Biology subjects

Moncla, L. H.

Publications and source records attributed to Moncla, L. H..

16 recordsLinked to original sources

bioRxiv2026

H5N5 virus transmission is driven by repeated cross-Atlantic introductions and transmission among high latitude seabirds

In November 2025, the first global H5N5 infection was reported in a person in Washington State. Previously, these viruses had only been detected in seabirds and shorebirds near the Atlantic Ocean, suggesting potentially distinct ecology from dominant H5N1 strains. Using 354 global H5N5 genomes, we show that H5N5 viruses have been carried by high latitude seabirds and shorebirds across the Atlantic at least 9 times, with introductions more frequent in the fall and spring. We reconstruct a plausible path of cross-continental movement via Arctic or sub-Arctic regions, followed by a year of cryptic circulation prior to human spillover. These data show that H5N5 viruses have undergone far more intercontinental movements than previously recognized, and exhibit host and geographic patterns that are fundamentally distinct from dominant H5N1 lineages. The distinct host ecology, geography, and movement, paired with the capacity to infect a person, suggest that enhanced surveillance may be warranted.

evolutionary biology↗

bioRxiv2026

Host type governs influenza evolutionary strategy across reservoir and spillover hosts

Despite its high propensity for host switching, the evolutionary mechanisms underlying influenza host adaptation remain unclear. H3Nx influenza viruses are uniquely generalist, with long-term lineages that circulate in avian, human, swine, equine, and canine hosts. Using 13,295 H3Nx sequences, we quantified host-specific adaptive evolution and developed a pipeline to map reassortment events onto trees with measures of statistical uncertainty. We find that while H3Nx viruses in mammals undergo adaptive evolution in HA and NA, viruses in birds experience very little directional selection. Instead, avian lineages exhibit high rates of reassortment, frequently generating novel reassortant lineages that persist transiently and turn over rapidly. 29.8-47.4% of all avian reassortant lineages are purged within the first year of circulation, and reassortment shows no fitness benefit in birds. In contrast, reassorted lineages in swine are more likely to persist long-term, suggesting that reassortment in swine may be broadly beneficial. Segment-specific reassortment patterns were also distinct between avian and mammalian viruses, with NA reassorting more frequently than expected in birds, but less frequently than expected in swine. Reassortment events are enriched between mammalian, but not avian, host switches, suggesting that reassortment may be most beneficial for mediating host switches among mammalian species. Together, our data suggest that host differences drive fundamentally different evolutionary outcomes for influenza viruses, transitioning from reassortment-dominant evolution in their avian reservoir, to varying degrees of adaptation upon establishment in mammals.

evolutionary biology↗

bioRxiv2026

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens of human spillovers. National surveillance strategies generally provide only a single representative sequence per poultry outbreak, precluding fine-scale geographic transmission inference or studies of within-outbreak evolution. We produced high-quality deep sequence data from 46 infected Galliformes and Anseriformes sampled from commercial farm and live bird market (LBM) outbreaks in Pennsylvania from 2023-2025. We found that H5N1 viruses were introduced into Pennsylvania at least 68 independent times. We recover independent origins of live bird market outbreaks within the same county 3 weeks apart, and transmission between Pennsylvania LBM and New York commercial birds, suggesting high transmission risk within the Northeast live bird market distribution system. Analyses of within-farm variant populations show frequent variant sharing between samples from the same outbreak, suggesting that variants are propagated among epidemiologically linked infections. We identified 9 known adaptive mutations in these samples, including one instance of PB2 D701N in a LBM chicken sample, suggesting that while rare, concerning mammalian adaptive mutations can be present within these domestic outbreaks. Our data suggest that domestic bird outbreaks support high circulating diversity and wide transmission bottlenecks, increasing the risk of minority variants arising and propagating between infections. These data can help inform targeted biosecurity measures and better quantify the risk of viral adaptation during agricultural outbreaks.

genomics↗

bioRxiv2026

Frequent seasonal reassortment between high and low path viruses drives the diversification of influenza A/H5N1

Since 2021, highly pathogenic (HPAI) H5N1 viruses have spread across the Americas, diversifying via reassortment into new genotypes that have spilled into humans and livestock, raising fears of a new influenza pandemic. Pandemic lineages are typically associated with reassortment, but we currently have limited understanding of where and when reassortment is expected to occur, which limits our ability to assess pandemic risks. Using a dataset of 9,052 full-genome sequences, we show that reassortment and novel genotype formation are associated with seasonal variation in low pathogenicity avian influenza (LPAI) cases and with the spatial and host distributions of viral transmission. We pinpoint ducks, geese, and the Central flyway as frequent sources of new genotypes, and show that reassortment rates vary seasonally, driven by mixing between high- and low-pathogenicity viruses. Cattle spillover genotypes (B3.13 and D1.1) evolved during periods of high reassortment, implicating reassortment as a common occurrence in lineages evolving during particular time periods. Together, these findings reframe reassortment as a predictable ecological process, with direct implications for how surveillance and pandemic risk assessment should be designed.

evolutionary biology↗

bioRxiv2026

Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens

MotivationGenome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide near real-time insight into these dynamics. ResultsNextstrain provides continually updated real-time genomic surveillance for 21 viruses and the bacterial pathogen Mycobacterium tuberculosis, with most analyses relying solely on open sequence data. Each pathogen includes steps to fetch and curate open data, classify sequences using established nomenclature systems, perform phylogenetic analyses, and share the results publicly. These analyses are automated, with most running daily to provide continually updated snapshots of pathogen evolution. Availability and ImplementationAll source code is available at https://github.com/nextstrain. Phylogenetic results can be visualized and downloaded at https://nextstrain.org/pathogens, and open sequence data and curated metadata are available at https://nextstrain.org/pathogens/files.

bioinformatics↗

bioRxiv2026

Dynamics and control of highly pathogenic H5 avian influenza in a threatened pelican population

The ongoing epizootic of highly pathogenic avian influenza (HPAI) continues to cause massive deaths in wildlife. Fundamental understanding of its disease ecology in natural populations is urgently needed. This knowledge has been hindered by the difficulty of acquiring data on epidemic dynamics. Here, using data collected from a threatened population of Dalmatian pelicans (Pelecanus crispus), we recover the epidemiological and evolutionary history of one of the largest HPAI wildlife mortality events. The results show that this devastating outbreak was likely seeded by a single introduction associated with movement of the species. By estimating epidemiological features of two consecutive outbreaks in the same population, we show that panzootic H5N1 since 2022 likely exhibits higher transmissibility and longer shedding time in non-reservoir birds, compared to previous H5NX subtypes. We also evaluate effectiveness of past and future control measures: carcass removal during the outbreak is shown to have surprisingly little impact on mitigating the mortality; and current H5 vaccines relying on capture and injection to deliver cannot establish herd immunity in a wildlife population. The results provide the first field evidence supporting the hypothesis that viral fitness difference of H5N1 to previous H5NX subtypes is the key cause of the expanded epizootic and panzootic since 2022, and on highly debated HPAI management strategies in wildlife populations. Author SummarySince late 2021, a panzootic of H5N1 highly pathogenic avian influenza (HPAI) has caused unprecedented mass mortality in wildlife. Many severely affected species are critical for ecosystem functions, including several threatened and endangered species. However, fundamental knowledge of HPAI disease ecology in natural populations is still lacking, and the effectiveness of potential controls is under debate. Here, using data collected from one of the largest HPAI outbreak in wild animals - over 1700 deaths (80% of the population) in a threatened population of Dalmatian pelicans in Greece, for the first time we recover the transmission dynamics of H5N1 in a migratory bird population. Based on the recovered dynamics, we show that removing carcasses during the outbreak was surprisingly ineffective, and future potential vaccination would require a novel delivery method to establish population immunity in wildlife. Our study provides new insight in the epidemiology of HPAI clade 2.3.4.4b in wildlife, and provides a foundation for assessing interventions within this complicated system.

ecology↗

bioRxiv2025

Fatal Human H3N8 Influenza Virus has a Moderate Pandemic Risk

In China, low pathogenic avian influenza (LPAI) H3N8 virus is widespread among chickens and has recently caused three zoonotic infections, with the last one in 2023 being fatal. Here we evaluated the relative pandemic risk of this 2023 zoonotic H3N8 influenza virus, utilizing our previously published decision tree. Serological analysis indicated that a large proportion of the human population does not have any cross-neutralizing antibodies against this H3N8 strain. LPAI H3N8 displayed a dual affinity for 2-3 and 2-6 sialic acids and replicated efficiently in human bronchial epithelial cells. Furthermore, we observed H3N8 transmission via direct contact but not aerosols to ferrets with pre-existing H3N2 immunity. Although pre-existing H3N2 immunity resulted in a shortened disease course in ferrets, it did not reduce disease severity or replication in the respiratory tract. This study suggests that this zoonotic H3N8 strain has moderate pandemic potential and emphasizes the continued need for avian influenza surveillance.

microbiology↗

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↗

bioRxiv2024

Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America

Since late 2021, a panzootic of highly pathogenic H5N1 has devastated wild birds, agriculture, and mammals. Analysis of 1,818 Hemagglutinin sequences from wild birds, domestic birds and mammals revealed that the North American panzootic was driven by [~]9 introductions into the Atlantic and Pacific Flyways, followed by rapid dissemination via wild, migratory birds. Transmission was primarily driven by Anseriformes, while non-canonical species acted as dead-end hosts. Unlike the epizootic of 2015, outbreaks in domestic birds were driven by [~]46-113 independent introductions from wild birds that persisted for up to 6 months. Backyard birds were infected [~]9 days earlier on average than commercial poultry, suggesting potential as "early warning signals" for transmission upticks. We find that wild birds are an emerging source of H5N1 in North America, necessitating enhanced, continuous surveillance. Prevention of agricultural outbreaks may now require novel strategies that reduce transmission at the wild bird/agriculture interface.

ecology↗

bioRxiv2024

Pre-existing H1N1 immunity reduces severe disease with bovine H5N1 influenza virus

The emergence of highly pathogenic H5N1 avian influenza in dairy cattle herds across the United States has caused multiple mild human infections. There is an urgent need to understand the risk of spillover into humans. Here, we show that pre-existing immunity from the 2009 H1N1 pandemic influenza virus provided protection from mortality and severe clinical disease to ferrets intranasally infected with bovine H5N1. H1N1 immune ferrets exhibited a differential tissue tropism with little bovine H5N1 viral dissemination to organs outside the respiratory tract and significantly less H5N1 virus found in nasal secretions and the respiratory tract. Additionally, ferrets with H1N1 prior immunity produced antibodies that cross-reacted with H5N1 neuraminidase protein. Taken together, these results suggest that mild disease in humans may be linked to prior immunity to human seasonal influenza viruses.

microbiology↗

bioRxiv2024

The Evolution and Epidemiology of H3N2 Canine Influenza Virus After 20 Years in Dogs

The H3N2 canine influenza virus (CIV) emerged from an avian reservoir in Asia around 2004. As the virus has now been circulating entirely among dogs for 20 years, we here update our understanding of the evolution of virus in its new host. As a host-switched virus, H3N2 CIV will also reveal any host-adaptive changes arising during thousands of infections within its new host, and our analysis showed that the virus has evolved at a constant rate. CIV was first introduced into North America in 2015 from Korea, and we specifically examined the epidemiology of the virus among dogs in North America since then, including local outbreaks, regional die-outs, and repeated reintroduction from Asia. The H3N2 CIV now appears endemic only in China after dying out in South Korea around 2017. Virus lineages circulating in China appear to have seeded the most recent US outbreaks - with 2 or 3 introductions into North America during the past 3 years. Combining clinical reports, diagnostic testing data, and analysis of viral genomes we show that the virus spreads rapidly among dogs in kennels and shelters in different regions - likely dying out locally after all those animals become infected and immune. The overall epidemic therefore requires longer-distance dispersal of virus to initiate outbreaks in new locations. Patterns of spread in the USA may select viruses most adapted to those dense populations, which may lack the properties required for efficient long-distance transfers to other dog populations that would keep the virus in prolonged circulation. IMPORTANCEViruses occasionally jump into new hosts to cause epidemics and may spread widely due to movement of humans or animals, or their viruses, with profound consequences for global health. The emergence and epidemiology of new epidemic viruses in companion animals provides a model for understanding disease dynamics and evolution. The H3N2 canine influenza virus arose from an avian virus, and infected dogs provide many opportunities for human exposure. H3N2 CIV transmission is dominated by fast-moving outbreaks within dense populations in animal shelters or kennels, while sustaining the epidemic likely requires movement of virus to more distant dog populations. Viral spread within North Americahas only been sustained for a few years at a time after which the virus dies out. The epidemiological and evolutionary dynamics of this virus in this structured host population shows how an acute respiratory pathogen can emerge and spread in a new host and population.

microbiology↗

bioRxiv2024

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

H5 influenza is a potential pandemic threat. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to pandemic risk, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. Here we use pseudovirus deep mutational scanning to measure how all mutations to a clade 2.3.4.4b H5 HA affect each phenotype. We identify mutations that allow HA to better bind 2-6-linked sialic acids, and show that some viruses already carry mutations that stabilize HA. We also identify recent viral strains with reduced neutralization to sera elicited by candidate vaccine virus. Overall, the systematic nature of deep mutational scanning combined with the safety of pseudoviruses enables comprehensive characterization of mutations to inform surveillance of H5 influenza.

microbiology↗

bioRxiv2021

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

The recent emergence of divergent SARS-CoV-2 lineages has raised concerns about the role of selection within individual hosts in propagating novel variants. Of particular concern are variants associated with immune escape and/or enhanced transmissibility. Though growing evidence suggests that novel variants can arise during prolonged infections, most infections are acute. Understanding the extent to which variants emerge and transmit among acutely infected hosts is therefore critical for predicting the pace at which variants resistant to vaccines or conferring increased transmissibility might emerge in the majority of SARS-CoV-2 infections. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely infected individuals. We find that within-host diversity during acute infection is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household. Accordingly, we also find that within-host variants are rarely detected along phylogenetically linked infections in the broader community. Together, these findings suggest that efficient selection and transmission of novel SARS-CoV-2 variants is unlikely during typical, acute infection. One Sentence SummaryPatterns of SARS-CoV-2 within hosts suggest efficient selection and transmission of novel variants is unlikely during typical, acute infection.

evolutionary biology↗

bioRxiv2019

Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia

Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses. Author summaryH5N1 avian influenza viruses can cross species barriers and cause severe disease in humans. H5N1 viruses currently cannot replicate and transmit efficiently among humans, but animal infection studies and modeling experiments have suggested that human adaptation may require only a few mutations. However, data from natural spillover infection has been limited, posing a challenge for risk assessment. Here, we analyze a unique dataset of deep sequence data from H5N1 virus-infected humans and domestic ducks in Cambodia. We find that well-known markers of human receptor binding and replication arise in multiple, independent humans. We also find that 3 mutations detected within-host are enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adapting. However, we also show that within-host evolution in both humans and ducks are shaped heavily by purifying selection and genetic drift, and that a large fraction of within-host variation is never detected on the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-adapting mutations during natural infection. However, short infection times, purifying selection, and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a single infection.

microbiology↗

bioRxiv2019

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Viruses like influenza are infamous for their ability to adapt to new hosts. Retrospective studies of natural zoonoses and passaging in the lab have identified a modest number of host-adaptive mutations. However, it is unclear if these mutations represent all ways that influenza can adapt to a new host. Here we take a prospective approach to this question by completely mapping amino-acid mutations to the avian influenza virus polymerase protein PB2 that enhance growth in human cells. We identify numerous previously uncharacterized human-adaptive mutations. These mutations cluster on PB2s surface, highlighting potential interfaces with host factors. Some previously uncharacterized adaptive mutations occur in avian-to-human transmission of H7N9 influenza, showing their importance for natural virus evolution. But other adaptive mutations do not occur in nature because they are inaccessible via single-nucleotide mutations. Overall, our work shows how selection at key molecular surfaces combines with evolutionary accessibility to shape viral host adaptation.

microbiology↗

bioRxiv2018

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

BackgroundColombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.\n\nMethodsWe sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes ae-gypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.\n\nResultsWe attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeo-graphic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.\n\nConclusionsSimilarly to genomic epidemiologic studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. This more accurate dating of when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

genomics↗