Transmission parameters of vector-borne infections

Vector-borne infections are those for which the agent (virus, bacteria, or parasite) is transmitted from an infected host (animal or human) to another by a hematophagous arthropod (mosquito, tick, lice, and flea). Two parameters quantify the dynamics of a vector-borne infection: (1) the basic reproductive number (R(0)) that is the mean number of secondary infections transmitted from an infectious host by the bite of the vector and (2) the generation interval that explores the speed of occurrence of secondary cases transmitted by the vector from an infectious case. In a population in which some individuals are immune, the parameter of interest is the net reproduction number (R) function of R(0) and the proportion of those immune. For vector-borne infectious agents, R(0) is determined by the number of vectors in contact with a given individual (m), the number of a given vector bites/day on individuals (a), the daily survival rate of the vector (p), the duration of the pathogenic agent's development cycle in the vector (n), the proportion of infected vectors that are really infectious (vector competence) (b), the probability of agent transmission from a viremic individual to the vector for one bite (c) and the host's infectiousness clearance rate (r) with R(0)=(m.?a(2).?p(n)/-lnp).?b.?c/r. These parameters are related to geographic and climatic conditions and cannot, therefore, be extrapolated from one situation to another.     

The long-term dynamics of tuberculosis and other diseases with long serial intervals: implications of and for changing reproduction numbers.

The net and basic reproduction numbers are among the most widely-applied concepts in infectious disease epidemiology. A net reproduction number (the average number of secondary infectious cases resulting from each case in a given population) of above 1 is conventionally associated with an increase in incidence; the basic reproduction number (defined analogously for a ''totally susceptible'' population) provides a standard measure of the ''transmission potential'' of an infection. Using a model of the epidemiology of tuberculosis in England and Wales since 1900, we demonstrate that these measures are difficult to apply if disease can follow reinfection, and that they lose their conventional interpretations if important epidemiological parameters, such as the rate of contact between individuals, change over the time interval between successive cases in a chain of transmission (the serial interval). The net reproduction number for tuberculosis in England and Wales appears to have been approximately 1 from 1900 until 1950, despite concurrent declines in morbidity and mortality rates, and it declined rapidly in the second half of this century. The basic reproduction number declined from about 3 in 1900, reached 2 by 1950, and first fell below 1 in about 1960. Reductions in effective contact between individuals over this period, measured in terms of the average number of individuals to whom each case could transmit the infection, meant that the conventional basic reproduction number measure (which does not consider subsequent changes in epidemiological parameters) for a given year failed to reflect the ''actual transmission potential'' of the infection. This latter property is better described by a variant of the conventional measure which takes secular trends in contact into account. These results are relevant for the interpretation of trends in any infectious disease for which epidemiological parameters change over time periods comparable to the infectious period, incubation period or serial interval.     

新型冠状病毒感染不同阶段的传染性研究进展

新型冠状病毒(新冠病毒)感染不同阶段的传染性特征是调查病例感染来源、确定密切接触者范围和病例隔离时间等防控措施的重要基础。本文通过对国内外文献、技术报告与专业指南等资料进行综述,基于病原学和流行病学两个维度的研究结果,探讨新冠病毒感染者在潜伏期、临床症状期和恢复期阶段的传染性特征。现有研究提示,新冠病毒感染者在潜伏期末和发病期均可分离到具有感染性的病毒,发病4~6 d后在上呼吸道样本中病毒载量达到高峰,随后开始下降,提示在潜伏期末和发病1周内的传染性相对较强。个别病例在恢复期尽管可再次检出新冠病毒核酸,但未发现具有传染性的证据。     

Bayesian parameter inference for dynamic infectious disease modelling: rotavirus in Germany

Understanding infectious disease dynamics using epidemic models based on ordinary differential equations requires the calibration of model parameters from data. A commonly used approach in practice to simplify this task is to fix many parameters on the basis of expert or literature information. However, this not only leaves the corresponding uncertainty unexamined but often also leads to biased inference for the remaining parameters because of dependence structures inherent in any given model. In the present work, we develop a Bayesian inference framework that lessens the reliance on such external parameter quantifications by pursuing a more data‐driven calibration approach. This includes a novel focus on residual autocorrelation combined with model averaging techniques in order to reduce these estimates’ dependence on the underlying model structure. We applied our methods to the modelling of age‐stratified weekly rotavirus incidence data in Germany from 2001 to 2008 using a complex susceptible–infectious–susceptible‐type model complemented by the stochastic reporting of new cases. As a result, we found the detection rate in the eastern federal states to be more than four times higher compared with that of the western federal states (19.0% vs 4.3%), and also the infectiousness of symptomatically infected individuals was estimated to be more than 10 times higher than that of asymptomatically infected individuals (95% credibility interval: 8.1–19.6). Not only do these findings give valuable epidemiological insight into the transmission processes, we were also able to examine the considerable impact on the model‐predicted transmission dynamics when fixing parameters beforehand. Copyright © 2013 John Wiley & Sons, Ltd.     

Effectiveness of Contact Tracing for Viral Disease Mitigation and Suppression: Evidence-Based Review

BackgroundContact tracing in association with quarantine and isolation is an important public health tool to control outbreaks of infectious diseases. This strategy has been widely implemented during the current COVID-19 pandemic. The effectiveness of this nonpharmaceutical intervention is largely dependent on social interactions within the population and its combination with other interventions. Given the high transmissibility of SARS-CoV-2, short serial intervals, and asymptomatic transmission patterns, the effectiveness of contact tracing for this novel viral agent is largely unknown.ObjectiveThis study aims to identify and synthesize evidence regarding the effectiveness of contact tracing on infectious viral disease outcomes based on prior scientific literature.MethodsAn evidence-based review was conducted to identify studies from the PubMed database, including preprint medRxiv server content, related to the effectiveness of contact tracing in viral outbreaks. The search dates were from database inception to July 24, 2020. Outcomes of interest included measures of incidence, transmission, hospitalization, and mortality.ResultsOut of 159 unique records retrieved, 45 (28.3%) records were reviewed at the full-text level, and 24 (15.1%) records met all inclusion criteria. The studies included utilized mathematical modeling (n=14), observational (n=8), and systematic review (n=2) approaches. Only 2 studies considered digital contact tracing. Contact tracing was mostly evaluated in combination with other nonpharmaceutical interventions and/or pharmaceutical interventions. Although some degree of effectiveness in decreasing viral disease incidence, transmission, and resulting hospitalizations and mortality was observed, these results were highly dependent on epidemic severity (R0 value), number of contacts traced (including presymptomatic and asymptomatic cases), timeliness, duration, and compliance with combined interventions (eg, isolation, quarantine, and treatment). Contact tracing effectiveness was particularly limited by logistical challenges associated with increased outbreak size and speed of infection spread.ConclusionsTimely deployment of contact tracing strategically layered with other nonpharmaceutical interventions could be an effective public health tool for mitigating and suppressing infectious outbreaks by decreasing viral disease incidence, transmission, and resulting hospitalizations and mortality.     

2011-2017年重庆市南岸区学校传染病突发公共卫生事件分析

目的 分析2011—2017年南岸区学校传染病突发公共卫生事件流行特征,为探索适合本区实际的学校传染病综合防控措施提供依据。方法 采用描述流行病学方法。结果 2011—2017年累计报告学校传染病突发公共卫生事件50起,占全区事件发生总数94.34% 。发病1939例,无死亡病例报告,平均罹患率为3.30%;呼吸道传染病疫情为主要事件占 66%,其次为肠道传染病占34%;疫情发生时间主要在4—6月及9—10月;报告事件数最多的前3位街镇依次为南坪镇、长生桥镇及涂山镇;小学报告疫情起数最多,共27起,占54%,其次是幼儿园,15起,占30%;呼吸道传染病疫情持续平均时间及首发病例发病至疫情报告间隔平均时间均高于肠道传染病。结论 学校是传染病突发公共卫生事件的高发场所,呼吸道传染病为疫情防控重点和难点。南岸区需加强以呼吸道及肠道传染病为重点的学校传染病疫情监测,联合区教委督促学校积极落实传染病防控准备,同时,进一步推动南岸区疫苗接种工作,避免疫情扩散。     

Epidemiology of transmissible diseases after elimination

Elimination of an infectious disease is often understood to mean the total absence of cases in a population. This situation can occur only if the entire population is immune as a result of either natural disease or vaccination. However, this costly and unrealistic scenario is not necessary to ensure elimination, more appropriately defined as a situation in which sustained transmission cannot occur and secondary spread from importations of disease will end naturally, without intervention. The authors describe the size and duration of outbreaks caused by imported infections after indigenous transmission has been eliminated. They show that the status of the elimination process can be monitored by assessing the proportion of cases imported and the distribution of outbreak sizes. Measles in Canada, the United States, and the United Kingdom provides a good example of the relevance of these criteria. Surveillance of the size and duration of these outbreaks enables maintenance of elimination to be monitored.     

2010年深圳市学校与托幼机构传染病爆发疫情分析

目的了解2010年深圳市学校与托幼机构传染病爆发疫情的流行病学特征。方法应用描述性流行病学方法对深圳市2010年学校传染病爆发疫情进行分析。结果 2010年深圳市学校与托幼机构传染病爆发疫情263起,其中以小学最为常见,占43.4%;传染病爆发疫情以3、4、9月为多,占70%以上;爆发疫情为乙类、丙类和非法定传染病,主要病种为流感、手足口病和急性出血性结膜炎;在263起传染病爆发疫情中,经肠道传播的占60.8%,其次为呼吸道传播占39.2%。发病2 610例,波及人数39 149人,罹患率为6.7%。结论 2010年深圳市学校与托幼机构传染病爆发疫情主要为丙类传染病,传播途径以肠道传播为主,经呼吸道传播为次;高发人群仍然是幼儿及小学生。     

Transmission dynamics of primary pneumonic plague in the USA

Plague is thought to have killed millions during three catastrophic pandemics. Primary pneumonic plague, the most severe form of the disease, is transmissible from person-to-person and has the potential for propagating epidemics. Efforts to quantify its transmission potential have relied on published data from large outbreaks, an approach that artificially inflates the basic reproductive number (R(0)) and skews the distribution of individual infectiousness. Using data for all primary pneumonic plague cases reported in the USA from 1900 to 2009, we determined that the majority of cases will fail to transmit, even in the absence of antimicrobial treatment or prophylaxis. Nevertheless, potential for sustained outbreaks still exists due to superspreading events. These findings challenge current concepts regarding primary pneumonic plague transmission.     

A Bayesian MCMC approach to study transmission of influenza: application to household longitudinal data

We propose a transmission model to estimate the main characteristics of influenza transmission in households. The model details the risks of infection in the household and in the community at the individual scale. Heterogeneity among subjects is investigated considering both individual susceptibility and infectiousness. The model was applied to a data set consisting of the follow-up of influenza symptoms in 334 households during 15 days after an index case visited a general practitioner with virologically confirmed influenza.Estimating the parameters of the transmission model was challenging because a large part of the infectious process was not observed: only the dates when new cases were detected were observed. For each case, the data were augmented with the unobserved dates of the start and the end of the infectious period. The transmission model was included in a 3-levels hierarchical structure: (i) the observation level ensured that the augmented data were consistent with the observed data, (ii) the transmission level described the underlying epidemic process, (iii) the prior level specified the distribution of the parameters. From a Bayesian perspective, the joint posterior distribution of model parameters and augmented data was explored by Markov chain Monte Carlo (MCMC) sampling.The mean duration of influenza infectious period was estimated at 3.8 days (95 per cent credible interval, 95 per cent CI [3.1,4.6]) with a standard deviation of 2.0 days (95 per cent CI [1.1,2.8]). The instantaneous risk of influenza transmission between an infective and a susceptible within a household was found to decrease with the size of the household, and established at 0.32 person day(-1) (95 per cent CI [0.26,0.39]); the instantaneous risk of infection from the community was 0.0056 day(-1) (95 per cent CI [0.0029,0.0087]). Focusing on the differences in transmission between children (less than 15 years old) and adults, we estimated that the former were more likely to transmit than adults (posterior probability larger than 99 per cent), but that the mean duration of the infectious period was similar in children (3.6 days, 95 per cent CI [2.3,5.2]) and adults (3.9 days, 95 per cent CI [3.2,4.9]). The posterior probability that children had a larger community risk was 76 per cent and the posterior probability that they were more susceptible than adults was 79 per cent.     

Tuberculosis outbreak investigations in the United States, 2002-2008

To understand circumstances of tuberculosis transmission that strain public health resources, we systematically reviewed Centers for Disease Control and Prevention (CDC) staff reports of US outbreaks in which CDC participated during 2002-2008 that involved ≥3 culture-confirmed tuberculosis cases linked by genotype and epidemiology. Twenty-seven outbreaks, representing 398 patients, were reviewed. Twenty-four of the 27 outbreaks involved primarily US-born patients; substance abuse was another predominant feature of outbreaks. Prolonged infectiousness because of provider- and patient-related factors was common. In 17 outbreaks, a drug house was a notable contributing factor. The most frequently documented intervention to control the outbreak was prioritizing contacts according to risk for infection and disease progression to ensure that the highest risk contacts were completely evaluated. US-born persons with reported substance abuse most strongly characterized the tuberculosis outbreaks in this review. Substance abuse remains one of the greatest challenges to controlling tuberculosis transmission in the United States.     

深圳市2009-2012年学校及托幼机构传染病暴发疫情分析

目的了解深圳市2009-2012年学校及托幼机构传染病暴发疫情流行病学特征,为做好学校及托幼机构传染病疫情防制提供科学依据。方法收集深圳市2009-2012年学校及托幼机构传染病暴发疫情资料,运用描述性流行病学方法对数据进行分析。结果深圳市2009-2012年学校及托幼机构共报告传染病暴发疫情1308起,发病10443例,发病率为4.50%。其中疫情高峰出现在3、6、9和12月,占70%以上;疫情在小学发生最多,占45.87%;以呼吸道传染病为主,占68.27%;主要病种有流行性感冒、手足口病、水痘、流行性腮腺炎。结论深圳市小学和托幼机构是传染病的高发场所,应加强其呼吸道和肠道传染病的预防控制工作。     

Modeling potential responses to smallpox as a bioterrorist weapon.

We constructed a mathematical model to describe the spread of smallpox after a deliberate release of the virus. Assuming 100 persons initially infected and 3 persons infected per infectious person, quarantine alone could stop disease transmission but would require a minimum daily removal rate of 50% of those with overt symptoms. Vaccination would stop the outbreak within 365 days after release only if disease transmission were reduced to <0.85 persons infected per infectious person. A combined vaccination and quarantine campaign could stop an outbreak if a daily quarantine rate of 25% were achieved and vaccination reduced smallpox transmission by > or = 33%. In such a scenario, approximately 4,200 cases would occur and 365 days would be needed to stop the outbreak. Historical data indicate that a median of 2,155 smallpox vaccine doses per case were given to stop outbreaks, implying that a stockpile of 40 million doses should be adequate.     

Trends in primary and secondary syphilis and HIV infections in men who have sex with men--San Francisco and Los Angeles, California, 1998-2002

Because syphilis infection facilitates acquisition and transmission of human immunodeficiency virus (HIV), recent outbreaks of syphilis among men who have sex with men (MSM) in major U.S. cities, including San Francisco and Los Angeles, and reported increases in sexual risk behavior have raised concerns about potential increases in HIV transmission. In 2002, MSM accounted for the majority of primary and secondary (P&S) syphilis cases in men reported in San Francisco (93%) and Los Angeles (81%). To investigate a potential change in HIV incidence associated with the syphilis outbreaks in the two cities, local, state, and federal health officials analyzed data from HIV counseling and testing centers and a municipal sexually transmitted disease (STD) clinic. This report describes the results of that investigation, which indicated that, as of 2002, the outbreaks of syphilis had not had a substantial impact on HIV incidence among MSM in these two cities. However, the continued increase in syphilis cases in MSM underscores the need for integrated HIV- and STD-prevention strategies to control syphilis outbreaks and prevent potential increases in HIV infections (6,7) and for further systematic studies of HIV incidence among MSM infected with syphilis.     

Estimating the transmission parameters of pneumococcal carriage in households

This paper analyses Streptococcus pneumoniae transmission dynamics in households using longitudinal data on pneumococcal (Pnc) carriage in the United Kingdom. Ten consecutive swabs were taken at 4-week intervals from all members of 121 households. The family status is derived from the observed Pnc carriage status of each family member. Transition matrices are built for each family size and composition containing the observed frequency of transitions between family statuses over a 28-day interval. A density-dependent transmission model is fitted to derive maximum-likelihood estimates of the duration of carriage and acquisition rates from the community and from infected individuals within the household. Parameter values are estimated for children (< 5 years) and adults (5+ years). The duration of carriage is longer in children < 5 years of age than in older family members (51 vs. 19 days). Children are 3-4 times more likely than adults to acquire Pnc infection from the community. Transmission rates within the household suggest that adults are more infectious but less susceptible than children. Transmission within the household is most important in large families. The proportion of household-acquired infection ranges from 29 to 46% in households of three persons to 38-50% in larger households. Evidence of density-dependent within-household transmission is found, although the strength of this relationship is not clear from the model estimates.     

Establishing herd immunity against Ebola through vaccination

ObjectivesIn response to recent concern regarding Ebola outbreaks, this study aims to (1) determine the relationship between vaccination coverage and herd immunity, (2) determine the vaccination coverage necessary to establish herd immunity for previous Ebola viruses, and (3) recommend vaccination coverage thresholds for future Ebola viruses.MethodsHerd immunity thresholds needed to block transmission of Ebola virus were determined using vaccine efficacy and number of secondary cases per infected case during an entire infectious period.ResultsIn past Ebola outbreaks 42.2–63.0% of the population would need to be vaccinated in order to prevent transmission and outbreaks. Assuming 80% vaccine efficacy as reported by phase I clinical trials, 52.7–78.7% of the population would require vaccination coverage in order to establish herd immunity. In recent ring vaccination trials which considered the vaccine to be 100% effective after 10 days, 42.2–63.0% of the population would need to be vaccinated.ConclusionFor future Ebola outbreaks, the spread of the virus can be prevented by vaccinating certain percentages of the population depending on vaccine efficacy and number of secondary cases per infected case.     

Analysis of the incubation period for measles in the epidemic in Greenland in 1951 using a variance components model.

This paper presents a model for analysing the incubation period of highly infectious diseases in populations where almost all susceptibles become infected during an epidemic. The model leads to a simple method for estimating the variance of the duration of the incubation period without any distributional assumptions. Further, the influence of covariates on the duration of the incubation period can be analysed. Data from the epidemic of measles in Greenland in 1951 are analysed and it is found that intersymptom times are correlated within households, suggesting that secondary cases are infected almost simultaneously. This result is inconsistent with a variation in the times of infection of secondary cases within a household which is often assumed when analysing data on measles. Prophylactic treatment did not prevent infection in the epidemic in Greenland, but it is found that the incubation period tended to be shorter for persons not receiving prophylactic treatment.     

青海省2012-2018年学校突发公共卫生事件流行病学特征分析

目的 分析青海省2012-2018年学校等集体机构突发公共卫生事件的流行病学特征,为学校疫情防控提供科学依据。方法 采用描述流行病学方法、对“突发公共卫生事件报告管理信息系统”2012 年1 月1 日- 2018年12 月31 日青海省网络直报的学校突发公共卫生事件进行分析。结果 2012-2018年青海省共报告学校突发公共卫生事件92起,报告病例3319例,分别占总报告事件的84.40%和报告病例总数的92.81%,其他传染病（水痘）的事件数和发病数均高于丙类传染病的事件数和发病数,丙类高于乙类传染病的事件数和发病数。发病居前三位的事件有水痘、流行性腮腺炎和手足口病,季节上呈现了春秋（5月和10月）双高峰现象。学校传染病疫情高发地区为农村中小学校、高发人群为县中学生和城市幼儿园。首发病例发病与疫情报告的时间间隔中位数为10d,疫情持续时间中位数为30d。结论 建议加强疫情监测,提高识别疫情的敏感性,提升各级医疗机构思想报告意识,做到早发现、早报告、早处置的同时积极开展多形式培训,是防控传染病疫情的关键。     

Transmission routes of influenza A(H1N1)pdm09: analyses of inflight outbreaks

Knowledge about the infection transmission routes is significant for developing effective intervention strategies. We searched the PubMed databases and identified 10 studies with 14 possible inflight influenza A(H1N1)pdm09 outbreaks. Considering the different mechanisms of the large-droplet and airborne routes, a meta-analysis of the outbreak data was carried out to study the difference in attack rates for passengers within and beyond two rows of the index case(s). We also explored the relationship between the attack rates and the flight duration and/or total infectivity of the index case(s). The risk ratios for passengers seated within and beyond the two rows of the index cases were 1.7 (95% confidence interval (CI) 0.98–2.84) for syndromic secondary cases and 4.3 (95% CI 1.25–14.54) for laboratory-confirmed secondary cases. Furthermore, with an increase of the product of the flight duration and the total infectivity of the index cases, the overall attack rate increased linearly. The study indicates that influenza A(H1N1)pdm09 may mainly be transmitted via the airborne route during air travel. A standardised approach for the reporting of such inflight outbreak investigations would help to provide more convincing evidence for such inflight transmission events.Key words: Airborne route, inflight outbreaks, influenza, meta-analysis