Nonlinear effect of climate on plague during the third pandemic in China

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.

The 2016 Severe Floods and Incidence of Hemorrhagic Fever With Renal Syndrome in the Yangtze River Basin

Importance

Hemorrhagic fever with renal syndrome (HFRS), a neglected zoonotic disease, has received only short-term attention in postflood prevention and control initiatives, possibly because of a lack of evidence regarding the long-term association of flooding with HFRS.

Objectives

To quantify the association between severe floods and long-term incidence of HFRS in the Yangtze River basin and to examine the modifying role of geographical factors in this association.

Design, Setting, and Participants

This cross-sectional study collected data on HFRS cases between July 1, 2013, and June 30, 2019, from 58 cities in 4 provinces (Anhui, Hubei, Hunan, and Jiangxi) in the Yangtze River basin of China, with a breakpoint of flooding in July 2016, generating monthly data. The 3 years after July 2016 were defined as the postflood period, while the 3 years before the breakpoint were defined as the control period. Statistical analysis was performed from October to December 2023.

Exposures

City-level monthly flooding, elevation, ruggedness index, and closest distance from each city to the Yangtze River and its tributaries.

Main Outcomes and Measures

The primary outcomes were the number of city-level monthly HFRS cases and the number of type 1 (spring or summer) and type 2 (autumn or winter) HFRS cases.

Results

A total of 11 745 patients with HFRS were reported during the study period: 5216 patients (mean [SD] age, 47.1 [16.2] years; 3737 men [71.6%]) in the control period and 6529 patients (mean [SD] age, 49.8 [15.8] years; 4672 men [71.6%]) in the postflood period. The pooled effects of interrupted time series analysis indicated a long-term association between flooding and HFRS incidence (odds ratio, 1.38; 95% CI, 1.13-1.68), with type 1 cases being at highest risk (odds ratio, 1.71; 95% CI, 1.40-2.09). The metaregression results indicated that elevation and ruggedness index were negatively associated with the risk of HFRS, while the distance to rivers interacted with these associations.

Conclusions and Relevance

This cross-sectional study of the long-term association between flooding and HFRS incidence, as well as the modification effects of geographical factors, suggests that severe floods were associated with an increased risk of HFRS within 3 years. This study provides evidence for the development of HFRS prevention and control strategies after floods.

Relationship between climatic factors and the flea index of two plague hosts in Xilingol League, Inner Mongolia Autonomous Region

Climatic factors are closely associated with the occurrence of vector-borne diseases, and they also influence the distribution of vectors. The occurrence of plague is closely related to the population dynamics of fleas and their host animals, as well as climatic conditions. This study focused on Xilingol League, utilizing climatic and flea index data from 2012 to 2021. Spearman correlation and "Boruta" importance analysis were conducted to screen for climatic variables. A generalized additive model (GAM) was employed to investigate the influence of climatic factors and rodent density on the flea index. GAM analysis revealed distinct trends in flea index among different rodent hosts. For Meriones unguiculatus, the flea index declined with increased density and with higher humidity, yet rose with greater lagged sunshine duration. For Spermophilus dauricus, an initial increase in flea index with density was observed, followed by a decrease, and a rise in the index was noted when ground temperatures were low. This study reveals the nonlinear interactions and lag effects among climatic factors, density, and flea index. Climatic factors and density variably influence the flea index of two Yersinia pestis hosts. This research advances the prediction and early warning efforts for plague control, providing a theoretical basis for rodent and flea eradication strategies.

Impacts of climate change on the potential distribution of Pulex simulans and Polygenis gwyni

Pulex simulans and Polygenis gwyni are vectors of many flea-borne diseases. They were widely recorded in the United States and Mexico between 1970 and 2000. Maximum entropy models were used to explore the habitats of both fleas under different climate scenarios to provide the scientific basis for the surveillance and control of flea-borne diseases. We screened climate variables by principal component analysis and Pearson's correlation test and evaluated model performance by ROC curve. ArcMap was used to visualize expressions. Under current climatic conditions, the medium and highly suitable areas for P. simulans are estimated to be 9.16 × 106 km2 and 4.97 × 106 km2, respectively. These regions are predominantly located in South America, along the Mediterranean coast of Europe, the southern part of the African continent, the Middle East, North China, and Australia. For P. gwyni, the medium and highly suitable areas under current climatic conditions are approximately 4.01 × 106 and 2.04 × 106 km2, respectively, with the primary distribution in North China extending to the Himalayas, near the Equator in Africa, and in a few areas of Europe. Under future climate scenarios, in the SSP3-7.0 scenario for the years 2081-2100, the area of high suitability for P. simulans is projected to reach its maximum. Similarly, in the SSP2-4.5 scenario for 2061-2080, the area of high suitability for P. gwyni is expected to reach its maximum. Under global climate change, there is a large range in the potential distribution for both fleas, with an overall upward trend in the area of habitat under future climate scenarios. Governments should develop scientific prevention and control measures to prevent the invasive alien species flea.

Relationship Between Climate Change and Marmot Plague of Marmota himalayana Plague Focus - the Altun Mountains of the Qinghai-Xizang Plateau, China, 2000-2022

Introduction

Plague is a zoonotic disease that occurs naturally in specific geographic areas. Climate change can influence the populations of the plague host or vector, leading to variations in the occurrence and epidemiology of plague in animals.

Methods

In this study, we collected meteorological and plague epidemiological data from the Marmota himalayana plague focus in the Altun Mountains of the Qinghai-Xizang Plateau. The data spanned from 2000 to 2022. We describe the climatic factors and plague epidemic conditions and we describe their analysis by Pearson's correlation.

Results

During the period from 2000 to 2022, the isolation rates of Yersinia pestis (Y.pestis) from marmots and fleas were 9.27% (451/4,864) and 7.17% (118/1,646), respectively. Additionally, we observed a positive rate of F1 antibody of 11.25% (443/3,937) in marmots and 18.16% (142/782) in dogs. With regards to climate, there was little variation, and a decreasing trend in blowing-sand days was observed. The temperature in the previous year showed a negative correlation with the Y. pestis isolation rate in marmots (r=-0.555, P=0.011) and the positive rate of F1 antibody in marmots (r=-0.552, P=0.012) in the current year. The average annual precipitation in the previous two years showed a positive correlation with marmot density (r=0.514, P=0.024), while blowing-sand days showed a negative correlation with marmot density (r=-0.701, P=0.001). Furthermore, the average annual precipitation in the previous three years showed a positive correlation with the isolation rate of Y. pestis from marmots (r=0.666, P=0.003), and blowing-sand days showed a negative correlation with marmot density (r=-0.597, P=0.009).

Conclusions

The findings of this study indicate that there is a hysteresis effect of climate change on the prevalence of plague. Therefore, monitoring climate conditions can offer significant insights for implementing timely preventive and control measures to combat plague epidemics.

A systematic review of the clinical profile of patients with bubonic plague and the outcome measures used in research settings

BACKGROUND

Plague is a zoonotic disease that, despite affecting humans for more than 5000 years, has historically been the subject of limited drug development activity. Drugs that are currently recommended in treatment guidelines have been approved based on animal studies alone-no pivotal clinical trials in humans have yet been completed. As a result of the sparse clinical research attention received, there are a number of methodological challenges that need to be addressed in order to facilitate the collection of clinical trial data that can meaningfully inform clinicians and policy-makers. One such challenge is the identification of clinically-relevant endpoints, which are informed by understanding the clinical characterisation of the disease-how it presents and evolves over time, and important patient outcomes, and how these can be modified by treatment.

METHODOLOGY/PRINCIPAL FINDINGS

This systematic review aims to summarise the clinical profile of 1343 patients with bubonic plague described in 87 publications, identified by searching bibliographic databases for studies that meet pre-defined eligibility criteria. The majority of studies were individual case reports. A diverse group of signs and symptoms were reported at baseline and post-baseline timepoints-the most common of which was presence of a bubo, for which limited descriptive and longitudinal information was available. Death occurred in 15% of patients; although this varied from an average 10% in high-income countries to an average 17% in low- and middle-income countries. The median time to death was 1 day, ranging from 0 to 16 days.

CONCLUSIONS/SIGNIFICANCE

This systematic review elucidates the restrictions that limited disease characterisation places on clinical trials for infectious diseases such as plague, which not only impacts the definition of trial endpoints but has the knock-on effect of challenging the interpretation of a trial's results. For this reason and despite interventional trials for plague having taken place, questions around optimal treatment for plague persist.

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.

The indirect impacts of nonpharmacological COVID-19 control measures on other infectious diseases in Yinchuan, Northwest China: a time series study

BACKGROUND

Various nonpharmaceutical interventions (NPIs) against COVID-19 continue to have an impact on socioeconomic and population behaviour patterns. However, the effect of NPIs on notifiable infectious diseases remains inconclusive due to the variability of the disease spectrum, high-incidence endemic diseases and environmental factors across different geographical regions. Thus, it is of public health interest to explore the influence of NPIs on notifiable infectious diseases in Yinchuan, Northwest China.

METHODS

Based on data on notifiable infectious diseases (NIDs), air pollutants, meteorological data, and the number of health institutional personnel in Yinchuan, we first fitted dynamic regression time series models to the incidence of NIDs from 2013 to 2019 and then estimated the incidence for 2020. Then, we compared the projected time series data with the observed incidence of NIDs in 2020. We calculated the relative reduction in NIDs at different emergency response levels in 2020 to identify the impacts of NIPs on NIDs in Yinchuan.

RESULTS

A total of 15,711 cases of NIDs were reported in Yinchuan in 2020, which was 42.59% lower than the average annual number of cases from 2013 to 2019. Natural focal diseases and vector-borne infectious diseases showed an increasing trend, as the observed incidence in 2020 was 46.86% higher than the estimated cases. The observed number of cases changed in respiratory infectious diseases, intestinal infectious diseases and sexually transmitted or bloodborne diseases were 65.27%, 58.45% and 35.01% higher than the expected number, respectively. The NIDs with the highest reductions in each subgroup were hand, foot, and mouth disease (5854 cases), infectious diarrhoea (2157 cases) and scarlet fever (832 cases), respectively. In addition, it was also found that the expected relative reduction in NIDs in 2020 showed a decline across different emergency response levels, as the relative reduction dropped from 65.65% (95% CI: -65.86%, 80.84%) during the level 1 response to 52.72% (95% CI: 20.84%, 66.30%) during the level 3 response.

CONCLUSIONS

The widespread implementation of NPIs in 2020 may have had significant inhibitory effects on the incidence of respiratory infectious diseases, intestinal infectious diseases and sexually transmitted or bloodborne diseases. The relative reduction in NIDs during different emergency response levels in 2020 showed a declining trend as the response level changed from level 1 to level 3. These results can serve as essential guidance for policy-makers and stakeholders to take specific actions to control infectious diseases and protect vulnerable populations in the future.

The role of reservoir species in mediating plague's dynamic response to climate

The distribution and transmission of Yersinia pestis, the bacterial agent of plague, responds dynamically to climate, both within wildlife reservoirs and human populations. The exact mechanisms mediating plague's response to climate are still poorly understood, particularly across large environmentally heterogeneous regions encompassing several reservoir species. A heterogeneous response to precipitation was observed in plague intensity across northern and southern China during the Third Pandemic. This has been attributed to the response of reservoir species in each region. We use environmental niche modelling and hindcasting methods to test the response of a broad range of reservoir species to precipitation. We find little support for the hypothesis that the response of reservoir species to precipitation mediated the impact of precipitation on plague intensity. We instead observed that precipitation variables were of limited importance in defining species niches and rarely showed the expected response to precipitation across northern and southern China. These findings do not suggest that precipitation-reservoir species dynamics never influence plague intensity but that instead, the response of reservoir species to precipitation across a single biome cannot be assumed and that limited numbers of reservoir species may have a disproportional impact upon plague intensity.

Epidemiological Characteristics of Human and Animal Plague in Yunnan Province, China, 1950 to 2020

This study analyzed the epidemiological characteristics of 3,464 human plague cases and the distribution pattern of 4,968 Yersinia pestis isolates from humans, hosts, and vector insects from 1950 to 2020 among two natural plague foci in Yunnan Province, China. These foci include the Rattus flavipectus plague focus of the Yunnan, Guangdong, and Fujian provinces and the Apodemus chevrieri-Eothenomys miletus plague focus of the highlands of northwestern Yunnan Province. The case fatality rate for plague in humans was 18.39% (637/3,464), and the total isolation rate of Y. pestis was 0.17% (4,968/2,975,288). Despite that the frequency of human cases declined rapidly, the animal plague fluctuated greatly, alternating between activity and inactivity in these foci. The tendency among human cases can be divided into 4 stages, 1950 to 1955, 1956 to 1989, 1990 to 2005, and 2006 to 2020. Bubonic plague accounted for the majority of cases in Yunnan, where pneumonic and septicemic plague rarely occurred. The natural plague foci have been in a relatively active state due to the stability of local ecology. Dense human population and frequent contact with host animals contribute to the high risk of human infection. This study systematically analyzed the epidemic pattern of human plague and the distribution characteristics of Y. pestis in the natural plague foci in Yunnan, providing a scientific basis for further development and adjustment of plague prevention and control strategies. IMPORTANCE Yunnan is the origin of the third plague pandemic. The analysis of human and animal plague characteristics of plague foci in Yunnan enlightens the prevention and control of the next plague pandemics. The plague characteristics of Yunnan show that human plague occurred when animal plague reached a certain scale, and strengthened surveillance of animal plague and reducing the density of host animals and transmission vectors contribute to the prevention and control of human plague outbreaks. The phenomenon of alternation between the resting period and active period of plague foci in Yunnan further proves the endogenous preservation mechanism of plague.

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.

Correlation analysis between the occurrence of epidemic in ancient China and solar activity

As the globe has witnessed the pandemic, epidemic diseases exert a strong impact on human beings and ecosystems. Since the Sun is the primary energy source of the Earth, some scientific pioneers attempted to search for the discernible relation between solar activity and the incidence of epidemics. In this study, the periodic changes and trends of ancient Chinese epidemic data were analyzed in comparison with those of sunspot numbers, a solar activity proxy. The results show that the epidemic and solar activity changes are in good agreement to a certain extent, especially during the Gleissberg and the de Vries cycles. The wavelet coherence shows that the frequency of the epidemic data and sunspot numbers are highly associated. In addition, results from the ensemble empirical mode decomposition illustrate consistent variations in low-frequency decompositions. This study has important implications for further understanding of the potential impact of solar activity on Earth's biosphere, the underlying mechanism of which needs further exploration.

Climate Change Drives the Transmission and Spread of Vector-Borne Diseases: An Ecological Perspective

Climate change affects ecosystems and human health in multiple dimensions. With the acceleration of climate change, climate-sensitive vector-borne diseases (VBDs) pose an increasing threat to public health. This paper summaries 10 publications on the impacts of climate change on ecosystems and human health; then it synthesizes the other existing literature to more broadly explain how climate change drives the transmission and spread of VBDs through an ecological perspective. We highlight the multi-dimensional nature of climate change, its interaction with other factors, and the impact of the COVID-19 pandemic on transmission and spread of VBDs, specifically including: (1) the generally nonlinear relationship of local climate (temperature, precipitation and wind) and VBD transmission, with temperature especially exhibiting an n-shape relation; (2) the time-lagged effect of regional climate phenomena (the El Niño-Southern Oscillation and North Atlantic Oscillation) on VBD transmission; (3) the u-shaped effect of extreme climate (heat waves, cold waves, floods, and droughts) on VBD spread; (4) how interactions between non-climatic (land use and human mobility) and climatic factors increase VBD transmission and spread; and (5) that the impact of the COVID-19 pandemic on climate change is debatable, and its impact on VBDs remains uncertain. By exploring the influence of climate change and non-climatic factors on VBD transmission and spread, this paper provides scientific understanding and guidance for their effective prevention and control.

Broad-scale climate variation drives the dynamics of animal populations: a global multi-taxa analysis

Climate is a major extrinsic factor affecting the population dynamics of many organisms. The Broad-Scale Climate Hypothesis (BSCH) was proposed by Elton to explain the large-scale synchronous population cycles of animals, but the extent of support and whether it differs among taxa and geographical regions is unclear. We reviewed publications examining the relationship between the population dynamics of multiple taxa worldwide and the two most commonly used broad-scale climate indices, El Niño-Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO). Our review and synthesis (based on 561 species from 221 papers) reveals that population changes of mammals, birds and insects are strongly affected by major oceanic shifts or irregular oceanic changes, particularly in ENSO- and NAO-influenced regions (Pacific and Atlantic, respectively), providing clear evidence supporting Elton's BSCH. Mammal and insect populations tended to increase during positive ENSO phases. Bird populations tended to increase in positive NAO phases. Some species showed dual associations with both positive and negative phases of the same climate index (ENSO or NAO). These findings indicate that some taxa or regions are more or less vulnerable to climate fluctuations and that some geographical areas show multiple weather effects related to ENSO or NAO phases. Beyond confirming that animal populations are influenced by broad-scale climate variation, we document extensive patterns of variation among taxa and observe that the direct biotic and abiotic mechanisms for these broad-scale climate factors affecting animal populations are very poorly understood. A practical implication of our research is that changes in ENSO or NAO can be used as early signals for pest management and wildlife conservation. We advocate integrative studies at both broad and local scales to unravel the omnipresent effects of climate on animal populations to help address the challenge of conserving biodiversity in this era of accelerated climate change.

Climate Change and Vector-Borne Diseases in China: A Review of Evidence and Implications for Risk Management

Simple Summary

Vector-borne diseases are among the most rapidly spreading infectious diseases and are widespread all around the world. In China, many types of vector-borne diseases have been prevalent in different regions, which is a serious public health problem with significant association with meteorological factors and weather events. Under the background of current severe climate change, the outbreaks and transmission of vector-borne diseases have been proven to be impacted greatly due to rapidly changing weather conditions. This study summarizes research progress on the association between climate conditions and all types of vector-borne diseases in China. A total of seven insect-borne diseases, two rodent-borne diseases, and a snail-borne disease were included, among which dengue fever is the most concerning mosquito-borne disease. Temperature, rainfall, and humidity have the most significant effect on vector-borne disease transmission, while the association between weather conditions and vector-borne diseases shows vast differences in China. We also make suggestions about future research based on a review of current studies.

Abstract

Vector-borne diseases have posed a heavy threat to public health, especially in the context of climate change. Currently, there is no comprehensive review of the impact of meteorological factors on all types of vector-borne diseases in China. Through a systematic review of literature between 2000 and 2021, this study summarizes the relationship between climate factors and vector-borne diseases and potential mechanisms of climate change affecting vector-borne diseases. It further examines the regional differences of climate impact. A total of 131 studies in both Chinese and English on 10 vector-borne diseases were included. The number of publications on mosquito-borne diseases is the largest and is increasing, while the number of studies on rodent-borne diseases has been decreasing in the past two decades. Temperature, precipitation, and humidity are the main parameters contributing to the transmission of vector-borne diseases. Both the association and mechanism show vast differences between northern and southern China resulting from nature and social factors. We recommend that more future research should focus on the effect of meteorological factors on mosquito-borne diseases in the era of climate change. Such information will be crucial in facilitating a multi-sectorial response to climate-sensitive diseases in China.

Spatiotemporal Variations of Plague Risk in the Tibetan Plateau from 1954-2016

Plague persists in the plague natural foci today. Although previous studies have found climate drives plague dynamics, quantitative analysis on animal plague risk under climate change remains understudied. Here, we analyzed plague dynamics in the Tibetan Plateau (TP) which is a climate-sensitive area and one of the most severe animal plague areas in China to disentangle variations in marmot plague enzootic foci, diffusion patterns, and their possible links with climate and anthropogenic factors. Specifically, we developed a time-sharing ecological niche modelling framework to identify finer potential plague territories and their temporal epidemic trends. Models were conducted by assembling animal records and multi-source ecophysiological variables with actual ecological effects (both climatic predictors and landscape factors) and driven by matching plague strains to periods corresponding to meteorological datasets. The models identified abundant animal plague territories over the TP and suggested the spatial patterns varied spatiotemporal dimension across the years, undergoing repeated spreading and contractions. Plague risk increased in the 1980s and 2000s, with the risk area increasing by 17.7 and 55.5 thousand km², respectively. The 1990s and 2010s were decades of decreased risk, with reductions of 71.9 and 39.5 thousand km², respectively. Further factor analysis showed that intrinsic conditions (i.e., elevation, soil, and geochemical landscape) provided fundamental niches. In contrast, climatic conditions, especially precipitation, led to niche differentiation and resulted in varied spatial patterns. Additionally, while increased human interference may temporarily reduce plague risks, there is a strong possibility of recurrence. This study reshaped the plague distribution at multiple time scales in the TP and revealed multifactorial synergistic effects on the spreading and contraction of plague foci, confirming that TP plague is increasingly sensitive to climate change. These findings may facilitate groups to take measures to combat the plague threats and prevent potential future human plague from occurring.

Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic

The Black Death (1347–1352 ce) is the most renowned pandemic in human history, believed by many to have killed half of Europe’s population. However, despite advances in ancient DNA research that conclusively identified the pandemic’s causative agent (bacterium Yersinia pestis), our knowledge of the Black Death remains limited, based primarily on qualitative remarks in medieval written sources available for some areas of Western Europe. Here, we remedy this situation by applying a pioneering new approach, ‘big data palaeoecology’, which, starting from palynological data, evaluates the scale of the Black Death’s mortality on a regional scale across Europe. We collected pollen data on landscape change from 261 radiocarbon-dated coring sites (lakes and wetlands) located across 19 modern-day European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that a large portion of the population, upwards of half, died within a few years in the 21 historical regions we studied. While we can confirm that the Black Death had a devastating impact in some regions, we found that it had negligible or no impact in others. These inter-regional differences in the Black Death’s mortality across Europe demonstrate the significance of cultural, ecological, economic, societal and climatic factors that mediated the dissemination and impact of the disease. The complex interplay of these factors, along with the historical ecology of plague, should be a focus of future research on historical pandemics.

Historical accounts of the mortality outcomes of the Black Death plague pandemic are variable across Europe, with much higher death tolls suggested in some areas than others. Here the authors use a ‘big data palaeoecology’ approach to show that land use change following the pandemic was spatially variable across Europe, confirming heterogeneous responses with empirical data.

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.

Genetic source tracking of human plague cases in Inner Mongolia-Beijing, 2019

On 12 November 2019, one couple from the Sonid Left Qi (County) in the Inner Mongolia Autonomous Region was diagnosed with pneumonic plague in Beijing. The wife acquired the infection from her husband. Thereafter, two bubonic plague cases were identified in Inner Mongolia on November 16th and 24th. In this study, genome-wide single nucleotide polymorphism (SNP) analysis was used to identify the phylogenetic relationship of Yersinia pestis strains isolated in Inner Mongolia. Strains isolated from reservoirs in 2018 and 2019 in Inner Mongolia, together with the strain isolated from Patient C, were further clustered into 2.MED3m, and two novel lineages (2.MED3q, 2.MED3r) in the 2.MED3 population. According to the analysis of PCR-based molecular subtyping methods, such as the MLVA 14 scheme and seven SNP allele sequencing, Patients A/B and D were classified as 2.MED3m. In addition, strains from rodents living near the patients' residences were clustered into the same lineage as patients. Such observations indicated that human plague cases originated from local reservoirs. Corresponding phylogenetic analysis also indicated that rodent plague strains in different areas in Inner Mongolia belong to different epizootics rather than being caused by spreading from the same epizootic in Meriones unguiculatus in 2019.

Modeling the complete spatiotemporal spread of the COVID-19 epidemic in mainland China

Objectives

The novel coronavirus (COVID-19) epidemic is reaching its final phase in China. The epidemic data are available for a complete assessment of epidemiological parameters in all regions and time periods.

Methods

This study aims to present a spatiotemporal epidemic model based on spatially stratified heterogeneity (SSH) to simulate the epidemic spread. A susceptible-exposed/latent-infected-removed (SEIR) model was constructed for each SSH-identified stratum (each administrative city) to estimate the spatiotemporal epidemiological parameters of the outbreak.

Results

We estimated that the mean latent and removed periods were 5.40 and 2.13 days, respectively. There was an average of 1.72 latent or infected persons per 10,000 Wuhan travelers to other locations until January 20th, 2020. The space-time basic reproduction number (R₀) estimates indicate an initial value between 2 and 3.5 in most cities on this date. The mean period for R₀ estimates to decrease to 80%, and 50% of initial values in cities were an average of 14.73 and 19.62 days, respectively.

Conclusions

Our model estimates the complete spatiotemporal epidemiological characteristics of the outbreak in a space-time domain. These findings will help enhance a comprehensive understanding of the outbreak and inform the strategies of prevention and control in other countries worldwide.

The delayed effect of cooling reinforced the NAO-plague connection in pre-industrial Europe

Previous studies on the connection between climate and plague were mostly conducted without considering the influence of large-scale atmospheric circulations and long-term historical observations. The current study seeks to reveal the sophisticated role of climatic control on plague by investigating the combined effect of North Atlantic Oscillation (NAO) and temperature on plague outbreaks in Europe from 1347 to 1760 CE. Moving correlation analysis is applied to explore the non-linear relationship between NAO and plague transmission over time. Also, we apply the cross-correlation function to identify the role of temperature in mediating the NAO-plague connection and the lead-lag relationship in between. Our statistical results show that the pathway from climate change to plague incidence is distinctive in its spatial, temporal, and non-linear patterns. The multi-decadal temperature change exerted a 15-22 years lagged impact on the NAO-plague correlation in different European regions. The NAO-plague correlation in Atlantic-Central Europe primarily remained positive, while the correlation in Mediterranean Europe switched between positive and negative alternately. The modulating effect of temperature over the NAO-plague correlation increases exponentially with the magnitude of the temperature anomaly, but the effect is negligible between 0.3 and -0.3 °C anomaly. Our findings show that a lagged influence from the temperature extremes dominantly controls the correlation between NAO and plague incidence. A forecast from our study suggests that large-scale plague outbreaks are unlikely to happen in Europe if NAO remains at its current positive phase during the earth's future warming.

Human Plague Case Diagnosed in Ningxia Tracked to Animal Reservoirs — Inner Mongolia Autonomous Region, China, 2021

What is already known about this topic?

There were a total of 4 and 3 human plague cases that occurred in the Inner Mongolia Autonomous Region in 2019 and 2020, respectively, with 1 and 2 deaths in 2019 and 2020 respectively, which indicated that plague still poses a significant threat to human health especially for farmers, shepherds, or residents living in native plague foci.

What is added by this report?

On August 14, 2021, 1 patient from the Otog Qi (County) in the Inner Mongolia sought treatment in Yinchuan City (the capital of Ningxia Hui Autonomous Region), where the patient was diagnosed with bubonic plague and secondary septicemic plague. The genetic source tracking of associated Yersiniapestis strains indicated that human plague cases were infected from animal reservoirs in Inner Mongolia.

What are the implications for public health practice?

Major threats of plague to residents living in native plague foci are the infection by bites of bacterium-bearing fleas or direct contact with diseased or dead plague-infected animals. And the ability of early diagnostic is very critical for county-level hospital in native plague foci.

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.

Acceleration of plague outbreaks in the second pandemic

Historical records reveal the temporal patterns of a sequence of plague epidemics in London, United Kingdom, from the 14th to 17th centuries. Analysis of these records shows that later epidemics spread significantly faster ("accelerated"). Between the Black Death of 1348 and the later epidemics that culminated with the Great Plague of 1665, we estimate that the epidemic growth rate increased fourfold. Currently available data do not provide enough information to infer the mode of plague transmission in any given epidemic; nevertheless, order-of-magnitude estimates of epidemic parameters suggest that the observed slow growth rates in the 14th century are inconsistent with direct (pneumonic) transmission. We discuss the potential roles of demographic and ecological factors, such as climate change or human or rat population density, in driving the observed acceleration.

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.

Climate and society in long-term perspective: Opportunities and pitfalls in the use of historical datasets

Recent advances in paleoclimatology and the growing digital availability of large historical datasets on human activity have created new opportunities to investigate long-term interactions between climate and society. However, noncritical use of historical datasets can create pitfalls, resulting in misleading findings that may become entrenched as accepted knowledge. We demonstrate pitfalls in the content, use and interpretation of historical datasets in research into climate and society interaction through a systematic review of recent studies on the link between climate and (a) conflict incidence, (b) plague outbreaks and (c) agricultural productivity changes. We propose three sets of interventions to overcome these pitfalls, which involve a more critical and multidisciplinary collection and construction of historical datasets, increased specificity and transparency about uncertainty or biases, and replacing inductive with deductive approaches to causality. This will improve the validity and robustness of interpretations on the long-term relationship between climate and society. This article is categorized under: Climate, History, Society, Culture > Disciplinary Perspectives.

Identifying the spatiotemporal clusters of plague occurrences in China during the Third Pandemic

Plague, a devastating infectious disease caused by Yersinia pestis, has killed millions of people in the past and is still active in the natural foci of the world today. Understanding the spatiotemporal patterns of plague outbreaks in history is critically important, as it may help to facilitate prevention and control of potential future outbreaks. In this study, we explored spatiotemporal clusters of human plague occurrences in China using a machine-learning clustering method and reconstructed the potential transmission pattern during the Third Pandemic (1772-1964). We succeeded in identifying 6 clusters in the space domain (2D) and 13 clusters in the spatiotemporal domain (3D). Our results suggest that there were several temporal outbreaks and transmissions of plague in different spatial clusters. Together with the spatiotemporal nearest neighbor approach (ST-NNA), this method could allow us to have a clearer look at the spatiotemporal patterns of plague.

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

Quantitative knowledge about which natural and anthropogenic factors influence the global spread of plague remains sparse. We estimated the worldwide spreading velocity of plague during the Third Pandemic, using more than 200 years of extensive human plague case records and genomic data, and analyzed the association of spatiotemporal environmental factors with spreading velocity. Here, we show that two lineages, 2.MED and 1.ORI3, spread significantly faster than others, possibly reflecting differences among strains in transmission mechanisms and virulence. Plague spread fastest in regions with low population density and high proportion of pasture- or forestland, findings that should be taken into account for effective plague monitoring and control. Temperature exhibited a nonlinear, U-shaped association with spread speed, with a minimum around 20 °C, while precipitation showed a positive association. Our results suggest that global warming may accelerate plague spread in warm, tropical regions and that the projected increased precipitation in the Northern Hemisphere may increase plague spread in relevant regions.

Human plague system associated with rodent diversity and other environmental factors

Plague remains a threat to public health and is considered as a re-emerging infectious disease today. Rodents play an important role as major hosts in plague persistence and driving plague outbreaks in natural foci; however, few studies have tested the association between host diversity in ecosystems and human plague risk. Here we use zero-inflated generalized additive models to examine the association of species richness with human plague presence (where plague outbreaks could occur) and intensity (the average number of annual human cases when they occurred) in China during the Third Pandemic. We also account for transportation network density, annual precipitation levels and human population size. We found rodent species richness, particularly of rodent plague hosts, is positively associated with the presence of human plague. Further investigation shows that species richness of both wild and commensal rodent plague hosts are positively correlated with the presence, but only the latter correlated with the intensity. Our results indicated a positive relationship between rodent diversity and human plague, which may provide suggestions for the plague surveillance system.

Quantifying the effects of climate and anthropogenic change on regional species loss in China

Human-induced environmental and climate change are widely blamed for causing rapid global biodiversity loss, but direct estimation of the proportion of biodiversity lost at local or regional scales are still infrequent. This prevents us from quantifying the main and interactive effects of anthropogenic environmental and climate change on species loss. Here, we demonstrate that the estimated proportion of species loss of 252 key protected vertebrate species at a county level of China during the past half century was 27.2% for all taxa, 47.7% for mammals, 28.8% for amphibians and reptiles and 19.8% for birds. Both human population increase and species richness showed significant positive correlations with species loss of all taxa combined, mammals, birds, and amphibians and reptiles. Temperature increase was positively correlated with all-taxa and bird species loss. Precipitation increase was negatively correlated with species loss of birds. Human population change and species richness showed more significant interactions with the other correlates of species loss. High species richness regions had higher species loss under the drivers of human environmental and climate change than low-richness regions. Consequently, ongoing human environmental and climate changes are expected to perpetuate more negative effects on the survival of key vertebrate species, particularly in high-biodiversity regions.

A historical evaluation of Chinese tongue diagnosis in the treatment of septicemic plague in the pre-antibiotic era, and as a new direction for revolutionary clinical research applications

Chinese tongue diagnosis was initially developed to quickly and efficiently diagnose and prescribe medicine, while at the same time allowing the doctor to have minimal contact with the patient. At the time of its compiling, the spread of Yersinia pestis, often causing septicaemia and gangrene of the extremities, may have discouraged doctors to come in direct contact with their patients and take the pulse. However, in recent decades, modern developments in the field of traditional Chinese medicine, as well as the spread of antibiotics in conjunction with the advancements of microbiology, have overshadowed the original purpose of this methodology. Nevertheless, the fast approaching post-antibiotic era and the development of artificial intelligence may hold new applications for tongue diagnosis. This article focuses on the historical development of what is the world's earliest tongue diagnosis monograph, and discusses the directions that such knowledge may be used in future clinical research.

Pre-industrial plague transmission is mediated by the synergistic effect of temperature and aridity index

Background

Although the linkage between climate change and plague transmission has been proposed in previous studies, the dominant approach has been to address the linkage with traditional statistical methods, while the possible non-linearity, non-stationarity and low frequency domain of the linkage has not been fully considered. We seek to address the above issue by investigating plague transmission in pre-industrial Europe (AD1347–1760) at both continental and country levels.

Methods

We apply Granger Causality Analysis to identify the casual relationship between climatic variables and plague outbreaks. We then apply Wavelet Analysis to explore the non-linear and non-stationary association between climate change and plague outbreaks.

Results

Our results show that 5-year lagged temperature and aridity index are the significant determinants of plague outbreaks in pre-industrial Europe. At the multi-decadal time scale, there are more frequent plague outbreaks in a cold and arid climate. The synergy of temperature and aridity index, rather than their individual effect, is more imperative in driving plague outbreaks, which is valid at both the continental and country levels.

Conclusions

Plague outbreaks come after cold and dry spells. The multi-decadal climate variability is imperative in driving the cycles of plague outbreaks in pre-industrial Europe. The lagged and multi-decadal effect of climate change on plague outbreaks may be attributable to the complexity of ecological, social, or climate systems, through which climate exerts its influence on plague dynamics. These findings may contribute to improve our understanding of the epidemiology of plague and other rodent-borne or flea-borne infectious diseases in human history.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3045-5) contains supplementary material, which is available to authorized users.

Climate warming and humans played different roles in triggering Late Quaternary extinctions in east and west Eurasia

Climate change and humans are proposed as the two key drivers of total extinction of many large mammals in the Late Pleistocene and Early Holocene, but disentangling their relative roles remains challenging owing to a lack of quantitative evaluation of human impact and climate-driven distribution changes on the extinctions of these large mammals in a continuous temporal-spatial dimension. Here, our analyses showed that temperature change had significant effects on mammoth (genus Mammuthus), rhinoceros (Rhinocerotidae), horse (Equidae) and deer (Cervidae). Rapid global warming was the predominant factor driving the total extinction of mammoths and rhinos in frigid zones from the Late Pleistocene and Early Holocene. Humans showed significant, negative effects on extirpations of the four mammalian taxa, and were the predominant factor causing the extinction or major extirpations of rhinos and horses. Deer survived both rapid climate warming and extensive human impacts. Our study indicates that both the current rates of warming and range shifts of species are much faster than those from the Late Pleistocene to Holocene. Our results provide new insight into the extinction of Late Quaternary megafauna by demonstrating taxon-, period- and region-specific differences in extinction drivers of climate change and human disturbances, and some implications about the extinction risk of animals by recent and ongoing climate warming.

Scale-dependent climatic drivers of human epidemics in ancient China

A wide range of climate change-induced effects have been implicated in the prevalence of infectious diseases. Disentangling causes and consequences, however, remains particularly challenging at historical time scales, for which the quality and quantity of most of the available natural proxy archives and written documentary sources often decline. Here, we reconstruct the spatiotemporal occurrence patterns of human epidemics for large parts of China and most of the last two millennia. Cold and dry climate conditions indirectly increased the prevalence of epidemics through the influences of locusts and famines. Our results further reveal that low-frequency, long-term temperature trends mainly contributed to negative associations with epidemics, while positive associations of epidemics with droughts, floods, locusts, and famines mainly coincided with both higher and lower frequency temperature variations. Nevertheless, unstable relationships between human epidemics and temperature changes were observed on relatively smaller time scales. Our study suggests that an intertwined, direct, and indirect array of biological, ecological, and societal responses to different aspects of past climatic changes strongly depended on the frequency domain and study period chosen.

Climate change and human infectious diseases: A synthesis of research findings from global and spatio-temporal perspectives

The life cycles and transmission of most infectious agents are inextricably linked with climate. In spite of a growing level of interest and progress in determining climate change effects on infectious disease, the debate on the potential health outcomes remains polarizing, which is partly attributable to the varying effects of climate change, different types of pathogen-host systems, and spatio-temporal scales. We summarize the published evidence and show that over the past few decades, the reported negative or uncertain responses of infectious diseases to climate change has been growing. A feature of the research tendency is the focus on temperature and insect-borne diseases at the local and decadal scale. Geographically, regions experiencing higher temperature anomalies have been given more research attention; unfortunately, the Earth's most vulnerable regions to climate variability and extreme events have been less studied. From local to global scales, agreements on the response of infectious diseases to climate change tend to converge. So far, an abundance of findings have been based on statistical methods, with the number of mechanistic studies slowly growing. Research gaps and trends identified in this study should be addressed in the future.

Navigable rivers facilitated the spread and recurrence of plague in pre-industrial Europe

Infectious diseases have become a rising challenge to mankind in a globalizing world. Yet, little is known about the inland transmission of infectious diseases in history. In this study, we based on the spatio-temporal information of 5559 plague (Yersinia pestis) outbreaks in Europe and its neighboring regions in AD1347–1760 to statistically examine the connection between navigable rivers and plague outbreak. Our results showed that 95.5% of plague happened within 10 km proximity of navigable rivers. Besides, the count of plague outbreak was positively correlated with the width of river and negatively correlated with the distance between city and river. This association remained robust in different regression model specifications. An increase of 100 m in the width of river and a shortening of 1 km distance between city and river resulted in 9 and 0.96 more plague outbreaks in our study period, respectively. Such relationship shows a declining trend over our study period due to the expansion of city and technological advancement in overland transportation. This study elucidates the key role of navigable river in the dissemination of plague in historical Europe.

The trophic responses of two different rodent-vector-plague systems to climate change

Plague, the causative agent of three devastating pandemics in history, is currently a re-emerging disease, probably due to climate change and other anthropogenic changes. Without understanding the response of plague systems to anthropogenic or climate changes in their trophic web, it is unfeasible to effectively predict years with high risks of plague outbreak, hampering our ability for effective prevention and control of the disease. Here, by using surveillance data, we apply structural equation modelling to reveal the drivers of plague prevalence in two very different rodent systems: those of the solitary Daurian ground squirrel and the social Mongolian gerbil. We show that plague prevalence in the Daurian ground squirrel is not detectably related to its trophic web, and that therefore surveillance efforts should focus on detecting plague directly in this ecosystem. On the other hand, plague in the Mongolian gerbil is strongly embedded in a complex, yet understandable trophic web of climate, vegetation, and rodent and flea densities, making the ecosystem suitable for more sophisticated low-cost surveillance practices, such as remote sensing. As for the trophic webs of the two rodent species, we find that increased vegetation is positively associated with higher temperatures and precipitation for both ecosystems. We furthermore find a positive association between vegetation and ground squirrel density, yet a negative association between vegetation and gerbil density. Our study thus shows how past surveillance records can be used to design and improve existing plague prevention and control measures, by tailoring them to individual plague foci. Such measures are indeed highly needed under present conditions with prevailing climate change.

Genome and Evolution of Yersinia pestis

This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.

Perspectives on Yersinia pestis: A Model for Studying Zoonotic Pathogens

Yersinia pestis is a typical zoonotic bacterial pathogen. The following reasons make this pathogen a model for studying zoonotic pathogens: (1) Its unique lifestyle makes Y. pestis an ideal model for studying host-vector-environment-pathogen interactions; (2) population diversity characters in Y. pestis render it a model species for studying monomorphic bacterial evolution; (3) the pathogenic features of bacteria provide us with good opportunities to study human immune responses; (4) typical animal and vector models of Y. pestis infection create opportunities for experimental studies on pathogenesis and evolution; and (5) repeated pandemics and local outbreaks provide us with clues about the infectious disease outbreaks that have occurred in human history.

Plague: A Disease Which Changed the Path of Human Civilization

Plague caused by Yersinia pestis is a zoonotic infection, i.e., it is maintained in wildlife by animal reservoirs and on occasion spills over into human populations, causing outbreaks of different entities. Large epidemics of plague, which have had significant demographic, social, and economic consequences, have been recorded in Western European historical documents since the sixth century. Plague has remained in Europe for over 1400 years, intermittently disappearing, yet it is not clear if there were reservoirs for Y. pestis in Western Europe or if the pathogen was rather reimported on different occasions from Asian reservoirs by human agency. The latter hypothesis thus far seems to be the most plausible one, as it is sustained by both ecological and climatological evidence, helping to interpret the phylogeny of this bacterium.

The seesaw effect of winter temperature change on the recruitment of cotton bollworms Helicoverpa armigera through mismatched phenology

Knowing how climate change affects the population dynamics of insect pests is critical for the future of integrated pest management. Rising winter temperatures from global warming can drive increases in outbreaks of some agricultural pests. In contrast, here we propose an alternative hypothesis that both extremely cold and warm winters can mismatch the timing between the eclosion of overwintering pests and the flowering of key host plants. As host plants normally need higher effective cumulative temperatures for flowering than insects need for eclosion, changes in flowering time will be less dramatic than changes in eclosion time, leading to a mismatch of phenology on either side of the optimal winter temperature. We term this the "seesaw effect." Using a long-term dataset of the Old World cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in northern China, we tested this seesaw hypothesis by running a generalized additive model for the effects of the third generation moth in the preceding year, the winter air temperature, the number of winter days below a critical temperature and cumulative precipitation during winter on the demography of the overwintering moth. Results confirmed the existence of the seesaw effect of winter temperature change on overwintering populations. Pest management should therefore consider the indirect effect of changing crop phenology (whether due to greenhouse cultivation or to climate change) on pest outbreaks. As arthropods from mid- and high latitudes are actually living in a cooler thermal environment than their physiological optimum in contrast to species from lower latitudes, the effects of rising winter temperatures on the population dynamics of arthropods in the different latitudinal zones should be considered separately. The seesaw effect makes it more difficult to predict the average long-term population dynamics of insect pests at high latitudes due to the potential sharp changes in annual growth rates from fluctuating minimum winter temperatures.

When phenology matters: age-size truncation alters population response to trophic mismatch

Climate-induced shifts in the timing of life-history events are a worldwide phenomenon, and these shifts can de-synchronize species interactions such as predator–prey relationships. In order to understand the ecological implications of altered seasonality, we need to consider how shifts in phenology interact with other agents of environmental change such as exploitation and disease spread, which commonly act to erode the demographic structure of wild populations. Using long-term observational data on the phenology and dynamics of a model predator–prey system (fish and zooplankton in Windermere, UK), we show that age–size truncation of the predator population alters the consequences of phenological mismatch for offspring survival and population abundance. Specifically, age–size truncation reduces intraspecific density regulation due to competition and cannibalism, and thereby amplifies the population sensitivity to climate-induced predator–prey asynchrony, which increases variability in predator abundance. High population variability poses major ecological and economic challenges as it can diminish sustainable harvest rates and increase the risk of population collapse. Our results stress the importance of maintaining within-population age–size diversity in order to buffer populations against phenological asynchrony, and highlight the need to consider interactive effects of environmental impacts if we are to understand and project complex ecological outcomes.

The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China

Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.

Wet climate and transportation routes accelerate spread of human plague

Currently, large-scale transmissions of infectious diseases are becoming more closely associated with accelerated globalization and climate change, but quantitative analyses are still rare. By using an extensive dataset consisting of date and location of cases for the third plague pandemic from 1772 to 1964 in China and a novel method (nearest neighbour approach) which deals with both short- and long-distance transmissions, we found the presence of major roads, rivers and coastline accelerated the spread of plague and shaped the transmission patterns. We found that plague spread velocity was positively associated with wet conditions (measured by an index of drought and flood events) in China, probably due to flood-driven transmission by people or rodents. Our study provides new insights on transmission patterns and possible mechanisms behind variability in transmission speed, with implications for prevention and control measures. The methodology may also be applicable to studies of disease dynamics or species movement in other systems.

Linking climate change to population cycles of hares and lynx

The classic 10-year population cycle of snowshoe hares (Lepus americanus, Erxleben 1777) and Canada lynx (Lynx canadensis, Kerr 1792) in the boreal forests of North America has drawn much attention from both population and community ecologists worldwide; however, the ecological mechanisms driving the 10-year cyclic dynamic pattern are not fully revealed yet. In this study, by the use of historic fur harvest data, we constructed a series of generalized additive models to study the effects of density dependence, predation, and climate (both global climate indices of North Atlantic Oscillation index (NAO), Southern Oscillation index (SOI) and northern hemispheric temperature (NHT) and local weather data including temperature, rainfall, and snow). We identified several key pathways from global and local climate to lynx with various time lags: rainfall shows a negative, and snow shows a positive effect on lynx; NHT and NAO negatively affect lynx through their positive effect on rainfall and negative effect on snow; SOI positively affects lynx through its negative effect on rainfall. Direct or delayed density dependency effects, the prey effect of hare on lynx and a 2-year delayed negative effect of lynx on hare (defined as asymmetric predation) were found. The simulated population dynamics is well fitted to the observed long-term fluctuations of hare and lynx populations. Through simulation, we find density dependency and asymmetric predation, only producing damped oscillation, are necessary but not sufficient factors in causing the observed 10-year cycles; while extrinsic climate factors are important in producing and modifying the sustained cycles. Two recent population declines of lynx (1940-1955 and after 1980) were likely caused by ongoing climate warming indirectly. Our results provide an alternative explanation to the mechanism of the 10-year cycles, and there is a need for further investigation on links between disappearance of population cycles and global warming in hare-lynx system.

Analysis of effects of meteorological factors on dengue incidence in Sri Lanka using time series data

In tropical and subtropical regions of eastern and South-eastern Asia, dengue fever (DF) and dengue hemorrhagic fever (DHF) outbreaks occur frequently. Previous studies indicate an association between meteorological variables and dengue incidence using time series analyses. The impacts of meteorological changes can affect dengue outbreak. However, difficulties in collecting detailed time series data in developing countries have led to common use of monthly data in most previous studies. In addition, time series analyses are often limited to one area because of the difficulty in collecting meteorological and dengue incidence data in multiple areas. To gain better understanding, we examined the effects of meteorological factors on dengue incidence in three geographically distinct areas (Ratnapura, Colombo, and Anuradhapura) of Sri Lanka by time series analysis of weekly data. The weekly average maximum temperature and total rainfall and the total number of dengue cases from 2005 to 2011 (7 years) were used as time series data in this study. Subsequently, time series analyses were performed on the basis of ordinary least squares regression analysis followed by the vector autoregressive model (VAR). In conclusion, weekly average maximum temperatures and the weekly total rainfall did not significantly affect dengue incidence in three geographically different areas of Sri Lanka. However, the weekly total rainfall slightly influenced dengue incidence in the cities of Colombo and Anuradhapura.

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.