Vaccination and the population structure of antigenically diverse pathogens that exchange genetic material

Mutations make pandemics worse or better: modeling SARS-CoV-2 variants and imperfect vaccination

COVID-19 is a respiratory disease triggered by an RNA virus inclined to mutations. Since December 2020, variants of COVID-19 (especially Delta and Omicron) continuously appeared with different characteristics that influenced death and transmissibility emerged around the world. To address the novel dynamics of the disease, we propose and analyze a dynamical model of two strains, namely native and mutant, transmission dynamics with mutation and imperfect vaccination. It is also assumed that the recuperated individuals from the native strain can be infected with mutant strain through the direct contact with individual or contaminated surfaces or aerosols. We compute the basic reproduction number, R 0 , which is the maximum of the basic reproduction numbers of native and mutant strains. We prove the nonexistence of backward bifurcation using the center manifold theory, and global stability of disease-free equilibrium whenR 0 < 1 , that is, vaccine is effective enough to eliminate the native and mutant strains even if it cannot provide full protection. Hopf bifurcation appears when the endemic equilibrium loses its stability. An intermediate mutation rate ν 1 leads to oscillations. When ν 1 increases over a threshold, the system regains its stability and exhibits an interesting dynamics called endemic bubble. An analytical expression for vaccine-induced herd immunity is derived. The epidemiological implication of the herd immunity threshold is that the disease may effectively be eradicated if the minimum herd immunity threshold is attained in the community. Furthermore, the model is parameterized using the Indian data of the cumulative number of confirmed cases and deaths of COVID-19 from March 1 to September 27 in 2021, using MCMC method. The cumulative cases and deaths can be reduced by increasing the vaccine efficacies to both native and mutant strains. We observe that by considering the vaccine efficacy against native strain as 90%, both cumulative cases and deaths would be reduced by 0.40%. It is concluded that increasing immunity against mutant strain is more influential than the vaccine efficacy against it in controlling the total cases. Our study demonstrates that the COVID-19 pandemic may be worse due to the occurrence of oscillations for certain mutation rates (i.e., outbreaks will occur repeatedly) but better due to stability at a lower infection level with a larger mutation rate. We perform sensitivity analysis using the Latin Hypercube Sampling methodology and partial rank correlation coefficients to illustrate the impact of parameters on the basic reproduction number, the number of cumulative cases and deaths, which ultimately sheds light on disease mitigation.

Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation

Pathogen adaptation to public health interventions such as vaccination may take tortuous routes and involve multiple mutations at different locations in the pathogen genome, acting on distinct phenotypic traits. Yet how these multi-locus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: pathogen escape from the vaccine-induced immune response and adjustments to pathogen virulence affecting transmission or clearance. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines blocking infection, reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, favouring whichever adaptation is more accessible. Our work provides a timely alternative to the variant-centred perspective on pathogen adaptation and captures the effect of different types of vaccine on the interference between multiple adaptive mutations.

Pneumococcal Competition Modulates Antibiotic Resistance in the Pre-Vaccination Era: A Modelling Study

The ongoing emergence of antibiotic resistant strains and high frequencies of antibiotic resistance of Streptococcus pneumoniae poses a major public health challenge. How and which ecological and evolutionary mechanisms maintain the coexistence of antibiotic resistant and susceptible strains remains largely an open question. We developed an individual-based, stochastic model expanding on a previous pneumococci modelling framework. We explore how between- and within-host mechanisms of competition can sustain observed levels of resistance to antibiotics in the pre-vaccination era. Our framework considers that within-host competition for co-colonization between resistant and susceptible strains can arise via pre-existing immunity (immunological competition) or intrinsic fitness differences due to resistance costs (ecological competition). We find that beyond stochasticity, population structure or movement, competition at the within-host level can explain observed resistance frequencies. We compare our simulation results to pneumococcal antibiotic resistance data in the European region using approximate Bayesian computation. Our results demonstrate that ecological competition for co-colonization can explain the variation in co-existence of resistant and susceptible pneumococci observed in the pre-vaccination era. Furthermore, we show that within-host pneumococcal competition can facilitate the maintenance of resistance in the pre-vaccination era. Accounting for these competition-related components of pneumococcal dynamics can improve our understanding of drivers for the emergence and maintenance of antibiotic resistance in pneumococci.

Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae

The bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis, and septicemia. Available vaccines target only a subset of serotypes, so vaccination is often accompanied by a rise in the frequency of nonvaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among nonvaccine serotypes. Building on previous multilocus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation of serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in a rapid increase in the frequency of preexisting resistant variants of nonvaccine serotypes due to the removal of competition from vaccine serotypes.

Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae

The bacterial pathogen, Streptococcus pneumoniae (the pneumococcus), is a leading cause of life-threatening illness and death worldwide. Available conjugate vaccines target only a small subset (up to 13) of >90 known capsular serotypes of S. pneumoniae and, since their introduction, increases in non-vaccine serotypes have been recorded in several countries: a phenomenon termed Vaccine Induced Serotype Replacement (VISR). Here, using a combination of mathematical modelling and whole genome analysis, we show that targeting particular serotypes through vaccination can also cause their metabolic and virulence-associated components to transfer through recombination to non-vaccine serotypes: a phenomenon we term Vaccine-Induced Metabolic Shift (VIMS). Our results provide a novel explanation for changes observed in the population structure of the pneumococcus following vaccination, and have important implications for strain-targeted vaccination in a range of infectious disease systems.

The evolutionary consequences of alternative types of imperfect vaccines

The emergence and spread of mutant pathogens that evade the effects of prophylactic interventions, including vaccines, threatens our ability to control infectious diseases globally. Imperfect vaccines (e.g. those used against influenza), while not providing life-long immunity, confer protection by reducing a range of pathogen life-history characteristics; conversely, mutant pathogens can gain an advantage by restoring the same range of traits in vaccinated hosts. Using an SEIR model motivated by equine influenza, we investigate the evolutionary consequences of alternative types of imperfect vaccination, by comparing the spread rate of three types of mutant pathogens, in response to three types of vaccines. All mutant types spread faster in response to a transmission-blocking vaccine, relative to vaccines that reduce the proportion of exposed vaccinated individuals becoming infectious, and to vaccines that reduce the length of the infectious period; this difference increases with increasing vaccine efficacy. We interpret our results using the first published Price equation formulation for an SEIR model, and find that our main result is explained by the effects of vaccines on the equilibrium host distribution across epidemiological classes. In particular, the proportion of vaccinated infectious individuals among all exposed and infectious hosts, which is relatively higher in the transmission-blocking vaccine scenario, is important in explaining the faster spread of mutant strains in response to that vaccine. Our work illustrates the connection between epidemiological and evolutionary dynamics, and the need to incorporate both in order to explain and interpret findings of complicated infectious disease dynamics.

No coexistence for free: neutral null models for multistrain pathogens

In most pathogens, multiple strains are maintained within host populations. Quantifying the mechanisms underlying strain coexistence would aid public health planning and improve understanding of disease dynamics. We argue that mathematical models of strain coexistence, when applied to indistinguishable strains, should meet criteria for both ecological neutrality and population genetic neutrality. We show that closed clonal transmission models which can be written in an "ancestor-tracing" form that meets the former criterion will also satisfy the latter. Neutral models can be a parsimonious starting point for studying mechanisms of strain coexistence; implications for past and future studies are discussed.

Mimics and magnets: the importance of color and ecological facilitation in floral deception

Plants that lack floral rewards can attract pollinators if they share attractive floral signals with rewarding plants. These deceptive plants should benefit from flowering in close proximity to such rewarding plants, because pollinators are locally conditioned on floral signals of the rewarding plants (mimic effect) and because pollinators are more abundant close to rewarding plants (magnet effect). We tested these ideas using the non-rewarding South African plant Eulophia zeyheriana (Orchidaceae) as a study system. Field observations revealed that E. zeyheriana is pollinated solely by solitary bees belonging to a single species of Lipotriches (Halictidae) that appears to be closely associated with the flowers of Wahlenbergia cuspidata (Campanulaceae), a rewarding plant with which the orchid is often sympatric. The pale blue color of the flowers of E. zeyheriana differs strongly from flowers of its congeners, but is very similar to that of flowers of W. cuspidata. Analysis of spectral reflectance patterns using a bee vision model showed that bees are unlikely to be able to distinguish the two species in terms of flower color. A UV-absorbing sunscreen was applied to the flowers of the orchid in order to alter their color, and this resulted in a significant decline in pollinator visits, thus indicating the importance of flower color for attraction of Lipotriches bees. Pollination success in the orchid was strongly affected by proximity to patches of W. cuspidata. This was evident from one of two surveys of natural populations of the orchid, as well as experiments in which we translocated inflorescences of the orchid either into patches of W. cuspidata or 40 m outside such patches. Flower color and location of E. zeyheriana plants relative to rewarding magnet patches are therefore key components of the exploitation by this orchid of the relationship between W. cuspidata and Lipotriches bee pollinators.

Virulence evolution in response to vaccination: the case of malaria

One theory of why some pathogens are virulent (i.e., they damage their host) is that they need to extract resources from their host in order to compete for transmission to new hosts, and this resource extraction can damage the host. Here we describe our studies in malaria that test and support this idea. We go on to show that host immunity can exacerbate selection for virulence and therefore that vaccines that reduce pathogen replication may select for more virulent pathogens, eroding the benefits of vaccination and putting the unvaccinated at greater risk. We suggest that in disease contexts where wild-type parasites can be transmitted through vaccinated hosts, evolutionary outcomes need to be considered.

Of mice and men: asymmetric interactions between Bordetella pathogen species

In a recent experiment, we found that mice previously infected with Bordetella pertussis were not protected against a later infection with Bordetella parapertussis, while primary infection with B. parapertussis conferred cross-protection. This challenges the common assumption made in most mathematical models for pathogenic strain dynamics that cross-immunity between strains is symmetric. Here we investigate the potential consequences of this pattern on the circulation of the two pathogens in human populations. To match the empirical dominance of B. pertussis, we made the additional assumption that B. parapertussis pays a cost in terms of reduced fitness. We begin by exploring the range of parameter values that allow the coexistence of the two pathogens, with or without vaccination. We then track the dynamics of the system following the introduction of anti-pertussis vaccination. Our results suggest that (1) in order for B. pertussis to be more prevalent than B. parapertussis, the former must have a strong competitive advantage, possibly in the form of higher infectivity, and (2) because of asymmetric cross-immunity, the introduction of anti-pertussis vaccination should have little effect on the absolute prevalence of B. parapertussis. We discuss the evidence supporting these predictions, and the potential relevance of this model for other pathogens.

Short report: rare Plasmodium falciparum merozoite surface protein 1 19-kda (msp-1(19)) haplotypes identified in Mali using high-throughput genotyping methods

Genetic diversity in malaria vaccine antigens may compromise malaria vaccine efficacy, so it is important to understand this diversity and the processes that generate it. By applying new high-throughput genotyping methods to a large sample of infections from Mali (N = 1369), seven new 19-kDa merozoite surface protein 1 (MSP-1(19)) haplotypes were identified. Herein we report the sequences of these new haplotypes and discuss their possible origins. Although they are present in < 1% of the samples examined, the existence of these rare haplotypes reveals a greater degree of diversity at this locus than previously reported and highlights the potential for Plasmodium to evolve under selective pressure from the immune system and from such interventions as vaccines and drugs.

Vaccination and the dynamics of immune evasion

Vaccines exert strong selective pressures on pathogens, favouring the spread of antigenic variants. We propose a simple mathematical model to investigate the dynamics of a novel pathogenic strain that emerges in a population where a previous strain is maintained at low endemic level by a vaccine. We compare three methods to assess the ability of the novel strain to invade and persist: algebraic rate of invasion; deterministic dynamics; and stochastic dynamics. These three techniques provide complementary predictions on the fate of the system. In particular, we emphasize the importance of stochastic simulations, which account for the possibility of extinctions of either strain. More specifically, our model suggests that the probability of persistence of an invasive strain (i) can be minimized for intermediate levels of vaccine cross-protection (i.e. immune protection against the novel strain) and (ii) is lower if cross-immunity acts through a reduced infectious period rather than through reduced susceptibility.

Host intra-clutch variation, cuckoo egg matching and egg rejection by great reed warblers

Prevailing theory predicts that lower levels of intra-clutch variation in host eggs facilitate the detection of brood parasitism. We assessed egg matching using both human vision and UV-VIS spectrophotometry and then followed the nest fate of great reed warblers naturally parasitised by European cuckoos. Rejection was predicted by the following three variables: matching between cuckoo and host eggs on the main chromatic variable defined by principal components analysis of the egg spectra (which has a strong loading in the UV); the number of host eggs in the nest; and human estimates of intra-clutch variation. The first variable is not correlated to human estimates of matching, which do not predict rejection. In line with another recent study, rejection rates were predicted by higher levels of intra-clutch variation in the host eggs, suggesting that higher rather than lower levels of intra-clutch variation can facilitate the discrimination of cuckoo eggs by hosts. We suggest that the importance of intra-clutch variation is context dependent, with intra-clutch variation being important when there is good matching between the host and the cuckoo eggs. Our results also suggest that both spectrometric and human visual assessments of egg matching and intra-clutch variation are prudent: the former provide the best method of estimating reflectance variation, whereas the latter include some assessment of patterns of maculation.

The transmission and control of mastitis in dairy cows: A theoretical approach

A multi-species model that incorporates the transmission of both major and minor mastitis pathogens as well as the interaction between them via coinfection of a quarter is fitted to data from seven dairy herds. The results suggest that major and minor pathogens can interact, on occasion, in a counter-intuitive way with implications for the control of clinical mastitis. The key finding is that delaying culling of cows with major pathogen infections for more than 100 days post infection could result in a higher prevalence of major pathogen infections, whereas early culling would reduce the levels. A theoretical exploration of current and proposed control strategies is carried out, informed by parameters estimated from the model and data. The results at each stage suggest of areas of further research such as: field-testing of the hypotheses presented; the exploration of a stochastic formulation of the model; analysis of the raw repeated measures data; application of control theory to determine the most effective combination of control strategies; inclusion of economic factors into the modelling framework.

AGE-DEPENDENT EPIDEMIOLOGICAL PATTERNS AND STRAIN DIVERSITY IN HELMINTH PARASITES

Field studies of schistosomes and the major intestinal nematodes Trichuris trichiura and Ascaris lumbricoides repeatedly demonstrate that the intensity and prevalence of infection exhibit marked dependency on host age. Peak levels of infection typically occur in hosts aged between 10 and 14 yr in endemically infected communities. It has widely been assumed that the slow acquisition of resistance in adults is caused by repeated exposure to the same antigenic repertoire of a single parasite strain. Consequently, these empirical patterns have previously been taken to suggest that human immunity to helminth parasites confers poor protection against reinfection. Here, an alternative explanation is suggested on the basis of results from a simplified model of helminth transmission. It is proposed that the empirical observations can be attributed to the circulation of multiple helminth strains that each elicit highly protective immunity. If this hypothesis is correct, estimates of epidemiological parameters from field data and the potential for control of helminth diseases might require reevaluation.

Mathematical models of vaccination

Mathematical models of epidemics have a long history of contributing to the understanding of the impact of vaccination programmes. Simple, one-line models can predict target vaccination coverage that will eradicate an infectious agent, whilst other questions require complex simulations of stochastic processes in space and time. This review introduces some simple ordinary differential equation models of mass vaccination that can be used to address important questions about the predicted impact of vaccination programmes. We show how to calculate the threshold vaccination coverage rate that will eradicate an infection, explore the impact of vaccine-induced immunity that wanes through time, and study the competitive interactions between vaccine susceptible and vaccine resistant strains of infectious agent.

Imperfect vaccines and the evolution of pathogen virulence

Vaccines rarely provide full protection from disease. Nevertheless, partially effective (imperfect) vaccines may be used to protect both individuals and whole populations. We studied the potential impact of different types of imperfect vaccines on the evolution of pathogen virulence (induced host mortality) and the consequences for public health. Here we show that vaccines designed to reduce pathogen growth rate and/or toxicity diminish selection against virulent pathogens. The subsequent evolution leads to higher levels of intrinsic virulence and hence to more severe disease in unvaccinated individuals. This evolution can erode any population-wide benefits such that overall mortality rates are unaffected, or even increase, with the level of vaccination coverage. In contrast, infection-blocking vaccines induce no such effects, and can even select for lower virulence. These findings have policy implications for the development and use of vaccines that are not expected to provide full immunity, such as candidate vaccines for malaria.

Meiotic recombination, cross-reactivity, and persistence in Plasmodium falciparum

We incorporate a representation of Plasmodium falciparum recombination within a discrete-event model of malaria transmission. We simulate the introduction of a new parasite genotype into a human population in which another genotype has reached equilibrium prevalence and compare the emergence and persistence of the novel recombinant forms under differing cross-reactivity relationships between the genotypes. Cross-reactivity between the parental (initial and introduced) genotypes reduces the frequency of appearance of recombinants within three years of introduction from 100% to 14%, and delays their appearance by more than a year, on average. Cross-reactivity between parental and recombinant genotypes reduces the frequency of appearance to 36% and increases the probability of recombinant extinction following appearance from 0% to 83%. When a recombinant is cross-reactive with its parental types, its probability of extinction is influenced by cross-reactivity between the parental types in the opposite manner; that is, its probability of extinction after appearance decreases. Frequencies of P. falciparum outcrossing are mediated by frequencies of mixed-genotype infections in the host population, which are in turn mediated by the structure of cross-reactivity between parasite genotypes. The three leading hypotheses about how meiosis relates to oocyst production lead to quantitative, but no qualitative, differences in these results.

Acquisition of new capsular genes among clinical isolates of antibiotic-resistant Streptococcus pneumoniae

Antibiotic-resistant clones of Streptococcus pneumoniae are recognizable through a combination of unique molecular, microbiological, and serological properties. In the course of surveillance of epidemic clones of S. pneumoniae, several isolates were identified that shared the clone-specific pulsed-field gel electrophoretic (PFGE) pattern and antibiotype but expressed serotypes atypical for the particular clone. A selected group of isolates belonging to the Spanish/USA clone but expressing serotypes 19, 14, or 3, instead of the expected serotype 23F, were tested using DNA probes for each of the 18 open reading frames (ORFs) of the 23F capsular locus. In no case were there any 23F-specific genes retained, with the possible exception of genes already known to be common to the capsular loci involved. Analysis of the sequence of the capsular locus of a penicillin-resistant serotype 23F isolate from Mexico showed that part of the cpsA gene of this strain, as well as genes cpsQ and cpsR, had high degrees of identity to the sequence of the homologous genes in isolates expressing serotype 19F. The capsular locus of this Mexican strain may have originated from an in vivo capsular switch event in which the original 19F locus was replaced by 23F-specific capsular genes.

Sex allocation and population structure in apicomplexan (protozoa) parasites

Establishing the selfing, rate of parasites is important for studies in clinical and epidemiological medicine as well as evolutionary biology Sex allocation theory offers a relatively cheap and easy way to estimate selfing rates in natural parasite populations. Local mate competition (LMC) theory predicts that the optimal sex ratio (r*; defined as proportion males) is related to the selfing rate (s) by the equation r* = (1-s)/2. In this paper, we generalize the application of sex allocation theory across parasitic protozoa in the phylum Apicomplexa. This cosmopolitan phylum consists entirely of parasites, and includes a number of species of medical and veterinary importance. We suggest that LMC theory should apply to eimeriorin intestinal parasites. As predicted, data from 13 eimeriorin species showed a female-biased sex ratio, with the sex ratios suggesting high levels of selfing (0.8-1.0). Importantly, our estimate of the selfing rate in one of these species, Toxoplasma gondii, is in agreement with previous genetic analyses. In contrast, we predict that LMC theory will not apply to the groups in which syzygy occurs (adeleorins, gregarines and piroplasms). Syzygy occurs when a single male gametocyte and a single female gametocyte pair together physically or in close proximity, just prior to fertilization. As predicted, data from four adeleorin species showed sex ratios not significantly different from 0.5.

Population structure of pathogens: the role of immune selection

Sunetra Gupta and Roy Anderson discuss how the balance between host immune responses against conserved and variable antigens shapes the population structure of pathogens. At one extreme, immune selection against polymorphic determinants can cause pathogen populations to self-organize spontaneously into discrete antigenic types that may either be maintained over long periods or undergo cyclical or chaotic fluctuations. At the other extreme, diversity may be drastically reduced by competition induced by a strong immune response against a conserved determinant. Where does each pathogen lie along this continuum? How would this knowledge influence our attempts to control an infectious disease?

Population biology, evolution, and infectious disease: convergence and synthesis

Traditionally, the interest of population and evolutionary biologists in infectious diseases has been almost exclusively in their role as agents of natural selection in higher organisms. Recently, this interest has expanded to include the genetic structure and evolution of microparasite populations, the mechanisms of pathogenesis and the immune response, and the population biology, ecology, and evolutionary consequences of medical and public health interventions. This article describes recent work in these areas, emphasizing the ways in which quantitative, population-biological approaches have been contributing to the understanding of infectious disease and the design and evaluation of interventions for their treatment and prevention.

Vaccine design, evaluation, and community-based use for antigenically variable infectious agents

A major challenge for vaccine design and development, and for trials of new vaccines, is to tackle antigenically variable infectious agents. Here we outline a few general conceptual issues and then discuss new frameworks that are being developed to help understand how vaccination might change the distribution, abundance, and type of strains in a population. Herd Immunity is a key concept in population-based immunisation programmes and has to be considered in vaccine design and use even though it may cause a conflict between the needs of the individual versus those of the community. This issue is of increasing importance since once common infections are becoming rare due to effective vaccination. Concomitantly, adverse effects arising from immunisation are becoming more apparent as infection-induced morbidity declines to very low levels. Efficacy is widely regarded as a key criterion in vaccine design but duration of protection is of equal importance. Whether it is possible to produce effective vaccines to antigenically diverse pathogens remains uncertain but progress towards this goal will be enhanced by a better understanding of the population genetics of the target infectious agent facilitated by molecular epidemiological studies to assess the genetic constitution of pathogen populations and changes therein over time.