Biology subjects

Neher, R.

Publications and source records attributed to Neher, R..

At least 19 recordsLinked to original sources

bioRxiv2025

Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment

The ongoing panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses is the largest in history, with unprecedented transmission to multiple mammalian species. Avian influenza A viruses of the H5 subtype circulate globally among birds and are classified into distinct clades based on their hemagglutinin (HA) genetic sequences. Thus, the ability to accurately and rapidly assign clades to newly sequenced isolates is key to surveillance and outbreak response. Co-circulation of endemic, low pathogenic avian influenza (LPAI) A(H5) lineages in North American and European wild birds necessitates the ability to rapidly and accurately distinguish between infections arising from these lineages and epizootic HPAI A(H5) viruses. However, currently available clade assignment tools are limited and often require command line expertise, hindering their utility for public health surveillance labs. To address this gap, we have developed datasets to enable A(H5) clade assignments with Nextclade, a drag-and-drop tool originally developed for SARS-CoV-2 genetic clade classification. Using annotated reference datasets for all historical A(H5) clades, clade 2.3.2.1 descendants, and clade 2.3.4.4 descendants provided by the Food and Agriculture Organization/World Health Organization/World Organisation for Animal Health (FAO/WHO/WOAH) H5 Working Group, we identified clade-defining mutations for every established clade to enable tree-based clade assignment. We then created three Nextclade datasets which can be used to assign clades to A(H5) HA sequences and call mutations relative to reference strains through a drag-and-drop interface. Nextclade assignments were benchmarked with 19,834 unique sequences not in the reference set using a pre-released version of LABEL, a well-validated and widely used command line software. Prospective assignment of new sequences with Nextclade and LABEL produced very well-matched assignments (match rates of 97.8% and 99.1% for the 2.3.2.1 and 2.3.4.4 datasets, respectively). The all-clades dataset also performed well (94.8% match rate) and correctly distinguished between all HPAI and LPAI strains. This tool additionally allows for the identification of polybasic cleavage site sequences and potential N-linked glycosylation sites. These datasets therefore provide an alternative, rapid method to accurately assign clades to new A(H5) HA sequences, with the benefit of an easy-to-use browser interface.

bioinformatics↗

bioRxiv2023

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016.

Mpox is often described as being endemic in West and Central Africa as a zoonotic disease that transmits through contact with the reservoir rodent host, likely a species of African squirrel. In May 2022, human cases of Mpox were detected spreading internationally beyond countries with known endemic reservoirs. At time of writing, 84,700 confirmed cases have been reported in 110 countries. When the first cases from 2022 were sequenced, it was seen that they shared 42 single nucleotide differences from the closest mpox virus (MPXV) genome sampled in 2018. This number of changes within 3-4 years is unexpectedly large and points to a much greater evolutionary rate than expected for a poxvirus. Strikingly, most nucleotide changes are of a specific type - a dinucleotide change from TC->TT or its reverse complement GA->AA. This mutation type is characteristic of the action of APOBEC3 deaminases; host-enzymes with reported antiviral function. Analysis of MPXV genomes sampled from 2017 to 2022 showed further evidence of TC->TT mutation pattern enrichment, with 93% of transmitted single nucleotide mutations since 2017 consistent with APOBEC3 editing. Assuming APOBEC-editing is characteristic of MPXV infection in human hosts, we propose an APOBEC clock that - at a rate of ~6 APOBEC3 mutations per year - estimates MPXV has been circulating in humans since 2016. This evolutionary pattern of host-enzyme editing has implications for the longer-term fitness of the virus in this epidemic as such mechanisms are primarily antiviral in function, but in the context of a poxvirus also provide a source of variation that may conceivably facilitate adaptation.

evolutionary biology↗

bioRxiv2022

PanGraph: scalable bacterial pan-genome graph construction

The genomic diversity of microbes is commonly parameterized as single nucleotide polymorphisms relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the wide-spread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. Traditional computational approaches towards whole-genome analysis either scale poorly with the number of genomes, or treat genomes as dissociated "bags of genes", and thus are not suited for this new era. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as an undirected path along vertices, which in turn, encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into a several common formats for either downstream analysis or immediate visualization.

bioinformatics↗

bioRxiv2022

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates

HIV-1 is a rapidly evolving virus able to evade host immunity through rapid adaptation during chronic infection. The HIV-1 group M has diversified since its zoonosis into several subtypes at a rate of the order of 10-3 changes per site per year. This rate varies between different parts of the genome and its inference is sensitive to the time scale and diversity spanned by the sequence data used. Higher rates are estimated on short time scales and particularly for within-host evolution, while rate estimates spanning decades or the entire HIV-1 pandemic tend to be lower. The underlying causes of this difference are not well understood. We investigate here the role of rapid reversions toward a preferred evolutionary sequence state on multiple time scales. We show that within-host reversion mutations are under positive selection and contribute substantially to sequence turnover, especially at conserved sites. We then use the rates of reversions and non-reversions estimated from longitudinal within-host data to parametrize a phylogenetic sequence evolution model. Sequence simulation of this model on HIV-1 phylogenies reproduces diversity and apparent evolutionary rates of HIV-1 in gag and pol, suggesting that a tendency to rapidly revert to a consensus-like state can explain much of the time dependence of evolutionary rate estimates in HIV-1.

evolutionary biology↗

bioRxiv2021

TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses

When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortments events from viral sequence data, little is known about its role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.

bioinformatics↗

bioRxiv2020

Limited predictability of amino acid substitutions in seasonal influenza viruses

Seasonal influenza viruses repeatedly infect humans in part because they rapidly change their antigenic properties and evade host immune responses, necessitating frequent updates of the vaccine composition. Accurate predictions of strains circulating in the future could therefore improve the vaccine match. Here, we studied the predictability of frequency dynamics and fixation of amino acid substitutions. Current frequency was the strongest predictor of eventual fixation, as expected in neutral evolution. Other properties, such as occurrence in previously characterized epitopes or high Local Branching Index (LBI) had little predictive power. Parallel evolution was found to be moderately predictive of fixation. While the LBI had little power to predict frequency dynamics, it was still successful at picking strains representative of future populations. The latter is due to a tendency of the LBI to be high for consensus-like sequences that are closer to the future than the average sequence. Simulations of models of adapting populations, in contrast, show clear signals of predictability. This indicates that the evolution of influenza HA and NA, while driven by strong selection pressure to change, is poorly described by common models of directional selection such as travelling fitness waves.

evolutionary biology↗

bioRxiv2020

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence-only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.

evolutionary biology↗

bioRxiv2020

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within host. They also suggest new avenues for improving influenza control.

evolutionary biology↗

bioRxiv2020

Complementation can maintain a quasispecies of drug sensitive and resistant HIV

HIV exists as multiple genotypes in a single infected individual referred to as a quasispecies. Here we reproduced a quasispecies by moderate selective pressure using an HIV reverse transcriptase inhibitor. The drug resistant genotype never completely supplanted the drug sensitive genotype, which stabilized at about 20 percent of viral sequences. Single-cell sequencing showed that resistant genotype frequency plateaued when cells were co-infected with sensitive and resistant genotypes, suggesting a sharing of viral proteins in co-infected cells (complementation) which masks genotypic differences. To test if complementation can confer phenotypic drug resistance, we co-transfected fluorescently labelled molecular clones of sensitive and resistant HIV and observed that genotypically sensitive virus from co-transfected cells was drug resistant. Resistant virus preferentially infected cells in tandem with drug sensitive HIV, explaining how co-infections of sensitive and resistant genotypes were initiated. Modelling this effect, we observed that a stable quasispecies could form at the experimental multiplicities of infection for the drug resistant and drug sensitive virus, showing that complementation can lead to a quasispecies in an HIV evolution experiment.

evolutionary biology↗

bioRxiv2020

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of viral pathogens within cities is crucial for effective prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic determinants of influenza transmission in a European city. We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed annually re-occurring geographic clusters of influenza incidences, mainly associated with net income, and independent of population density and living space. Vaccination against influenza was also mainly associated with household income and was linked to the likelihood of influenza-like illness within an urban quarter. Transmissions patterns within and between quarters were complex. High-resolution city-level epidemiological studies combined with social science surveys such as this will be essential for understanding seasonal and pandemic transmission chains and delivering tailored public health information and vaccination programs at the municipal level.

microbiology↗

bioRxiv2020

Efficient inference, potential, and limitations of site-specific substitution model

Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states or only change in concert with other sites. Most commonly used evolutionary models, however, ignore much of this complexity and at best account for variation in the rate at which different sites change. Here, we present an efficient algorithm to estimate more complex models that allow for site-specific preferences and explore the accuracy at which such models can be estimated from simulated data. We find that an iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences. Ignoring site-specific preferences during estimation of branch length of phylogenetic trees - an assumption of most phylogeny software - results in substantial underestimation comparable to the error incurred when ignoring rate variation. However, the joint estimation of branch lengths, site-specific rates, and site-specific preferences can suffer from identifiability problems and is typically unable to recover the correct branch lengths. Site-specific preferences estimated from large HIV pol alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of site-specific HIV substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.

evolutionary biology↗

bioRxiv2019

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

This report details current seasonal influenza circulation patterns as of August 2019 and makes projections up to September 2020 to coincide with selection of the 2020 Southern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that weve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu/nextstrain pipeline [1,2] with continual updates posted to nextstrain.org/flu. A/H3N2: A/H3N2 viruses continue to show substantial diversity in HA sequences with a deep split between 3c3.A and 3c2.A1b viruses. The most notable recent developments are the rapid rise of clade A1b/137F - a subclade of A1b/135K - in China and Bangladesh and clade A1b/197R - a subclade of A1b/131K - which dominates the ongoing season in Australia. Our models predict that A1b/137F and A1b/197R will be the dominant clades next year with A1b/197R accounting for most circulation. There is, however, large uncertainty in the true extent of A1b/137F circulation. A/H1N1pdm: The S183P substitution has risen to near fixation. The most successful subclade carrying this mutation is 183P-5 which has essentially replaced competing variants. A variant with substitutions 129D/185I is at 60% prevalence globally, while a second variant with substitution 130N is at 50% in North America and ~10% elsewhere. Substitutions at site 156 to D or K have arisen sporadically and result in loss of recognition by antisera raised against viruses with asparagine at position 156. Despite the large antigenic effect, viruses with mutations at site 156 dont seem to spread. Beyond variants at site 156, little to no antigenic evolution is evident in assays with ferret antisera. B/Vic: Antigenically drifted deletion variants at HA1 sites 162, 163 and 164 are now dominating global circulation and have all but taken over. The double deletion variant V1A.1 had previously been circulating at high frequency in the Americas. However, over the course of 2009, the triple deletion variant V1A.3 has increased in frequency globally and is now dominating in all geographic regions. Importantly, V1A.1 and V1A.3 variants appear antigenically distinct by HI assays with 4-8 fold reductions in log2 titer in both directions. B/Yam: B/Yam has not circulated in large numbers since the Northern Hemisphere season 2017/2018 and displays relatively little amino acid variation in HA or antigenic diversity. Amino acid variants at sites 229 and 232 have begun to circulate and population is now split between 229D/232D, 229N/232D and 229D/232N variants. These variants show little sign of antigenic difference in HI assays.

evolutionary biology↗

bioRxiv2018

Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing

Carbapenemase-producing bacteria are resistant against almost all commonly used betalactam and cephalosporin antibiotics and represent a growing public health crisis. Carbapenemases reside predominantly in mobile genetic elements and rapidly spread across genetic backgrounds and species boundaries. Here, we report more than one hundred finished, high quality genomes of carbapenemase producing enterobacteriaceae, P. aeruginosa and A. baumannii sequenced with Oxford Nanopore and Illumina technologies. We developed a number of high-throughput criteria to assess the quality of fully assembled genomes for which curated references do not exist. Using this diverse collection of closed genomes and plasmids, we demonstrate rapid movement of carbapenemase between genomic neighborhoods, sequence types, and across species boundaries with distinct patterns for different carbapenemases. Lastly, we present evidence of multiple ancestral recombination events between different Enterobacteriaceae MLSTs. Taken together, our samples suggest a hierarchical picture of genomic variation produced by the evolution of carbapenemase producing bacteria that will require new models to adequately understand and track.

microbiology↗

bioRxiv2018

Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen

Rapidly evolving pathogens like influenza viruses can persist by accumulating antigenic novelty fast enough to evade the adaptive immunity of the host population, yet without continuous accumulation of genetic diversity. This dynamical state is often compared to the Red Queen evolving as fast as it can just to maintain its foothold in the host population: Accumulation of antigenic novelty is balanced by the build-up of host immunity. Such Red Queen States (RQS) of continuous adaptation in large rapidly mutating populations are well understood in terms of Traveling Wave (TW) theories of population genetics. Here we shall make explicit the mapping of the established Multi-strain Susceptible-Infected-Recovered (SIR) model onto the TW theory and demonstrate that a pathogen can persist in RQS if cross-immunity is long-ranged and its population size is large populations allowing for rapid adaptation. We then investigate the stability of this state focusing on the rate of extinction and the rate of \"speciation\" defined as antigenic divergence of viral strains beyond the range of cross-inhibition. RQS states are transient, but in a certain range of evolutionary parameters can exist for the time long compared to the typical time to the most recent common ancestor (TMRCA). In this range the steady TW is unstable and the antigenic advance of the lead strains relative to the typical co-circulating viruses tends to oscillate. This results in large fluctuations in prevalence that facilitate extinction. We shall demonstrate that the rate of TW fission into antigenically uncoupled viral populations is related to fluctuations of TMRCA and construct a \"phase diagram\" identifying different regimes of viral phylodynamics as a function of evolutionary parameters.

evolutionary biology↗

bioRxiv2018

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused widespread serious respiratory and neurological disease. To investigate diversity, spread, and evolution of EV-D68 we performed near full-length deep sequencing in 54 samples obtained in Sweden during the 2014 and 2016 outbreaks. In most samples, intrapatient variability was low and dominated by rare synonymous variants, but three patients showed evidence of dual infections with distinct EV-D68 variants from the same subclade. Interpatient evolution showed a very strong temporal signal, with an evolutionary rate of 0.0038{+/-}0.0001 substitutions per site and year. Phylogenetic trees reconstructed from the sequences suggest that EV-D68 was introduced into Stockholm several times during the 2016 outbreak and then spread locally. Putative neutralization targets in the BC- and DE-loops of the VP1 protein are slightly more diverse within-host and tend to undergo more frequent substitution than other genomic regions. However, evolution in these loops does not appear to have driven the emergence of the 2016 B3-subclade directly from the 2014 B1-subclade. Instead, the most recent ancestor of both clades was dated to 2009. The study provides a comprehensive description of the intra- and interpatient evolution of EV-D68, including the first report of intrapatient diversity and dual infections. The new data along with publicly available EV-D68 sequences are included in an interactive phylodynamic analysis on nextstrain.org/enterovirus/d68 to facilitate timely EV-D68 tracking in the future.xs

microbiology↗

bioRxiv2018

Real-time analysis and visualization of pathogen sequence data

The rapid development of sequencing technologies has to led to an explosion of pathogen sequence data that are increasingly collected as part of routine surveillance or clinical diagnostics. In public health, sequence data is used to reconstruct the evolution of pathogens, anticipate future spread, and target interventions. In clinical settings whole genome sequences identify pathogens at the strain level, can be used to predict phenotypes such as drug resistance and virulence, and inform treatment by linking to closely related cases. However, the vast majority of sequence data are only used for specific narrow applications such as typing. Comprehensive analysis of these data could provide detailed insight into outbreak dynamics, but is not routinely done since fast, robust, and interpretable analysis work-flows are not in place. Here, we review recent developments in real-time analysis of pathogen sequence data with a particular focus on visualization and integration of sequence and phenotypic data.

microbiology↗

bioRxiv2018

Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019

This report details current seasonal influenza circulation patterns as of Feb 2018 and makes projections up to Feb 2019 to coincide with selection of the 2018-2019 Northern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that weve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.\n\nA/H3N2: H3N2 diversity has largely been replaced by subclades A1b, A2 and A3 within 3c2.A. Subclades A1b and A2 predominate in the population and each shows increases in frequency, mutations at epitope sites and evidence for minor changes to antigenic phenotype. Clade A1b may be marginally fitter than clade A2, but we expect both clades to persist into the future without a clear immediate winner.\n\nA/H1N1pdm: A clade comprising mutations S74R, S164T and I295V has recently swept to fixation. The rapidity of this sweep suggests a selective origin. However, there is no evidence of antigenic change.\n\nB/Vic: Very little B/Vic activity has been observed in recent months. A clade with a two codon deletion at sites HA1:162/163 has gradually risen in frequency. HI measurements suggest an 8 to 16-fold titer drop relative to the vaccine strain, but this antigenic change has not yet resulted in a rapid rise of this variant.\n\nB/Yam: Europe experienced a strong and early B/Yam season in absence of amino acid variation in HA or antigenic diversity. However, several mutations in NA have rapidly swept or risen to intermediate frequencies.

evolutionary biology↗

bioRxiv2017

Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

This report details current seasonal influenza circulation patterns as of Sep 2017 and makes projections up to Sep 2018 to coincide with selection of the 2018 Southern Hemisphere vaccine strain. This is not meant as a comprehensive report, but is instead intended as particular observations that weve made that may be of relevance. Please also note that observed patterns reflect the GISAID database and may not be entirely representative of underlying dynamics. All analyses are based on the nextflu pipeline [1] with continual updates posted to nextflu.org.\n\nA/H3N2H3N2 continues to diversify with many coexisting clades, all of which carry several amino acid mutations at previously characterized epitope sites. The majority of viruses fall into the 3c2.a clade which has been dominating globally for >3 years, but 3c3.a viruses continue to persist. The common ancestor of circulating H3N2 viruses is now more than 5 years old, which is rare for H3N2. Despite extensive genetic diversity, serological assays suggest limited, but non-zero, antigenic evolution. We expect multiple competing clades within 3c2.a to persist into the future with no clear immediate winner.\n\nA/H1N1pdmA clade comprising mutations S74R and I295V has recently risen to >60% global frequency. Although it shows no antigenic distinction by ferret HI data, the rapidity of its rise suggests a selective origin.\n\nB/VicA clade with a two amino acid deletion 162-/163-has altered serological properties and is increasing in frequency, albeit slowly. Two other clades (carrying mutations K209N and V87A/I175V) have increased in frequency moderately.\n\nB/YamA clade comprising M251V within clade 3 viruses continues to dominate. The is little genetic differentiation within this clade and no evidence of antigenic evolution.

evolutionary biology↗