From the Cover: Optimizing infectious disease interventions during an emerging epidemic

The emergence and global impact of the novel influenza A(H1N1)v highlights the continuous threat to public health posed by a steady stream of new and unexpected infectious disease outbreaks in animals and humans. Once an emerging epidemic is detected, public health authorities will attempt to mitigate the epidemic by, among other measures, reducing further spread as much as possible. Scarce and/or costly control measures such as vaccines, anti-infective drugs, and social distancing must be allocated while epidemiological characteristics of the disease remain uncertain. Here we present first principles for allocating scarce resources with limited data. We show that under a broad class of assumptions, the simple rule of targeting intervention measures at the group with the highest risk of infection per individual will achieve the largest reduction in the transmission potential of a novel infection. For vaccination of susceptible persons, the appropriate risk measure is force of infection; for social distancing, the appropriate risk measure is incidence of infection. Unlike existing methods that rely on detailed knowledge of group-specific transmission rates, the method described here can be implemented using only data that are readily available during an epidemic, and allows ready adaptation as the epidemic progresses. The need to observe risk of infection helps to focus the ongoing planning and design of new infectious disease surveillance programs; from the presented first principles for allocating scarce resources, we can adjust the prioritization of groups for intervention when new observations on an emerging epidemic become available.     

A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India

India's Late Cretaceous fossil mammals include the only undisputed pre-Tertiary Gondwanan eutherians, such as Deccanolestes. Recent studies have suggested a relationship between Deccanolestes and African and European Paleocene adapisoriculids, which have been variably identified as stem euarchontans, stem primates, lipotyphlan insectivores, or afrosoricids. Support for a close relationship between Deccanolestes and any of these placental mammal clades would be unique in representing a confirmed Mesozoic record of a placental mammal. However, some paleogeographic reconstructions place India at its peak isolation from all other continents during the latest Cretaceous, complicating reconstructions of the biogeographic history of the placental radiation. Recent fieldwork in India has recovered dozens of better-preserved specimens of Cretaceous eutherians, including several new species. Here, we incorporate these new specimens into an extensive phylogenetic analysis that includes every clade with a previously hypothesized relationship to Deccanolestes. Our results support a robust relationship between Deccanolestes and Paleocene adapisoriculids, but do not support a close affinity between these taxa and any placental clade, demonstrating that Deccanolestes is not a Cretaceous placental mammal and reinforcing the sizeable gap between molecular and fossil divergence time estimates for the placental mammal radiation. Instead, our expanded data push Adapisoriculidae, including Deccanolestes, into a much more basal position than in earlier analyses, strengthening hypotheses that scansoriality and arboreality were prevalent early in eutherian evolution. This comprehensive phylogeny indicates that faunal exchange occurred between India, Africa, and Europe in the Late Cretaceous-Early Paleocene, and suggests a previously unrecognized ～30 to 45 Myr "ghost lineage" for these Gondwanan eutherians.     

Brief Report: Adaptive staffing can mitigate essential worker disease and absenteeism in an emerging epidemic

Essential worker absenteeism has been a pressing problem in the COVID-19 pandemic. Nearly 20% of US hospitals experienced staff shortages, exhausting replacement pools and at times requiring COVID-positive healthcare workers to remain at work. To our knowledge there are no data-informed models examining how different staffing strategies affect epidemic dynamics on a network in the context of rising worker absenteeism. Here we develop a susceptible–infected–quarantined-recovered adaptive network model using pair approximations to gauge the effects of worker replacement versus redistribution of work among remaining healthy workers in the early epidemic phase. Parameterized with hospital data, the model exhibits a time-varying trade-off: Worker replacement minimizes peak prevalence in the early phase, while redistribution minimizes final outbreak size. Any “ideal” strategy requires balancing the need to maintain a baseline number of workers against the desire to decrease total number infected. We show that one adaptive strategy—switching from replacement to redistribution at epidemic peak—decreases disease burden by 9.7% and nearly doubles the final fraction of healthy workers compared to pure replacement.     

Proton pump inhibitors and an emerging epidemic of gastric fundic gland polyposis

Fundic gland polyps are now commonly recognized during endoscopy. These polyps are benign, often multiple and usually detected in the gastric body and fundus. In the past, these polyps were sometimes associated with familial adenomatous polyposis. In recent years, it has become evident that increasing numbers of these polyps are being detected during endoscopic studies, particularly in patients treated with proton pump inhibitors for prolonged periods. In some, dysplastic changes in these polyps have also been reported. Recent studies have suggested that there may be no increase in risk of colon cancer with long-term proton pump inhibitor therapy. While temporarily reassuring, ongoing vigilance, particularly in those genetically predisposed to colon cancer, is still warranted.     

The value of spatial information in MPA network design

The science of spatial fisheries management, which combines ecology, oceanography, and economics, has matured significantly. As a result, there have been recent advances in exploiting spatially explicit data to develop spatially explicit management policies, such as networks of marine protected areas (MPAs). However, when data are sparse, spatially explicit policies become less viable, and we must instead rely on blunt policies such as total allowable catches or imprecisely configured networks of MPAs. Therefore, spatial information has the potential to change management approaches and thus has value. We develop a general framework within which to analyze the value of information for spatial fisheries management and apply that framework to several US Pacific coast fisheries. We find that improved spatial information can increase fishery value significantly (>10% in our simulations), and that it changes dramatically the efficient management approach—switching from diffuse effort everywhere to a strategy where fishing is spatially targeted, with some areas under intensive harvest and others closed to fishing. Using all available information, even when incomplete, is essential to management success and may as much as double fishery value relative to using (admittedly incorrect) assumptions commonly invoked.     

Heart failure survival among older adults in the United States: a poor prognosis for an emerging epidemic in the Medicare population

OBJECTIVE: To describe the 6-year probability of survival for older adults after their first hospitalization for heart failure. SETTING: National Medicare hospital claims records for 1984 through 1986 and Medicare enrollment records from 1986 through 1992. DESIGN: We identified a national cohort of 170 239 (9% black patients) Medicare patients, 67 years or older, with no evidence of heart failure in 1984 or 1985, who were hospitalized and discharged for the first time in 1986 with a principal diagnosis of heart failure. For groups defined by race, sex, age, Medicaid eligibility, and comorbid conditions, we compared the probability of survival with Cox proportional hazards regression. RESULTS: Only 19% of black men, 16% of white men, 25% of black women, and 23% of white women survived 6 years. One third died within the first year. Men had lower median survival and 38% greater risk of mortality than did women (P<.05). White men had 10% greater risk of mortality than did black men (P<.05). Medicaid eligibility (white adults only) and diabetes were associated with increased mortality (P<.05). CONCLUSIONS: The prognosis for older adults with heart failure underscores the importance of prevention strategies and early detection and treatment modalities that can prevent, improve, or reverse myocardial dysfunction, particularly for the growing number of adults who are at increased risk for developing heart failure because of hypertension, diabetes, or myocardial infarction.     

Bayesian Phylogeographic Inference Suggests Japan as the Center for the Origin and Dissemination of Rice Stripe Virus

Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The origin and dispersal of RSV remain poorly understood, but an emerging hypothesis suggests that: (i) RSV originates from Yunnan, a southwest province of China; and (ii) some places of eastern China have acted as a center for the international dissemination of RSV. This hypothesis, however, has never been tested rigorously. Using a data set comprising more than 200 time-stamped coat protein gene sequences of RSV from Japan, China and South Korea, we reconstructed the phylogeographic history of RSV with Bayesian phylogeographic inference. Unexpectedly, the results did not support the abovementioned hypothesis. Instead, they suggested that RSV originates from Japan and Japan has been the major center for the dissemination of RSV in the past decades. Based on these data and the temporal dynamics of RSV reported recently by another group, we proposed a new hypothesis to explain the origin and dispersal of RSV. This new hypothesis may be valuable for further studies aiming to clarify the epidemiology of RSV. It may also be useful in designing management strategies against this devastating virus.     

Bayesian Phylodynamic Analysis Reveals the Dispersal Patterns of African Swine Fever Virus

The evolutionary and demographic history of African swine fever virus (ASFV) is potentially quite valuable for developing efficient and sustainable management strategies. In this study, we performed phylogenetic, phylodynamic, and phylogeographic analyses of worldwide ASFV based on complete ASFV genomes, B646L gene, and E183L gene sequences obtained from NCBI to understand the epidemiology of ASFV. Bayesian phylodynamic analysis and phylogenetic analysis showed highly similar results of group clustering between E183L and the complete genome. The evidence of migration and the demographic history of ASFV were also revealed by the Bayesian phylodynamic analysis. The evolutionary rate was estimated to be 1.14 × 10⁻⁵ substitution/site/year. The large out-migration from the viral population in South Africa played a crucial role in spreading the virus worldwide. Our study not only provides resources for the better utilization of genomic data but also reveals the comprehensive worldwide evolutionary history of ASFV with a broad sampling window across ~70 years. The characteristics of the virus spatiotemporal transmission are also elucidated, which could be of great importance for devising strategies to control the virus.     

鄱阳湖血吸虫病重疫区学生16年健康教育效果纵向观察

目的研制有效控制重疫区学生感染的血吸虫病健康教育干预模式,并观察其远期干预效果。方法应用实验研究方法,1992年基线调查后,1993-1999年和2000-2007年分别应用"信息传播+防护技能培训+奖惩激励"和"信息传播+行为参与+行为激励"干预实验组目标人群。结果干预前(1992)实验组和对照组血防知识知晓率、血防态度正确率、疫水接触率和血吸虫感染率均无显著差异。干预后1年(1993)实验组血防知识知晓率和血防态度正确率分别由干预前8.99、55.06提高到94.38、98.88;疫水接触率和血吸虫感染率分别由干预前14.55、13.94下降到1.87、2.25;对照组干预前后上述各项指标均无明显变化。干预后2-7年(1994-1999)实验组疫水接触率和血吸虫感染率均较干预前显著下降,但均未降至0。干预后8-15年(2000-2007)实验组均无疫水接触者和血吸虫感染者。结论应用"信息传播+行为参与+行为激励"模式干预可使重度疫区学生明显减轻甚至可完全避免血吸虫感染。     

安徽省恙虫病新疫源地疫情暴发特点及意义

目的 调查安徽省恙虫病新疫源地多起疫情暴发的流行病学和临床特点,阐明我国恙虫病疫源地分布的相应新变化.方法　采用现场流行病学调查、病史及检验结果分析、文献复习等方法,系统分析安徽省历次恙虫病疫情暴发的时间、地点、规模、地理、气候、虫媒、病原学、易感人群、临床特点及诊治情况.结果　2007年以来安徽省多次出现恙虫病疫情暴...     

2009-2015年沈阳地区布鲁氏菌病疫情的时空特征分析

目的 分析2009-2015年沈阳地区布鲁氏菌病(以下简称布病)的时空分布变化特征,为制定本地区布病防控策略提供循证依据。方法 布病监测方法按《全国人间布病监测方案》和《沈阳市人间布病监测方案》进行。2009-2015年人间布病疫情资料来自于沈阳市疾病预防控制中心传染病监测数据库。应用描述性流行病学方法分析布病疫情特征,进一步结合ArcMAP软件分析布病疫情的时空转换特征,绘制沈阳地区布病的时空分布图。结果 7年间沈阳地区共报告布病患者1 356例,其中2014年沈阳市区出现1例死亡病例;布病年均发病率的波动区间为(0.46~4.59)/10万,趋势性检验χ²=541.44,P<0.001,呈逐年递增趋势,而发病率增幅呈逐年递减趋势;春夏季为发病高峰期;病例以30~59岁男性农民居多。从时空分布图上看,2009年布病发病数和发病率最高的都是新民市,而到2015年发病数最高的是沈阳市区;发病率最高的是紧邻市区的法库县;从地理信息上来看,病例高发区由西部的新民市向东部的沈阳市和法库县推移,疫区范围也由2009年的7个地区,扩大为2015年的13个地区。结论 2009-2015年间沈阳地区布病疫情的时空变化特征为:随着时间的推移,疫区由局部地区扩展为整个地区, 病例高发区由西部的新民市向东部的沈阳市和法库县推移。     

Impact of an effective multidrug-resistant tuberculosis control programme in the setting of an immature HIV epidemic: system dynamics simulation model

This study sought to determine the impact of an effective programme of multidrug resistant tuberculosis control (MDRTB) on a population that is witnessing an explosive HIV epidemic among injecting drug users (IDUs), where the prevalence of MDRTB is already high. A transmission model was constructed that represents the dynamics of the drug-susceptible tuberculosis (DSTB), MDRTB and HIV spread among the adult population of Samara Oblast, Russia: from official notifications of tuberculosis and of HIV infection, estimates of MDRTB derived from surveillance studies, population data from official regional statistics, data on transmission probabilities from peer-reviewed publications and informed estimates, and policy-makers' estimates of IDU populations.Two scenarios of programme effectiveness for MDRTB were modelled and run over a period of 10 years to predict cumulative deaths. In a population of 3.3 million with a high prevalence of MDRTB, an emerging epidemic of HIV among IDUs, and a functioning directly observed therapy-short course (DOTS) programme, the model predicts that under low cure rates for MDRTB the expected cumulative deaths from tuberculosis will reach 6303 deaths including 1900 deaths from MDRTB at 10 years. Under high cure rate for MDRTB 4465 deaths will occur including 134 deaths from MDRTB. At 10 years there is little impact on HIV-infected populations from the MDRTB epidemic, but as the HIV epidemic matures the impact becomes substantial. When the model is extended to 20 years cumulative deaths from MDRTB become very high if cure rates for MDRTB are low and cumulative deaths in the HIV-infected population, likewise, are profoundly affected.In the presence of an immature HIV epidemic failure to actively control MDRTB may result in approximately a third more deaths than if effective treatment is given. As the HIV epidemic matures then the impact of MDRTB grows substantially if MDRTB control strategies are ineffective. The epidemiological starting point for these scenarios is present in many regions within the former Soviet Union and this analysis suggests control of MDRTB should be an urgent priority.