating experienced greater benefit than their untreated peers compared to those treated when the omicron variant was circulating, likely because earlier variants were more deadly and people had less prior immunity from previous infection or vaccination. By the time omicron was circulating, risk of death and hospitalization had fallen in general, so monoclonal antibody treatment had less overall benefit, but still clinically meaningful benefit, particularly in vulnerable patients, explained co-author Erin McCreary, Pharm.D., director of infectious diseases improvement and clinical research innovation at UPMC. “Right now, COVID-19 has a relatively low risk of death for the general population, but we have seen how quickly this virus can mutate and spread. Nobody can say with certainty that a future variant won’t be more deadly,” McCreary said. “Should that happen, our real-world data give reassurance that investing in the infrastructure and healthcare worker knowledge to quickly give antibody treatments keeps people in the communities we serve alive and out of the hospital.”

Study published April 4, 2023 (Annals of Int. Medicine):

https://doi.org/10.7326/M22-1286

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor binding domain (RBD) of the Spike (S)-protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors that target a conserved S2-region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2 and MERS-CoV, that have spilled over into humans in past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.

Published in Immunity (Feb. 15, 2023):

https://doi.org/10.1016/j.immuni.2023.02.005 

[11/30/2022] The U.S. Food and Drug Administration today announced bebtelovimab is not currently authorized for emergency use in the U.S. because it is not expected to neutralize Omicron subvariants BQ.1 and BQ.1.1., according to data included in the Health Care Provider Fact Sheet.  

Nowcast data from the Centers for Disease Control and Prevention published last week estimates that the combined proportion of COVID-19 cases caused by the Omicron BQ.1 and BQ.1.1 subvariants to be above 57% nationally, and already above 50% in all individual regions but one, and data shows a sustained trend of increasing prevalence across all regions. Given that a COVID-19 infection is likely to be caused by a non-susceptible SARS-CoV-2 variant, and consistent with the terms and conditions of the Letter of Authorization, bebtelovimab is not currently authorized for emergency use in any U.S. region at this time.   Eli Lilly and its authorized distributors have paused commercial distribution of bebtelovimab until further notice by the Agency. Additionally, the Administration for Strategic Preparedness and Response (ASPR) has paused the fulfillment of any pending requests under its Bebtelovimab Product Replacement Initiative.  The U.S. Government recommends all product be retained in the event that SARS-CoV-2 variants susceptible to bebtelovimab, which are currently circulating at lower prevalence, become more prevalent in the future in the United States. Retained product must be appropriately held in accordance with storage conditions detailed in the authorized Fact Sheet for Health Care Providers and the Letter of Authorization for bebtelovimab.  Health care providers should use other approved or authorized products that are expected to retain activity against BQ.1 and BQ.1.1 as they choose appropriate treatment options for patients, which include the following: 

• Paxlovid is authorized for the treatment of mild-to-moderate COVID-19 in adults and pediatric patients (12 years of age and older weighing at least 40 kg) with positive results of direct SARS-CoV-2 viral testing, and who are at high risk for progression to severe COVID-19, including hospitalization or death. 
• Veklury is approved for the treatment of adults and pediatric patients (28 days of age and older and weighing at least 3 kg) with positive results of direct SARS-CoV-2 viral testing, who are not hospitalized and have mild-to-moderate COVID-19 and are at high risk for progression to severe COVID-19, including hospitalization or death. 
• Lagevrio is authorized for the treatment of mild-to-moderate COVID-19 in adults with positive results of direct SARS-CoV-2 viral testing who are at high risk for progression to severe COVID-19, including hospitalization or death, and for whom alternative COVID-19 treatment options approved or authorized by FDA are not accessible or clinically appropriate. 

In addition, COVID-19 convalescent plasma with high titers of anti-SARS-CoV-2 antibodies is authorized for the treatment of COVID-19 in patients with immunosuppressive disease or receiving immunosuppressive treatment, in inpatient or outpatient settings. Individuals for whom COVID-19 vaccination is recommended should consider getting vaccinated with the primary series or, if vaccinated with the primary series, boosted with an updated bivalent vaccine when eligible to increase protection against the most serious consequences of COVID-19, including hospitalization and death. For more information related to the therapeutic management of non-hospitalized patients with mild-to-moderate COVID-19, refer to the NIH COVID-19 Treatment Guidelines.  

All treatment sites can continue ordering Paxlovid, Veklury, and Lagevrio by following the existing ordering processes and reporting procedures, as applicable.  FDA will continue to work with ASPR, the CDC, and the National Institutes of Health on surveillance of variants that may impact the use of the therapies authorized for emergency use. We will provide further updates and consider additional action as new information becomes available.

A new monoclonal antibody cocktail neutralizes a dangerous virus circulating West Africa: Lassa Virus.  Monoclonal antibodies are among our greatest assets in treating and preventing virus-induced disease. While the spotlight has focused squarely on Covid-19 monoclonal antibodies throughout the pandemic, antibody candidates for other severe pathogens have also made strides forward. Here we describe a new antibody cocktail that neutralizes a lesser known but nonetheless dangerous virus circulating West Africa: Lassa Virus.

What is Lassa Virus?

Lassa Virus is a pathogen responsible for Lassa hemorrhagic fever, which afflicts between 300,000 and 500,000 people per year, commonly in West African countries, including Nigeria, Liberia, Sierra Leone, Guinea, and Ghana. Lassa fever has a mortality rate of roughly one percent. Pregnant women are at the greatest risk of death, with up to a 90% fatality rate. The symptomatic cases present issues such as fever, headaches, vomiting, and muscle pain. Spread typically occurs via contact with infected mice excrement or urine, though direct contact spread from person to person is also common. Unfortunately, a vaccine is not yet available for the virus, and antivirals are weak at best. Lassa Virus, like SARS-CoV-2, is an RNA virus that constantly mutates. A therapy or prophylactic to fill the void of Lassa Virus drugs is needed.

Lassa Virus Monoclonal Antibody Therapy

Fortunately, a new candidate may be just around the corner. A group of researchers from the La Jolla Insitute for Immunology in California led by Dr. Erica Ollmann Saphire have identified a cocktail of three antibodies that bind and neutralize the Lassa Virus. This same group discovered a broadly accepted cocktail of monoclonal antibodies for Ebolavirus, which we have previously described. This cocktail arrived just in time as the current to treat the current epidemic caused by the Sudan strain of Ebolavirus in Nigeria.  The new Lassa Virus therapy, denoted Arevirumab-3, is comprised of three distinct antibodies, each one binding distinct regions of the Lassa Virus glycoprotein. The Lassa Virus spike protein comes in a set of three identical subunits embedded into the membrane. The virus is synthesized as a single long polypeptide and is cleaved into three parts, a leader sequence, GP1 which encodes the receptor-binding function, and GP2 embedded into the membrane (Figure 1).

8.9F inhibits virion-cell attachment by blocking the GPC/α-DG interaction

The first antibody, 8.9F, binds the top of the spike trimer, stretching across all three portions of the glycoprotein. 8.9F is an unusual antibody as the single antibody binds all three faces of the trimer. The antibody also binds the three cleavage sites of the GP1 subunits. It binds the portion of the glycoprotein that attaches to the host cell, directly inhibiting virion-cell attachment by mimicking the cell alpha-dystroglycan receptor. The 8.9F antibody also specifically binds a glycan, N119, which is required for neutralization activity. This glycan is required for alpha-dystroglycan receptor-binding, so 8.9F’s recognition is surprising.

A native N89 glycan plays a central role in 12.1F/LASV GPC recognition

The second antibody, 12.1F, binds to a separate site on GP1, directly interacting with N-glycans for neutralization activity. The antibody binds more membrane-proximal and has direct interaction with six crucial amino acid residues and critical glycans N89 and N109. To infect a cell, the Lassa Virus must bind the cell membrane and be engulfed by a cellular endosome. Then the protein undergoes a structural change to bind the LAMP-1 protein in the endosome interior. Binding to LAMP-1 is essential for fusion of viral and cell membranes and entry into the cytoplasm where replication occurs. 37.2D neutralizes LASV by locking the GPC trimer in an inactive configuration. The third antibody, 37.2D, binds two adjacent subunits of GP2. The antibody stretches across subunits, locking the trimer in place by binding conserved peptides and conserved glycans N390 and N395. 37.2D is special in that it attacks GP2 at a unique angle, stabilizing the pre-fusion trimer, preventing fusion activation and, therefore, infection. These three mechanisms work together to yield a highly effective antibody cocktail.  One critical question for monoclonal antibody treatment, is can the virus escape via mutation in the binding sites? Dr. Ollmann Saphire's team shows that such is the case for treatment with a single 8.9 F antibody. However, no resistance mutations arose when using the cocktail of all three antibodies, nor was the virus capable of escaping. The Arevirumab-3 antibody may provide a long-awaited answer to the lack of treatment and prevention of Lassa infections. This is particularly important for cases involving pregnant women and their fetuses. It will be important to reduce the costs of this antibody cocktail as much as possible so that it is available when needed in West Africa. Current technologies allow monoclonal antibodies to be produced at $200 and $250 per gram.

The next step in the development of the control of Lassa Fever is the development of a vaccine effective against all Lassa Virus variants. This work may serve as a guide for the creation of such a vaccine.