Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic

How virus migration and meteorological elements shape the seasonality of influenza a/H3N2: A case study in China

Recent global influenza resurgences, escalating to pandemics, emphasize the urgency for effective vaccinations. Despite their efficacy, vaccines offer limited protection against A/H3N2 variants. Thus, elucidating the spatial patterns and underlying drivers of A/H3N2 seasonality is critical for its management. However, the mechanisms governing this seasonality are not fully understood. The study conducted a collaborative and interdisciplinary analysis of influenza A/H3N2 epidemiology in China from 2012 to 2018, utilizing national influenza surveillance data, viral gene sequence data, and meteorological information. We initially examined the spatiotemporal distribution of influenza A/H3N2 across different temperate zones in China. Subsequently, we employed Bayesian "SkyGrid" reconstruction analysis to gain insights into the population dynamics of the influenza A/H3N2 virus within China's temperature zones. Additionally, we utilized generalized additive models (GAM) to assess the influence of meteorological factors on the seasonal prevalence of influenza A/H3N2. Our analysis of China's national influenza data revealed distinct seasonal patterns for A/H3N2: winter epidemics prevailed in temperate zones, while summer and autumn outbreaks occurred in subtropical and tropical areas. The seasonality of influenza A/H3N2 across China's diverse climatic zones is shaped by the interplay of virus migration and meteorological factors. Virus migration introduced new variant populations during seasonal epidemics of influenza A/H3N2 to different temperature zones in China, thereby seeding subsequent seasonal outbreaks. Our findings also indicate that meteorological elements trigger influenza A/H3N2 activity following virus migration. Moreover, the spatial variations in influenza A/H3N2 seasonality in China can be attributed to specific temperature thresholds, approximately 1 °C and 24 °C. These thresholds could serve as potential indicators for A/H3N2 prevalence. This insight is invaluable for tailoring region-specific prevention and control strategies in China and other regions with similar environmental conditions.

Pandemic Events Caused by Bacteria Throughout Human History and the Risks of Antimicrobial Resistance Today

During human history, many pandemic events have threatened and taken many human lives over the years. The deadliest outbreaks were caused by bacteria such as Yersinia pestis. Nowadays, antimicrobial resistance (AMR) in bacteria is a huge problem for the public worldwide, threatening and taking many lives each year. The present work aimed to gather current evidence published in scientific literature that addresses AMR risks. A literature review was conducted using the following descriptors: antimicrobial resistance, AMR, bacteria, and Boolean operators. The results showed that antimicrobial-resistant genes and antibiotic-resistant bacteria in organisms cause critical infectious diseases and are responsible for the infections caused by antibiotic-resistant bacteria (ARB). This review emphasizes the importance of this topic. It sheds light on the risk of reemerging infections and their relationship with AMR. In addition, it discusses the mechanisms and actions of antibiotics and the mechanisms behind the development of resistance by bacteria, focusing on demonstrating the importance of the search for new drugs, for which research involving peptides is fundamental.

Transoceanic pathogen transfer in the age of sail and steam

In the centuries following Christopher Columbus's 1492 voyage to the Americas, transoceanic travel opened unprecedented pathways in global pathogen circulation. Yet no biological transfer is a single, discrete event. We use mathematical modeling to quantify historical risk of shipborne pathogen introduction, exploring the respective contributions of journey time, ship size, population susceptibility, transmission intensity, density dependence, and pathogen biology. We contextualize our results using port arrivals data from San Francisco, 1850 to 1852, and from a selection of historically significant voyages, 1492 to 1918. We offer numerical estimates of introduction risk across historically realistic ranges of journey time and ship population size, and show that both steam travel and shipping regimes that involved frequent, large-scale movement of people substantially increased risk of transoceanic pathogen circulation.

High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China

Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.

Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

Plague, caused by Yersinia pestis, is a zoonotic disease that can reemerge and cause outbreaks following decades of latency in natural plague foci. However, the genetic diversity and spread pattern of Y. pestis during these epidemic-silent cycles remain unclear. In this study, we analyze 356 Y. pestis genomes isolated between 1952 and 2016 in the Yunnan Rattus tanezumi plague focus, China, covering two epidemic-silent cycles. Through high-resolution genomic epidemiological analysis, we find that 96% of Y. pestis genomes belong to phylogroup 1.ORI2 and are subdivided into two sister clades (Sublineage1 and Sublineage2) characterized by different temporal-spatial distributions and genetic diversity. Most of the Sublineage1 strains are isolated from the first epidemic-silent cycle, while Sublineage2 strains are predominantly from the second cycle and revealing a west to east spread. The two sister clades evolved in parallel from a common ancestor and independently lead to two separate epidemics, confirming that the pathogen responsible for the second epidemic following the silent interval is not a descendant of the causative strain of the first epidemic. Our results provide a mechanism for defining epidemic-silent cycles in natural plague foci, which is valuable in the prevention and control of future plague outbreaks.

Climate-driven marmot-plague dynamics in Mongolia and China

The incidence of plague has rebounded in the Americas, Asia, and Africa alongside rapid globalization and climate change. Previous studies have shown local climate to have significant nonlinear effects on plague dynamics among rodent communities. We analyzed an 18-year database of plague, spanning 1998 to 2015, in the foci of Mongolia and China to trace the associations between marmot plague and climate factors. Our results suggested a density-dependent effect of precipitation and a geographic location-dependent effect of temperature on marmot plague. That is, a significantly positive relationship was evident between risk of plague and precipitation only when the marmot density exceeded a certain threshold. The geographical heterogeneity of the temperature effect and the contrasting slopes of influence for the Qinghai-Tibet Plateau (QTP) and other regions in the study (nQTP) were primarily related to diversity of climate and landscape types.

Tracing the future of epidemics: Coincident niche distribution of host animals and disease incidence revealed climate-correlated risk shifts of main zoonotic diseases in China

Climate has critical roles in the origin, pathogenesis and transmission of infectious zoonotic diseases. However, large-scale epidemiologic trend and specific response pattern of zoonotic diseases under future climate scenarios are poorly understood. Here, we projected the distribution shifts of transmission risks of main zoonotic diseases under climate change in China. First, we shaped the global habitat distribution of main host animals for three representative zoonotic diseases (2, 6, and 12 hosts for dengue, hemorrhagic fever, and plague, respectively) with 253,049 occurrence records using maximum entropy (Maxent) modeling. Meanwhile, we predicted the risk distribution of the above three diseases with 197,098 disease incidence records from 2004 to 2017 in China using an integrated Maxent modeling approach. The comparative analysis showed that there exist highly coincident niche distributions between habitat distribution of hosts and risk distribution of diseases, indicating that the integrated Maxent modeling is accurate and effective for predicting the potential risk of zoonotic diseases. On this basis, we further projected the current and future transmission risks of 11 main zoonotic diseases under four representative concentration pathways (RCPs) (RCP2.6, RCP4.5, RCP6.0, and RCP8.5) in 2050 and 2070 in China using the above integrated Maxent modeling with 1,001,416 disease incidence records. We found that Central China, Southeast China, and South China are concentrated regions with high transmission risks for main zoonotic diseases. More specifically, zoonotic diseases had diverse shift patterns of transmission risks including increase, decrease, and unstable. Further correlation analysis indicated that these patterns of shifts were highly correlated with global warming and precipitation increase. Our results revealed how specific zoonotic diseases respond in a changing climate, thereby calling for effective administration and prevention strategies. Furthermore, these results will shed light on guiding future epidemiologic prediction of emerging infectious diseases under global climate change.

Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis

Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.

Yersinia pestis and Plague: some knowns and unknowns

Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen's physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y. pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.

Retrospective analysis of dissemination of the 2.MED1 phylogenetic branch of Yersinia pestis in the Caucasus

The 2.MED1 phylogenetic branch of Yersinia pestis of the medieval biovar became widespread in the Caspian Sea region, the Caucasus, and the Northern Aral Sea region in the 20th century, causing outbreaks and epizootics of plague there. Some of the formed natural foci of 2.MED1 still show epizootic activity and retain their epidemic potential. In this work, we carried out a phylogenetic analysis of 46 Y. pestis strains of the medieval biovar isolated in the Caucasus, the Caspian Sea, and the Northern Aral Sea regions during epidemic outbreaks and epizootics from 1922-2014. The obtained phylogenetic data, together with epidemiological and epizootological data accumulated over a period of about a hundred years, indicate the presence of two waves of penetration of the 2.MED1 branch into the Caucasus. The first occurred, apparently, in the first half of the 20th century as a result of the penetration of 2.MED1 from the foci of the Northern and North-Western Caspian Sea. The second wave was caused by the spread of 2.MED1 from the Northern Aral to the foci of the North-Western, Northern and Eastern Caspian Sea regions at the beginning of the second half of the 20th century, followed by introduction into the Pre-Caucasus and Transcaucasia. The rapid spread of 2.MED1 could be associated with the transfer of the pathogen by land and sea transport in the process of economic activity of the population.

No evidence for persistent natural plague reservoirs in historical and modern Europe

Caused by Yersinia pestis, plague ravaged the world through three known pandemics: the First or the Justinianic (6th-8th century); the Second (beginning with the Black Death during c.1338-1353 and lasting until the 19th century); and the Third (which became global in 1894). It is debatable whether Y. pestis persisted in European wildlife reservoirs or was repeatedly introduced from outside Europe (as covered by European Union and the British Isles). Here, we analyze environmental data (soil characteristics and climate) from active Chinese plague reservoirs to assess whether such environmental conditions in Europe had ever supported "natural plague reservoirs". We have used new statistical methods which are validated through predicting the presence of modern plague reservoirs in the western United States. We find no support for persistent natural plague reservoirs in either historical or modern Europe. Two factors make Europe unfavorable for long-term plague reservoirs: 1) Soil texture and biochemistry and 2) low rodent diversity. By comparing rodent communities in Europe with those in China and the United States, we conclude that a lack of suitable host species might be the main reason for the absence of plague reservoirs in Europe today. These findings support the hypothesis that long-term plague reservoirs did not exist in Europe and therefore question the importance of wildlife rodent species as the primary plague hosts in Europe.

Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution

Theoretical population genetics has long studied the arrival and geographic spread of adaptive variants through the analysis of mathematical models of dispersal and natural selection. These models take on a renewed interest in the context of the COVID-19 pandemic, especially given the consequences that novel adaptive variants have had on the course of the pandemic as they have spread through global populations. Here, we review theoretical models for the spatial spread of adaptive variants and identify areas to be improved in future work, toward a better understanding of variants of concern in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution and other contemporary applications. As we describe, characteristics of pandemics such as COVID-19-such as the impact of long-distance travel patterns and the overdispersion of lineages due to superspreading events-suggest new directions for improving upon existing population genetic models.

Sustained population decline of rodents is linked to accelerated climate warming and human disturbance

Background

During the past three decades, sustained population decline or disappearance of cycles in small rodents have been observed. Both anthropogenic disturbance and climate warming are likely to be potential drivers of population decline, but quantitative analysis on their distinct effects is still lacking.

Results

Using time series monitoring of 115 populations (80 populations from 18 known rodent species, 35 mixed populations from unknown species) from 1980 in China (spanning 20–33 yrs), we analyzed association of human disturbances and climate warming with population dynamics of these rodent species. We found 54 of 115 populations showed a decreasing trend since 1980, and 16 of 115 showed an increasing trend. Human disturbances and climate warming showed significant positive associations with the population declines of most rodent species, and the population declines were more pronounced in habitats with more intensified human disturbance such as cities and farmlands or in high-latitude regions which experienced more increase of temperature.

Conclusions

Our results indicate that the large-scale sustained population decline of small mammals in various ecosystems driven by the rapid increase of both climate warming and human disturbance is likely a signal of ecosystem dysfunction or transition. There is an urgent need to assess the risks of accelerated climate warming and human disturbance imposes on our ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02056-z.

Plague reservoir species throughout the world

Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.

Did Hydro-climatic Extremes, Positive Checks, and Economic Fluctuations Modulate the Epidemics Outbreaks in Late Imperial China?

Empirical research has shown that climate-related variables, the decline in economic well-being, and the mutual reinforcement of positive checks are the primary drivers of epidemic outbreaks in recent human history. However, their relative importance in causing the outbreak of epidemics is rarely examined quantitatively in a single study. I sought to address this issue by analyzing the 1402 epidemic incidents in China between 1841 and 1911, which partially overlaps partly with the Third Pandemic period. Fine-grained historical big data, multiple regression, and wavelet coherence analysis were employed. Statistical results show that economic fluctuations drove the country-wide epidemics outbreaks in China in inter-annual and decadal time scales. Economic fluctuations could cause short-term hardship and long-term impoverishment to the underprivileged social groups since a large portion of the Chinese population lived at the subsistence level in the past. The fluctuations might have sustained the repeated waves of epidemic outbreaks during the Third Pandemic period.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10745-021-00272-7.

COVID-19 and environment: a poignant reminder of sustainability in the new normal

The nexus of COVID-19 and environment is conspicuously deep-rooted. The roles of environmental factors in the origin, transmission and spread of COVID-19 and the mutual impact of the pandemic on the global environment have been the two perspectives to view this nexus. The present paper attempts to systematically review the existing literature to understand and explore the linkages of COVID-19 with environment and proposes conceptual frameworks to underline this nexus. Our study indicates a critical role of meteorological factors, ambient air pollutants and wastewater in severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) transmission-spread dynamics. The study also focuses on the direct and indirect impacts of COVID-19 on the regional and global environment. Most of the indirect environmental effects of COVID-19 were attributed to global human confinement that resulted from the implementation of the pandemic containment measures. This worldwide anthropogenic 'pause' sent ripples to all environmental compartments and presented a unique test bed to identify anthropogenic impacts on the earth's natural systems. The review further addresses emerging sustainability challenges in the new normal and their potential solutions. The situation warrants critical attention to the environment-COVID-19 nexus and innovative sustainable practices to address the ramifications of short- and long-term environmental impacts of the COVID-19 pandemic.

Graphical abstract

Evolution and circulation of Yersinia pestis in the Northern Caspian and Northern Aral Sea regions in the 20th-21st centuries

According to the whole genome SNP analysis of 38 Yersinia pestis strains isolated in the foci of the Northern Caspian and Northern Aral Sea regions in the 20th–early 21st centuries, between 1912 and 2015, the spatial and temporal structure of the 2.MED population of a medieval biovar in this region was determined. A phylogenetic branch 2.MED4 was identified which preceded the 2.MED1 branch that diverged later. 2.MED1 strains became the etiological agent of high-mortality plague outbreaks that occurred in the Northern Caspian region at the beginning of the 20th century. Later in the 20th century, the 2.MED1 branch became widespread in the Caspian Sea region, Caucasus, and vast areas of Central Asia. Based on the data of phylogenetic analysis, as well as epidemiological and epizootiological data, we reconstructed the paths of spread of the 2.MED1 branch in the Northern Caspian Sea region and in the Northern subzone of the Central Asian deserts. It is shown, that the reason for the activation of plague foci in the Northern Caspian region in the second half of the 20th century after a long inter-epizootic period caused by cyclical climate warming was the return of 2.MED1 from the foci of the Northern Aral Sea region. This led to the formation of stable plague foci in the Northern Caspian Sea region and Pre-Caucasus, which manifested epizootic activity in the second half of the 20th and early 21st centuries.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Modeling analysis revealed the distinct global transmission patterns of influenza A viruses and their influencing factors

Influenza A virus has caused huge damage to human health and poultry production worldwide, but its global transmission patterns and influencing factors remain unclear. Here, by using the Nearest Genetic Distance Approach with genetic sequences data, we reconstructed the global transmission patterns of 4 most common subtypes of influenza A virus (H1N1, H3N2, H5N1, and H7N9) and analyzed associations of transmission velocity of these influenza viruses with environmental factors. We found that the transmission patterns of influenza viruses and their associations with environmental factors were closely related to their host properties. H1N1 and H3N2, which are mainly held by humans, are transmitted between regions at high velocity and over long distances, which may be due to human transportation via airplane; while H5N1 and H7N9, which are mainly carried by animals, are transmitted locally at short distances and at low velocity, which may be facilitated by poultry transportation via railways or high ways. H1N1 and H3N2 spread faster in cold seasons, while H5N1 spread faster in both cold and warm seasons, and H7N9 spread faster in wet seasons. H1N1, H3N2, and H5N1 spread faster in places with both high and low human densities. Our study provided novel insights into the global transmission patterns, processes, and management strategies for influenza under accelerated global change.

Biovar-related differences apparent in the flea foregut colonization phenotype of distinct Yersinia pestis strains do not impact transmission efficiency

Background

Yersinia pestis is the flea-transmitted etiological agent of bubonic plague. Sylvatic plague consists of complex tripartite interactions between diverse flea and wild rodent species, and pathogen strains. Transmission by flea bite occurs primarily by the Y. pestis biofilm-mediated foregut blockage and regurgitation mechanism, which has been largely detailed by studies in the model interaction between Y. pestis KIM6+ and Xenopsylla cheopis. Here, we test if pathogen-specific traits influence this interaction by determining the dynamics of foregut blockage development in X. cheopis fleas among extant avirulent pCD1-Y. pestis strains, KIM6+ and CO92, belonging to distinct biovars, and a non-circulating mutant CO92 strain (CO92gly), restored for glycerol fermentation; a key biochemical difference between the two biovars.

Methods

Separate flea cohorts infected with distinct strains were evaluated for (i) blockage development, bacterial burdens and flea foregut blockage pathology, and (ii) for the number of bacteria transmitted by regurgitation during membrane feeding. Strain burdens per flea was determined for fleas co-infected with CO92 and KIM6+ strains at a ratio of 1:1.

Results

Strains KIM6+ and CO92 developed foregut blockage at similar rates and peak temporal incidences, but the CO92gly strain showed significantly greater blockage rates that peak earlier post-infection. The KIM6+ strain, however, exhibited a distinctive foregut pathology wherein bacterial colonization extended the length of the esophagus up to the feeding mouthparts in ~65% of blocked fleas; in contrast to 32% and 26%, respectively, in fleas blocked with CO92 and CO92gly. The proximity of KIM6+ to the flea mouthparts in blocked fleas did not result in higher regurgitative transmission efficiencies as all strains transmitted variable numbers of Y. pestis, albeit slightly lower for CO92gly. During competitive co-infection, strains KIM6+ and CO92 were equally fit maintaining equivalent infection proportions in fleas over time.

Conclusions

We demonstrate that disparate foregut blockage pathologies exhibited by distinct extant Y. pestis strain genotypes do not influence transmission efficiency from X. cheopis fleas. In fact, distinct extant Y. pestis genotypes maintain equivalently effective blockage and transmission efficiencies which is likely advantageous to maintaining continued successful plague spread and establishment of new plague foci.

Climate drivers of plague epidemiology in British India, 1898-1949

Plague, caused by Yersinia pestis infection, continues to threaten low- and middle-income countries throughout the world. The complex interactions between rodents and fleas with their respective environments challenge our understanding of human plague epidemiology. Historical long-term datasets of reported plague cases offer a unique opportunity to elucidate the effects of climate on plague outbreaks in detail. Here, we analyse monthly plague deaths and climate data from 25 provinces in British India from 1898 to 1949 to generate insights into the influence of temperature, rainfall and humidity on the occurrence, severity and timing of plague outbreaks. We find that moderate relative humidity levels of between 60% and 80% were strongly associated with outbreaks. Using wavelet analysis, we determine that the nationwide spread of plague was driven by changes in humidity, where, on average, a one-month delay in the onset of rising humidity translated into a one-month delay in the timing of plague outbreaks. This work can inform modern spatio-temporal predictive models for the disease and aid in the development of early-warning strategies for the deployment of prophylactic treatments and other control measures.