Lei Xu

Tian H, Yan C, Xu L, Büntgen U, Stenseth NC, Zhang Z: Scale-dependent climatic drivers of human epidemics in ancient China. Proc Natl Acad Sci U S A 2017.

Tian H, Yu P, Cazelles B, Xu L, Tan H, Yang J, Huang S, Xu B, Cai J, Ma C, Wei J, Li S, Qu J, Laine M, Wang J, Tong S, Stenseth NC, Xu B: Interannual cycles of Hantaan virus outbreaks at the human–animal interface in Central China are controlled by temperature and rainfall. Proc Natl Acad Sci U S A 2017:201701777.

Xu L, Stige LC, Chan KS, Zhou J, Yang J, Sang S, Wang M, Yang Z, Yan Z, Jiang T et al: Climate variation drives dengue dynamics. Proc Natl Acad Sci U S A 2017, 114(1):113-118.

Xu L, Schmid BV, Liu J, Si X, Stenseth NC, Zhang Z: The trophic responses of two different rodent-vector-plague systems to climate change. Proc Biol Sci 2015, 282

Xu L, Stige LC, Kausrud KL, Ben Ari T, Wang S, Fang X, Schmid BV, Liu Q, Stenseth NC, Zhang Z: Wet climate and transportation routes accelerate spread of human plague. P R Soc B 2014, 281(1780):20133159.

Ben-Ari T, Neerinckx S, Agier L, Cazelles B, Xu L, Zhang Z, Fang X, Wang S, Liu Q, Stenseth NC: Identification of Chinese plague foci from long-term epidemiological data. Proceedings of the National Academy of Sciences 2012, 109(21):8196-8201.(1800).

Xu L, Liu Q, Stige LC, Ben Ari T, Fang X, Chan KS, Wang S, Stenseth NC, Zhang Z: Nonlinear effect of climate on plague during the third pandemic in China. Proceedings of the National Academy of Sciences 2011, 108(25):10214-10219.

• Ma, Jian; Xu, Lei; Han, Qian; Gao, Jing; Yuan, Huihui & Dong, Kaixing [Show all 18 contributors for this article] (2025). The Indian Ocean Dipole drives imported-dominated dengue outbreaks in China: Mechanisms and predictions. PNAS Nexus. 4(11). doi: 10.1093/pnasnexus/pgaf350. Full text in Research Archive Show summary

  Dengue fever, influenced by climate dynamics and human mobility in nonendemic regions, remains poorly understood. We assessed the effects of large-scale climate features on domestic dengue outbreaks using data from China (2013–2021) and projections for 2023–2028, incorporating climate, human mobility, and environmental factors. A significant positive correlation (r = 0.89, P < 0.01) was found between domestic dengue incidence and overseas imported cases. Significant associations were also noted with domestic (F2.96, 25.78 = 518.03, P < 0.01) and international human mobility (F2.77, 25.78 = 66.84, P < 0.01), the Indian Ocean Dipole (IOD) index (F2.98, 25.78 = 522.84), and vectorial capacity (F2.92, 25.78 = 338.74, P < 0.01). IOD is the most influential climate feature, with a trend of intensification over time. The Extreme Gradient Boosting (XGBoost) algorithm incorporating IOD (r2 = 0.56) predicted outbreaks in 2025, 2026, and 2028. Our findings reveal that large-scale climate phenomenon, notably the IOD, and human mobility significantly influence dengue domestic outbreaks in China through a “dislocated impact.”

• Stenseth, Nils Christian; Dong, Kaixing; Cui, Yujun; Slavin, Philip; Xu, Lei & Yang, Ruifu [Show all 7 contributors for this article] (2024). The Ecology of Plague. In Atshabar, Bakyt B.; Stenseth, Nils Christian & Fair, Jeanne M. (Ed.), Plague: The Ecology of Natural Foci. Springer Nature. ISSN 9783031588303. p. 119–138. Full text in Research Archive
• Wang, Yuchen; Zhang, Chutian; Gao, Jing; Chen, Ziqi; Liu, Zhao & Huang, Jianbin [Show all 25 contributors for this article] (2024). Spatiotemporal trends of hemorrhagic fever with renal syndrome (HFRS) in China under climate variation. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 121(4). doi: 10.1073/pnas.2312556121. Full text in Research Archive Show summary

  Hemorrhagic fever with renal syndrome (HFRS) is a zoonotic disease caused by the rodent-transmitted orthohantaviruses (HVs), with China possessing the most cases globally. The virus hosts in China are Apodemus agrarius and Rattus norvegicus, and the disease spread is strongly influenced by global climate dynamics. To assess and predict the spatiotemporal trends of HFRS from 2005 to 2098, we collected historical HFRS data in mainland China (2005–2020), historical and projected climate and population data (2005–2098), and spatial variables including biotic, environmental, topographical, and socioeconomic. Spatiotemporal predictions and mapping were conducted under 27 scenarios incorporating multiple integrated representative concentration pathway models and population scenarios. We identify the type of magistral HVs host species as the best spatial division, including four region categories. Seven extreme climate indices associated with temperature and precipitation have been pinpointed as key factors affecting the trends of HFRS. Our predictions indicate that annual HFRS cases will increase significantly in 62 of 356 cities in mainland China. Rattus regions are predicted to be the most active, surpassing Apodemus and Mixed regions. Eighty cities are identified as at severe risk level for HFRS, each with over 50 reported cases annually, including 22 new cities primarily located in East China and Rattus regions after 2020, while 6 others develop new risk. Our results suggest that the risk of HFRS will remain high through the end of this century, with Rattus norvegicus being the most active host, and that extreme climate indices are significant risk factors. Our findings can inform evidence-based policymaking regarding future risk of HFRS.

• Yang, Ruifu; Atkinson, Steve; Chen, Ziqi; Cui, Yujun; Du, Zongmin & Han, Yanping [Show all 17 contributors for this article] (2023). Yersinia pestis and Plague: Some Knowns and Unknowns. Zoonoses. ISSN 2737-7474. 3(1), p. 1–24. doi: 10.15212/ZOONOSES-2022-0040. Full text in Research Archive Show summary

  Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress in 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 related to Y. pestis and plague. We notably focus on some key Y. pestis physiologic 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.

• Xiao, Yao; Xu, Lei; Zhang, Can; Zhu, Liehuang & Zhang, Yan (2023). Blockchain-Empowered Privacy-Preserving Digital Object Trading in the Metaverse. IEEE Multimedia. ISSN 1070-986X. 30(2), p. 81–90. doi: 10.1109/MMUL.2023.3246528. Full text in Research Archive
• Xu, Lei; Wang, Qian; Yang, Ruifu; Ganbold, Dalantai; Tsogbadrakh, Nyamdorj & Dong, Kaixing [Show all 13 contributors for this article] (2023). Climate-driven marmot-plague dynamics in Mongolia and China. Scientific Reports. 13(1), p. 1–9. doi: 10.1038/s41598-023-38966-1. Full text in Research Archive Show summary

  Abstract 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.

• Stenseth, Nils Christian; Tao, Yuxin; Zhang, Chutian; Bramanti, Barbara; Büntgen, Ulf & Cong, Xianbin [Show all 19 contributors for this article] (2022). No evidence for persistent natural plague reservoirs in historical and modern Europe. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 119(51). doi: 10.1073/pnas.2209816119. Full text in Research Archive Show summary

  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.

• Xu, Lei; Bao, Ting; Zhu, Liehuang & Zhang, Yan (2019). Trust-based privacy-preserving photo sharing in online social networks. IEEE transactions on multimedia. ISSN 1520-9210. 21(3), p. 591–602. doi: 10.1109/TMM.2018.2887019. Full text in Research Archive
• Xu, Lei; Stige, Leif Christian; Leirs, Herwig; Neerinckx, Simon; Gage, Kenneth L. & Yang, Ruifu [Show all 13 contributors for this article] (2019). Historical and genomic data reveal the influencing factors on global transmission velocity of plague during the Third Pandemic. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(24), p. 11833–11838. doi: 10.1073/pnas.1901366116. Full text in Research Archive Show summary

  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.

• Sun, Zhe; Xu, Lei; Schmid, Boris Valentijn; Dean, Katharine Rose; Zhang, Zhibin & Xie, Yan [Show all 14 contributors for this article] (2019). Human plague system associated with rodent diversity and other environmental factors. Royal Society Open Science. 6(6), p. 1–11. doi: 10.1098/rsos.190216. Full text in Research Archive Show summary

  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.

• Gai, Keke; Wu, Yulu; Zhu, Liehuang; Xu, Lei & Zhang, Yan (2019). Permissioned Blockchain and Edge Computing Empowered Privacy-Preserving Smart Grid Networks. IEEE Internet of Things Journal. ISSN 2327-4662. 6(5), p. 7992–8004. doi: 10.1109/JIOT.2019.2904303. Full text in Research Archive
• Sun, Zhe; Zhang, Zhibin; Liu, Qiyong; Lyu, Baolei; Fang, Xiye & Wang, Shuchun [Show all 9 contributors for this article] (2019). Identifying the spatiotemporal clusters of plague occurrences in China during the Third Pandemic. Integrative Zoology. ISSN 1749-4869. 15, p. 69–78. doi: 10.1111/1749-4877.12411. Full text in Research Archive
• Li, Ruiyun; Xu, Lei; Bjornstad, Ottar N.; Liu, Keke; Song, Tie & Chen, Aifang [Show all 9 contributors for this article] (2019). Climate-driven variation in mosquito density predicts the spatiotemporal dynamics of dengue. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(9), p. 3624–3629. doi: 10.1073/pnas.1806094116. Full text in Research Archive Show summary

  Dengue is a climate-sensitive mosquito-borne disease with increasing geographic extent and human incidence. Although the climate–epidemic association and outbreak risks have been assessed using both statistical and mathematical models, local mosquito population dynamics have not been incorporated in a unified predictive framework. Here, we use mosquito surveillance data from 2005 to 2015 in China to integrate a generalized additive model of mosquito dynamics with a susceptible–infected–recovered (SIR) compartmental model of viral transmission to establish a predictive model linking climate and seasonal dengue risk. The findings illustrate that spatiotemporal dynamics of dengue are predictable from the local vector dynamics, which in turn, can be predicted by climate conditions. On the basis of the similar epidemiology and transmission cycles, we believe that this integrated approach and the finer mosquito surveillance data provide a framework that can be extended to predict outbreak risk of other mosquito-borne diseases as well as project dengue risk maps for future climate scenarios.

• Liu, Keke; Sun, Jimin; Liu, Xiaobo; Li, Ruiyun; Wang, Yiguan & Lu, Liang [Show all 10 contributors for this article] (2018). Spatiotemporal patterns and determinants of dengue at county level in China from 2005-2017. International Journal of Infectious Diseases. ISSN 1201-9712. 77, p. 96–104. doi: 10.1016/j.ijid.2018.09.003. Full text in Research Archive
• Tian, Huaiyu; Yu, Pengbo; Cazelles, Bernard; Xu, Lei; Tan, Hua & Yang, Jing [Show all 18 contributors for this article] (2017). Interannual cycles of Hantaan virus outbreaks at the human–animal interface in Central China are controlled by temperature and rainfall. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 114(30), p. 8041–8046. doi: 10.1073/pnas.1701777114. Full text in Research Archive
• Tian, Huidong; Yan, Chuan; Xu, Lei; Büntgen, Ulf; Stenseth, Nils Christian & Zhang, Zhibin (2017). Scale-dependent climatic drivers of human epidemics in ancient China. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 114(49), p. 12970–12975. doi: 10.1073/pnas.1706470114. Full text in Research Archive
• Xu, Lei; Stige, Leif Christian; Chan, Kung-Sik; Zhou, Jie; Yang, Jun & Sang, Shaowei [Show all 17 contributors for this article] (2017). Climate variation drives dengue dynamics. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 114(1), p. 113–118. doi: 10.1073/pnas.1618558114. Full text in Research Archive Show summary

  Dengue, a viral infection transmitted between people by mosquitoes, is today one of the most rapidly spreading diseases in the world. Here, we report the analyses covering 11 years (2005–2015) from the city of Guangzhou in southern China. Using the first eight years of data to develop an ecological-based model for the dengue system, we reliably predict the following three years of dengue dynamics – years with exceptionally extensive dengue outbreaks. We demonstrate that climate conditions, through the effects of rainfall and temperature on mosquito abundance and dengue transmission rate, play key roles in explaining the temporal dynamics of dengue incidence in the human population. Our study thus contributes to a better understanding of dengue dynamics and provides a predictive tool for preventive dengue-reduction strategies.

• Bramanti, Barbara; Stenseth, Nils Christian; Walløe, Lars & Xu, Lei (2016). Plague: A disease which changed the path of human civilication. In Yang, Ruifu & Anisimov, Andrey (Ed.), Yersinia pestis: Retrospective and perspective. Springer. ISSN 9789402408881. p. 1–23. doi: 10.1007/978-024-0890-4_1. Full text in Research Archive
• Xu, Lei; Stige, Leif Christian; Kausrud, Kyrre Linné; Ari, Tamara Myriam Ben; Wang, Shuchun & Fang, Xiye [Show all 10 contributors for this article] (2014). Wet climate and transportation routes accelerate spread of human plague. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 281(1780). doi: 10.1098/rspb.2013.3159. Full text in Research Archive

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• Stenseth, Nils Christian; Bramanti, Barbara; Büntgen, Ulf; Fell, Henry G.; Cohn, Samuel & Sebbane, Florent [Show all 10 contributors for this article] (2023). Reply to Alfani: Reconstructing past plague ecology to understand human history. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 120(11). doi: 10.1073/pnas.2300760120. Full text in Research Archive
• Xu, Lei; Wang, Qian; Yang, Ruifu; Ganbold, Dalantai; Tsogbadrakh, Nyamdorj & Dong, Kaixing [Show all 13 contributors for this article] (2023). Author Correction: Climate-driven marmot-plague dynamics in Mongolia and China (Scientific Reports, (2023), 13, 1, (11906), 10.1038/s41598-023-38966-1). Scientific Reports. 13(1). doi: 10.1038/s41598-023-41800-3. Full text in Research Archive
• Xu, Lei (2016). Plague and climate variation in Central Asia and China. Full text in Research Archive

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