Biology subjects

Weissman, D.

Publications and source records attributed to Weissman, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Nucleoside-modified mRNA-based influenza vaccines circumvent problems associated with H3N2 vaccine strain egg-adaptation

Most human influenza vaccine antigens are produced in fertilized chicken eggs. Recent H3N2 egg-based vaccine antigens have limited effectiveness, partially due to egg-adaptive substitutions that alter the antigenicity of the hemagglutinin (HA) protein. The nucleoside-modified messenger RNA encapsulated in lipid nanoparticle (mRNA-LNP) vaccine platform is a promising alternative for egg-based influenza vaccines because mRNA-LNP-derived antigens are not subject to adaptive pressures that arise during the production of antigens in chicken eggs. Here, we compared H3N2-specific antibody responses in mice vaccinated with either 3c.2A H3-encoded mRNA-LNP or a conventional egg-based Fluzone vaccine (which included an egg-adapted 3c.2A antigen) supplemented with an MF59-like adjuvant. We tested mRNA-LNP encoding wild-type and egg-adapted 3c.2A H3 antigens. We found that mRNA-LNP encoding wild-type 3c.2A H3 elicited antibodies that neutralized the wild-type 3c.2A H3N2 virus more effectively relative to antibodies elicited by mRNA-LNP encoding egg-adapted 3c2.A H3 or the egg-based Fluzone vaccine. mRNA-LNP expressing either wild-type or egg-adapted 3c2.A H3 protected mice against infection with the wild-type 3c2.A H3N2, whereas the egg-based Fluzone vaccine did not. We found that both mRNA-LNP vaccines elicited high levels of group 2 HA stalk-reactive antibodies that likely contributed to protection in vivo. Our studies indicate that nucleoside-modified mRNA-LNP-based vaccines can circumvent problems associated with egg-adaptations with recent 3c2.A H3N2 viruses. SummaryThis study shows that the nucleoside-modified messenger RNA encapsulated in lipid nanoparticle (mRNA-LNP) vaccine platform is a promising alternative for egg-based influenza vaccines. We show that mRNA-LNP expressing H3 antigens elicit high levels of antibodies in mice and protect against H3N2 influenza virus infection.

microbiology↗

bioRxiv2022

Spatial structure alters the site frequency spectrum produced by hitchhiking

The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum (SFS) left by hitchhiking in the genomic region of a sweep in a population occupying a one-dimensional range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic three-part SFS at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly "surfed" on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the SFS produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in one-dimensional populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.

evolutionary biology↗

bioRxiv2022

mRNA-based vaccines against SARS-CoV-2 do not stimulate interferon stimulatory gene expression in individuals affected by Aicardi Goutieres Syndrome.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses threats to individuals with rare disease, in part because so little is known about the impact of COVID-19 infection and vaccination safety in rare disease populations. Of particular concern, given the overlap in disease manifestations and interferon dysregulation, are a group of heritable autoinflammatory conditions called type I interferonopathies. The most common of these, Aicardi Goutieres Syndrome (AGS), is caused by altered nucleic acid metabolism and sensing, resulting in additional concerns surrounding the use of mRNA vaccination approaches. To determine whether mRNA vaccines induce an interferon response in AGS, we applied mRNA SARS-CoV-2 vaccines to whole blood samples and assessed internalization and interferon signaling gene expression responses to the mRNA. In all cases (11 AGS and 11 control samples), interferon signatures did not significantly increase from baseline, regardless of baricitinib treatment status in the AGS subjects, and were even decreased, when using codon optimized SARS-CoV-2 di-proline modified spike sequence (S2P). Internalization of S2P in human dendritic cells was verified by Western Blot, and in control and AGS blood cells was verified by Luciferase activity. Although numbers of tested samples in this rare disease are small, based on these findings, we suggest that COVID vaccination is unlikely to directly stimulate the interferon signaling gene expression in AGS patients via response to mRNA internalization. The in vitro nature of this study cannot exclude an exaggerated interferon response to spike protein production at a systemic level in individuals with a primary heritable interferonopathy. In the context of continued SARS-CoV-2 spread in the community, we do not recommend withholding vaccination in this rare disease group. However, we recommend that vaccinations for AGS patients are provided in a controlled setting with appropriate observation and used with caution in individuals with prior vaccine associated adverse events.

immunology↗

bioRxiv2022

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, fundamental facts about the evolutionary origins of VOCs remain largely unknown. One major uncertainty is whether the VOCs evolved during transmission chains of many acute infections or during long-term infections within single individuals. We test the consistency of these two possible paths with the observed dynamics, focusing on the clustered emergence of the first three VOCs, Alpha, Beta, and Gamma, in late 2020, following a period of relative evolutionary stasis. We consider a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among multiple mutations that do not individually increase viral fitness--a "fitness plateau". Our results suggest that the timing and dynamics of the VOC emergence, together with the observed number of mutations in VOC lineages, are in best agreement with the VOC phenotype requiring multiple mutations and VOCs having evolved within single individuals with long-term infections.

evolutionary biology↗

bioRxiv2022

Modified E2 glycoprotein of hepatitis C virus enhances pro-inflammatory cytokines and protective immune response in mice

Hepatitis C virus (HCV) is characterized by a high number of chronic cases owing to an impairment of innate and adaptive immune responses. CD81 on the cell surface facilitates HCV entry by interacting with the E2 envelope glycoprotein. On the other hand, CD81/E2 binding on immune related cells may also influence host response outcome to HCV infection. Here, we performed site-specific amino acid substitution in the front layer of E2 sequence to reduce CD81 binding and evaluate HCV candidate vaccine potential. The altered sE2 protein (F442NYT), unlike sE2, displayed a significant reduction in CD81 binding, induced pro-inflammatory cytokines, and repressed anti-inflammatory response in primary monocyte-derived macrophages as antigen presenting cells. Further, sE2F442NYT stimulated CD4+T cell proliferation. Immunization of Balb/c mice with an E1/sE2F442NYT RNA-lipid nanoparticle (LNP) displayed improved IgG1 to IgG2a isotype switching, an increase in HCV pseudotype virus neutralizing antibodies, and resistance to challenge infection with a surrogate recombinant vaccinia virus expressing HCV E1-E2-NS2(aa134-966), unlike parental E1/sE2 immunization. Further investigation on modified E2 antigen for selection as antigen may provide helpful information for HCV vaccine development. One Sentence SummaryReduced HCV E2-CD81 binding and immune response

microbiology↗

bioRxiv2022

Targeted nanocarriers coopting pulmonary leukocytes for drug delivery to the injured brain

Selective drug delivery to injured regions of the brain is an elusive, but biomedically important, goal. It is tempting to co-opt migrating white blood cells (WBC) to carry drugs to the injured brain, using natural WBC tropism. Current approaches to load cargoes to WBC have limited utility, particularly in acute conditions, due to the need for time consuming ex vivo manipulation and loading of cells. Physiological, in vivo loading of WBC may be advantageous in this scenario. Here we devised such a strategy, capitalizing on the unique features of the direct blood exchange between brain and lungs. Mediators emanating from the injured brain directly travel to the pulmonary vasculature via venous flow. In response to these mediators, WBCs, transiently residing in the pulmonary microvascular lumen, disembark and flow with arterial blood to the brain microvasculature, where they adhere and transmigrate to the brain parenchyma via the local chemoattractant gradient. We posited that direct in vivo targeting of cargoes to the pulmonary WBC pool may provide drug transfer to brain via this natural mechanism. To test this, we intravenously injected agents targeted to intercellular adhesion molecule 1 (ICAM) in mice with acute brain inflammation caused by direct injection of tumor necrosis factor alpha (TNF-). We found that: A) At 2 hours, >20% of ICAM/NP accumulated in lungs, predominantly in WBCs; B) At 6 and 22 hours, ICAM/NP pulmonary uptake markedly decreased; C) In contrast, ICAM/NP uptake in brain increased ~5-fold in this time interval, concomitantly with migration of WBCs to the brain. Cranial window fluorescent microscopy confirmed WBC transport of ICAM/NP to the brain in TNF--challenged mice beyond the BBB. Importantly, demonstrating the pharmacologic relevance of this strategy, dexamethasone-loaded ICAM/liposomes abrogated brain edema in this model. In sum, coopting the natural homing of WBC from the lungs via ICAM-targeting to injured brain is an attractive strategy for precise interventions for treatment of acute brain injuries. VISUAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

pharmacology and toxicology↗

bioRxiv2022

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine

Coronavirus vaccines that are highly effective against SARS-CoV-2 variants are needed to control the current pandemic. We previously reported a receptor-binding domain (RBD) sortase A-conjugated ferritin nanoparticle (RBD-scNP) vaccine that induced neutralizing antibodies against SARS-CoV-2 and pre-emergent sarbecoviruses and protected monkeys from SARS-CoV-2 WA-1 infection. Here, we demonstrate SARS-CoV-2 RBD-scNP immunization induces potent neutralizing antibodies in non-human primates (NHPs) against all eight SARS-CoV-2 variants tested including the Beta, Delta, and Omicron variants. The Omicron variant was neutralized by RBD-scNP-induced serum antibodies with a mean of 10.6-fold reduction of ID50 titers compared to SARS-CoV-2 D614G. Immunization with RBD-scNPs protected NHPs from SARS-CoV-2 WA-1, Beta, and Delta variant challenge, and protected mice from challenges of SARS-CoV-2 Beta variant and two other heterologous sarbecoviruses. These results demonstrate the ability of RBD-scNPs to induce broad neutralization of SARS-CoV-2 variants and to protect NHPs and mice from multiple different SARS-related viruses. Such a vaccine could provide the needed immunity to slow the spread of and reduce disease caused by SARS-CoV-2 variants such as Delta and Omicron.

immunology↗

bioRxiv2022

Lipid nanoparticles delivering constitutively active STING mRNA as a novel anti-cancer therapeutic approach

Treating immunosuppressive tumors represents a major challenge in cancer therapies. Activation of STING signaling has shown remarkable potential to invigorate the immunologically cold tumor microenvironment (TME). However, we and others have shown that STING is silenced in many cancers, including pancreatic ductal adenocarcinoma (PDAC) and Merkel cell carcinoma (MCC), both of which are associated with an immune-dampened TME. In this study, we applied mRNA lipid nanoparticles (LNP) to deliver a permanently active gain-of-function STINGR284S mutant into PDAC and MCC cells. Expression of STINGR284S induces cytokines and chemokines crucial for promoting intratumoral infiltration of CD8+ T cells and, importantly, also leads to robust cancer cell death while avoiding T cell entry and toxicity. Our studies demonstrated that mRNA-LNP delivery of STINGR284S could be explored as a novel therapeutic tool to reactivate antitumor response in an array of STING-deficient cancers while overcoming the toxicity and limitations of conventional STING agonists.

bioengineering↗

bioRxiv2021

Combinatorial mRNA vaccination enhances protection against SARS-CoV-2 delta variant

Emergence of SARS-CoV-2 variants of concern (VOC), including the highly transmissible delta strain, has posed challenges to current COVID-19 vaccines that principally target the viral spike protein (S). Here, we report a nucleoside-modified mRNA vaccine that expresses the more conserved viral nucleoprotein (mRNA-N). We show that mRNA-N alone was able to induce a modest but significant control of SARS-CoV-2 in mice and hamsters. Critically, by combining mRNA-N with the clinically approved S-expressing mRNA vaccine (mRNA-S-2P), we found that combinatorial mRNA vaccination (mRNA-S+N) led to markedly enhanced protection against the SARS-CoV-2 delta variant compared to mRNA-S. In a hamster model, we demonstrated that while mRNA-S alone elicited significant control of the delta strain in the lungs ([~]45-fold reduction in viral loads compared to un-vaccinated control), its effectiveness in the upper respiratory tract was weak, whereas combinatorial mRNA-S+N vaccination induced markedly more robust control of the delta variant infection in the lungs ([~]450-fold reduction) as well as in the upper respiratory tract ([~]20-fold reduction). Immune analyses indicated that induction of N-specific immunity as well as augmented S-specific T-cell response and neutralizing antibody activity were collectively associated the enhanced protection against SARS-CoV-2 delta strain by combinatorial mRNA vaccination. These findings suggest that the combined effects of protection in the lungs and upper respiratory tract could both reduce the risk of severe disease as well as of infection and transmission.

microbiology↗

bioRxiv2021

Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles

The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA- LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.

immunology↗

bioRxiv2021

Chimeric spike mRNA vaccines protect against sarbecovirus challenge in mice

The emergence of SARS-CoV in 2003 and SARS-CoV-2 in 2019 highlights the need to develop universal vaccination strategies against the broader Sarbecovirus subgenus. Using chimeric spike designs, we demonstrate protection against challenge from SARS-CoV, SARS-CoV-2, SARS-CoV-2 B.1.351, bat CoV (Bt-CoV) RsSHC014, and a heterologous Bt-CoV WIV-1 in vulnerable aged mice. Chimeric spike mRNAs induced high levels of broadly protective neutralizing antibodies against high-risk Sarbecoviruses. In contrast, SARS-CoV-2 mRNA vaccination not only showed a marked reduction in neutralizing titers against heterologous Sarbecoviruses, but SARS-CoV and WIV-1 challenge in mice resulted in breakthrough infection. Chimeric spike mRNA vaccines efficiently neutralized D614G, UK B.1.1.7., mink cluster five, and the South African B.1.351 variant of concern. Thus, multiplexed-chimeric spikes can prevent SARS-like zoonotic coronavirus infections with pandemic potential. SentenceChimerized RBD, NTD, and S2 spike mRNA-LNPs protect mice against epidemic, zoonotic, and pandemic SARS-like viruses

microbiology↗

bioRxiv2021

SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys

Betacoronaviruses (betaCoVs) caused the severe acute respiratory syndrome (SARS) and Middle East Respiratory Syndrome (MERS) outbreaks, and now the SARS-CoV-2 pandemic. Vaccines that elicit protective immune responses against SARS-CoV-2 and betaCoVs circulating in animals have the potential to prevent future betaCoV pandemics. Here, we show that immunization of macaques with a multimeric SARS-CoV-2 receptor binding domain (RBD) nanoparticle adjuvanted with 3M-052-Alum elicited cross-neutralizing antibody responses against SARS-CoV-1, SARS-CoV-2, batCoVs and the UK B.1.1.7 SARS-CoV-2 mutant virus. Nanoparticle vaccination resulted in a SARS-CoV-2 reciprocal geometric mean neutralization titer of 47,216, and robust protection against SARS-CoV-2 in macaque upper and lower respiratory tracts. Importantly, nucleoside-modified mRNA encoding a stabilized transmembrane spike or monomeric RBD protein also induced SARS-CoV-1 and batCoV cross-neutralizing antibodies, albeit at lower titers. These results demonstrate current mRNA vaccines may provide some protection from future zoonotic betaCoV outbreaks, and provide a platform for further development of pan-betaCoV nanoparticle vaccines.

immunology↗

bioRxiv2020

Lipid nanoparticle encapsulated nucleoside-modified mRNA vaccines elicit polyfunctional HIV-1 antibodies comparable to proteins in nonhuman primates

Development of an effective AIDS vaccine remains a challenge. Nucleoside-modified mRNAs formulated in lipid nanoparticles (mRNA-LNP) have proved to be a potent mode of immunization against infectious diseases in preclinical studies, and are being tested for SARS-CoV-2 in humans. A critical question is how mRNA-LNP vaccine immunogenicity compares to that of traditional adjuvanted protein vaccines in primates. Here, we found that mRNA-LNP immunization compared to protein immunization elicited either the same or superior magnitude and breadth of HIV-1 Env-specific polyfunctional antibodies. Immunization with mRNA-LNP encoding Zika premembrane and envelope (prM-E) or HIV-1 Env gp160 induced durable neutralizing antibodies for at least 41 weeks. Doses of mRNA-LNP as low as 5 g were immunogenic in macaques. Thus, mRNA-LNP can be used to rapidly generate single or multi-component vaccines, such as sequential vaccines needed to protect against HIV-1 infection. Such vaccines would be as or more immunogenic than adjuvanted recombinant protein vaccines in primates.

immunology↗

bioRxiv2020

Inferring transmission bottleneck size from viral sequence data using a novel haplotype reconstruction method

The transmission bottleneck is defined as the number of viral particles transmitted from one host to another. Genome sequence data has been used to evaluate the size of the transmission bottleneck between humans infected with the influenza virus, however, the methods used to make these estimates have some limitations. Specifically, approaches using viral allele frequency data may not fully capture a process which involves the transmission of entire viral genomes. Here we set out a novel approach for inferring viral transmission bottlenecks; our method combines haplotype reconstruction, a method for inferring the composition of genomes in a viral population, with two maximum likelihood methods for bottleneck inference, tailored for small and large bottleneck sizes respectively. Our method allows for rapid calculation, and performs well when applied to data from simulated transmission events, being robust to errors in the haplotype reconstruction process. Applied to data from a previous household transmission study of influenza A infection we confirm the result that the majority of transmission events involve a small number of viruses, albeit with slightly looser bottlenecks being inferred, with between 1 and 13 particles transmitted in the majority of cases. While influenza A transmission involves a tight population bottleneck, the bottleneck is not so tight as to universally prevent the transmission of within-host viral diversity.

evolutionary biology↗

bioRxiv2019

HCMV glycoprotein B nucleoside-modified mRNA vaccine elicits antibody responses with greater durability and breadth than MF59-adjuvanted gB protein immunization

A vaccine to prevent maternal acquisition of human cytomegalovirus (HCMV) during pregnancy is a primary strategy to reduce the incidence of congenital disease. Similarly, vaccination of transplant recipients against HCMV has been proposed to prevent transplant-associated HCMV morbidity. The MF59-adjuvanted glycoprotein B protein subunit vaccine (gB/MF59) is the most efficacious tested to-date for both indications. We previously identified that gB/MF59 vaccination elicited poor neutralizing antibody responses and an immunodominant response against gB antigenic domain 3 (AD-3). Thus, we sought to test novel gB vaccines to improve functional antibody responses and reduce AD-3 immunodominance. Groups of juvenile New Zealand White rabbits were administered 3 sequential doses of full-length gB protein with an MF59-like squalene adjuvant (analogous to clinically-tested vaccine), gB ectodomain protein (lacking AD-3) with squalene adjuvant, or lipid nanoparticle (LNP)-packaged nucleoside-modified mRNA encoding full-length gB. The AD-3 immunodominant IgG response following human gB/MF59 vaccination was closely mimicked in rabbits, with 78% of binding antibodies directed against this region in the full-length gB protein group compared to 1% and 46% in the ectodomain and mRNA-LNP-vaccinated groups, respectively. All vaccines were highly immunogenic with similar kinetics and comparable peak gB-binding and functional antibody responses. Although gB ectodomain subunit vaccination reduced targeting of non-neutralizing epitope AD-3, it did not improve vaccine-elicited neutralizing or non-neutralizing antibody functions. gB nucleoside-modified mRNA-LNP-immunized rabbits exhibited enhanced durability of IgG binding to soluble and cell membrane-associated gB protein as well as HCMV-neutralizing function. Furthermore, the gB mRNA-LNP vaccine enhanced breadth of IgG binding responses against discrete gB peptide residues. Finally, low-magnitude gB-specific T cell activity was observed in the full-length gB protein and mRNA-LNP vaccine groups, though not in ectodomain-vaccinated rabbits. Altogether, these data suggest that the gB mRNA-LNP vaccine candidate, aiming to improve upon the partial efficacy of gB/MF59 vaccination, should be further evaluated in preclinical models.\n\nAuthor summaryHuman cytomegalovirus (HCMV) is the most common infectious cause of infant birth defects, resulting in permanent neurologic disability for one newborn child every hour in the United States. Furthermore, this virus causes significant morbidity and mortality in immune-suppressed transplant recipients. After more than a half century of research and development, we remain without a clinically-licensed vaccine or therapeutic to reduce the burden of HCMV-associated disease. In this study, we sought to improve upon the glycoprotein B protein vaccine (gB/MF59), the most efficacious HCMV vaccine evaluated in clinical trial, via targeted modifications to either the protein structure or vaccine formulation. An attempt to alter the protein structure to focus the immune response on vulnerable epitopes ( gB ectodomain) had little effect on the quality or function of the vaccine-elicited antibodies. However, a novel vaccine platform, nucleoside-modified mRNA formulated in lipid nanoparticles, increased the durability and breadth of vaccine-elicited immune responses. We propose that an mRNA-based gB vaccine may ultimately prove more efficacious than the gB/MF59 vaccine and should be further evaluated for its ability to elicit antiviral immune factors that can prevent both infant and transplant-associated disease caused by HCMV infection.

immunology↗

bioRxiv2018

Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?

The high-degree conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow T cell-inducing vaccines effective across different strains and subtypes. This conservation is not fully explained by functional constraint, since additional mutation(s) can compensate the replicative fitness loss of IAV escape-variant. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may only have a modest effect on transmission. Second, polymorphism of human MHC-I gene restricts the advantage of an escape-variant to only a small fraction of human population, who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell-escapevariants may result in compensatory increase in the responses to other epitopes of IAV. A combination of population genetics and epidemiological models is used to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape-variants. We conclude that the invasion of an escape-variant will be very slow with a timescale of decades or longer, even if the escape-variant does not have a replicative fitness loss. Our results suggest T cell-inducing vaccines may not engender the rapid evolution of IAV and serve as a foundation for future modeling works on the long-term effectiveness and impacts of T cell-inducing influenza vaccines. (Word count: 221)\n\nImportanceUniversal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear to which extent the T cell-inducing vaccines will select for viruses that escape the T cell responses. Our mathematical models suggest how the nature of CD8 T cell protection contributes to the conservation of the CD8 T cell epitopes of influenza A virus. Also, it points out the essential biological parameters and questions that need addressing by future experimental works. (Word count: 91)

immunology↗

bioRxiv2018

The expected time to cross extended fitness plateaus

For a population to acquire a complex adaptation requiring multiple individually neutral mutations, it must cross a plateau in the fitness landscape. We consider plateaus involving three mutations, and show that large populations can cross them rapidly via lineages that acquire multiple mutations while remaining at low frequency. Plateau-crossing is fastest for very large populations. At intermediate population sizes, recombination can greatly accelerate adaptation by combining independent mutant lineages to form triple-mutants. For more frequent recombination, such that the population is kept near linkage equilibrium, we extend our analysis to find simple expressions for the expected time to cross plateaus of arbitrary width.

evolutionary biology↗

bioRxiv2017

Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus

The bottleneck governing infectious disease transmission describes the size of the pathogen population transferred from a donor to a recipient host. Accurate quantification of the bottleneck size is of particular importance for rapidly evolving pathogens such as influenza virus, as narrow bottlenecks would limit the extent of transferred viral genetic diversity and, thus, have the potential to slow the rate of viral adaptation. Previous studies have estimated the transmission bottleneck size governing viral transmission through statistical analyses of variants identified in pathogen sequencing data. The methods used by these studies, however, did not account for variant calling thresholds and stochastic dynamics of the viral population within recipient hosts. Because these factors can skew bottleneck size estimates, we here introduce a new method for inferring transmission bottleneck sizes that explicitly takes these factors into account. We compare our method, based on beta-binomial sampling, with existing methods in the literature for their ability to recover the transmission bottleneck size of a simulated dataset. This comparison demonstrates that the beta-binomial sampling method is best able to accurately infer the simulated bottleneck size. We then apply our method to a recently published dataset of influenza A H1N1p and H3N2 infections, for which viral deep sequencing data from inferred donor-recipient transmission pairs are available. Our results indicate that transmission bottleneck sizes across transmission pairs are variable, yet that there is no significant difference in the overall bottleneck sizes inferred for H1N1p and H3N2. The mean bottleneck size for influenza virus in this study, considering all transmission pairs, was Nb = 196 (95% confidence interval 66-392) virions. While this estimate is consistent with previous bottleneck size estimates for this dataset, it is considerably higher than the bottleneck sizes estimated for influenza from other datasets.\n\nAuthor SummaryThe transmission bottleneck size describes the size of the pathogen population transferred from the donor to recipient host at the onset of infection and is a key factor in determining the rate at which a pathogen can adapt within a host population. Recent advances in sequencing technology have enabled the bottleneck size to be estimated from pathogen sequence data, though there is not yet a consensus on the statistical method to use. In this study, we introduce a new approach for inferring the transmission bottleneck size from sequencing data that accounts for the criteria used to identify sequence variants and stochasticity in pathogen replication dynamics. We show that the failure to account for these factors may lead to underestimation of the transmission bottleneck size. We apply this method to a previous dataset of human influenza A infections, showing that transmission is governed by a loose transmission bottleneck and that the bottleneck size is highly variable across transmission events. This work advances our understanding of the bottleneck size governing influenza infection and introduces a method for estimating the bottleneck size that can be applied to other rapidly evolving RNA viruses, such as norovirus and RSV.

microbiology↗