Philip A. Collender

Bio: Philip A. Collender is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Medicine & Disease surveillance. The author has an hindex of 8, co-authored 18 publications receiving 171 citations. Previous affiliations of Philip A. Collender include Emory University & University of California.

Modeling Biphasic Environmental Decay of Pathogens and Implications for Risk Analysis.

Abstract: As the appreciation for the importance of the environment in infectious disease transmission has grown, so too has interest in pathogen fate and transport. Fate has been traditionally described by simple exponential decay, but there is increasing recognition that some pathogens demonstrate a biphasic pattern of decay—fast followed by slow. While many have attributed this behavior to population heterogeneity, we demonstrate that biphasic dynamics can arise through a number of plausible mechanisms. We examine the identifiability of a general model encompassing three such mechanisms: population heterogeneity, hardening off, and the existence of viable-but-not-culturable states. Although the models are not fully identifiable from longitudinal sampling studies of pathogen concentrations, we use a differential algebra approach to determine identifiable parameter combinations. Through case studies using Cryptosporidium and Escherichia coli, we show that failure to consider biphasic pathogen dynamics can lead to ...

Modeling environmentally mediated rotavirus transmission: The role of temperature and hydrologic factors

Abstract: Rotavirus is considered a directly transmitted disease due to its high infectivity. Environmental pathways have, therefore, largely been ignored. Rotavirus, however, persists in water sources, and both its surface water concentrations and infection incidence vary with temperature. Here, we examine the potential for waterborne rotavirus transmission. We use a mechanistic model that incorporates both direct and waterborne transmission pathways, coupled with a hydrological model, and we simulate rotavirus transmission between two communities with interconnected water sources. To parameterize temperature dependency, we estimated temperature-dependent decay rates in water through a meta-analysis. Our meta-analysis suggests that rotavirus decay rates are positively associated with temperature (n = 39, P [Formula: see text] 0.001). This association is stronger at higher temperatures (over 20 °C), consistent with tropical climate conditions. Our model analysis demonstrates that water could disseminate rotavirus between the two communities for all modeled temperatures. While direct transmission was important for disease amplification within communities, waterborne transmission could also amplify transmission. In standing-water systems, the modeled increase in decay led to decreased disease, with every 1 °C increase in temperature leading to up to a 2.4% decrease in incidence. These effect sizes are consistent with prior meta-analyses, suggesting that environmental transmission through water sources may partially explain the observed associations between temperature and rotavirus incidence. Waterborne rotavirus transmission is likely most important in cooler seasons and in communities that use slow-moving or stagnant water sources. Even when indirect transmission through water cannot sustain outbreaks, it can seed outbreaks that are maintained by high direct transmission rates.

Early evidence of inactivated enterovirus 71 vaccine impact against hand, foot, and mouth disease in a major center of ongoing transmission in China, 2011-2018: a longitudinal surveillance study

Abstract: Background Enterovirus 71 (EV71) is a major causative agent of hand, foot, and mouth disease (HFMD), associated with severe manifestations of the disease. Pediatric immunization with inactivated EV71 vaccine was initiated in 2016 in the Asia-Pacific Region, including China. We analyzed time series of HFMD cases attributable to EV71, coxsackievirus A16 (CA16), and other enteroviruses in Chengdu, a major transmission center in China, to assess early impacts of immunization. Methods Reported HFMD cases were obtained from China's notifiable disease surveillance system. We compared observed post-vaccination incidence rates during 2017-18 with counterfactual predictions made from a negative binomial regression and a random forest model fitted to pre-vaccine years (2011-15). We fit a change point model to the full time series to evaluate whether the trend of EV71 HFMD changed following vaccination. Results Between 2011-18, 279,352 HFMD cases were reported in the study region. The average incidence rate of EV71 HFMD in 2017-2018 was 60% (95% prediction interval (PI): 41%-72%) lower than predicted in the absence of immunization, corresponding to an estimated 6,911 (95% PI: 3,246, 11,542) EV71 cases averted over two years. There were 52% (95% PI: 0.42, 0.60) fewer severe HFMD cases than predicted. However, the incidence rate of non-CA16 and non-EV71 HFMD was elevated in 2018. We identified a significant decline in the trend of EV71 HFMD four months into the post-vaccine period. Conclusions We provide the first real-world evidence that programmatic vaccination against EV71 is effective against childhood HFMD and present an approach to detect early vaccine impact or intended consequences from surveillance data.

Prenatal and early-life exposure to the Great Chinese Famine increased the risk of tuberculosis in adulthood across two generations.

Abstract: Global food security is a major driver of population health, and food system collapse may have complex and long-lasting effects on health outcomes. We examined the effect of prenatal exposure to the Great Chinese Famine (1958–1962)—the largest famine in human history—on pulmonary tuberculosis (PTB) across consecutive generations in a major center of ongoing transmission in China. We analyzed >1 million PTB cases diagnosed between 2005 and 2018 in Sichuan Province using age–period–cohort analysis and mixed-effects metaregression to estimate the effect of the famine on PTB risk in the directly affected birth cohort (F1) and their likely offspring (F2). The analysis was repeated on certain sexually transmitted and blood-borne infections (STBBI) to explore potential mechanisms of the intergenerational effects. A substantial burden of active PTB in the exposed F1 cohort and their offspring was attributable to the Great Chinese Famine, with more than 12,000 famine-attributable active PTB cases (>1.23% of all cases reported between 2005 and 2018). An interquartile range increase in famine intensity resulted in a 6.53% (95% confidence interval [CI]: 1.19–12.14%) increase in the ratio of observed to expected incidence rate (incidence rate ratio, IRR) in the absence of famine in F1, and an 8.32% (95% CI: 0.59–16.6%) increase in F2 IRR. Increased risk of STBBI was also observed in F2. Prenatal and early-life exposure to malnutrition may increase the risk of active PTB in the exposed generation and their offspring, with the intergenerational effect potentially due to both within-household transmission and increases in host susceptibility.

Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study.

Abstract: Summary Background Wuhan was the first epicentre of COVID-19 in the world, accounting for 80% of cases in China during the first wave. We aimed to assess household transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and risk factors associated with infectivity and susceptibility to infection in Wuhan. Methods This retrospective cohort study included the households of all laboratory-confirmed or clinically confirmed COVID-19 cases and laboratory-confirmed asymptomatic SARS-CoV-2 infections identified by the Wuhan Center for Disease Control and Prevention between Dec 2, 2019, and April 18, 2020. We defined households as groups of family members and close relatives who did not necessarily live at the same address and considered households that shared common contacts as epidemiologically linked. We used a statistical transmission model to estimate household secondary attack rates and to quantify risk factors associated with infectivity and susceptibility to infection, accounting for individual-level exposure history. We assessed how intervention policies affected the household reproductive number, defined as the mean number of household contacts a case can infect. Findings 27 101 households with 29 578 primary cases and 57 581 household contacts were identified. The secondary attack rate estimated with the transmission model was 15·6% (95% CI 15·2–16·0), assuming a mean incubation period of 5 days and a maximum infectious period of 22 days. Individuals aged 60 years or older were at a higher risk of infection with SARS-CoV-2 than all other age groups. Infants aged 0–1 years were significantly more likely to be infected than children aged 2–5 years (odds ratio [OR] 2·20, 95% CI 1·40–3·44) and children aged 6–12 years (1·53, 1·01–2·34). Given the same exposure time, children and adolescents younger than 20 years of age were more likely to infect others than were adults aged 60 years or older (1·58, 1·28–1·95). Asymptomatic individuals were much less likely to infect others than were symptomatic cases (0·21, 0·14–0·31). Symptomatic cases were more likely to infect others before symptom onset than after (1·42, 1·30–1·55). After mass isolation of cases, quarantine of household contacts, and restriction of movement policies were implemented, household reproductive numbers declined by 52% among primary cases (from 0·25 [95% CI 0·24–0·26] to 0·12 [0·10–0·13]) and by 63% among secondary cases (from 0·17 [0·16–0·18] to 0·063 [0·057–0·070]). Interpretation Within households, children and adolescents were less susceptible to SARS-CoV-2 infection but were more infectious than older individuals. Presymptomatic cases were more infectious and individuals with asymptomatic infection less infectious than symptomatic cases. These findings have implications for devising interventions for blocking household transmission of SARS-CoV-2, such as timely vaccination of eligible children once resources become available. Funding National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, US National Institutes of Health, and US National Science Foundation.

Evaluation of Phi6 Persistence and Suitability as an Enveloped Virus Surrogate.

Abstract: Recent outbreaks involving enveloped viruses, such as Ebola virus, have raised questions regarding the persistence of enveloped viruses in the water environment. Efforts have been made to find enveloped virus surrogates due to challenges investigating viruses that require biosafety-level 3 or 4 handling. In this study, the enveloped bacteriophage Phi6 was evaluated as a surrogate for enveloped waterborne viruses. The persistence of Phi6 was tested in aqueous conditions chosen based on previously published viral persistence studies. Our results demonstrated that the predicted T90 (time for 90% inactivation) of Phi6 under the 12 evaluated conditions varied from 24 min to 117 days depending on temperature, biological activity, and aqueous media composition. Phi6 persistence was then compared with persistence values from other enveloped viruses reported in the literature. The apparent suitability of Phi6 as an enveloped virus surrogate was dependent on the temperature and composition of the media tested. Of e...

병원성 바이러스와 지표성 바이러스의 생존에 관한 비교연구 ( Comparative Survival of Indicator Viruses and Enteric Viruses in Seawater and Sediment )

Abstract: Laboratory studies quantified the relative survival of F+ coliphages, B. fragilis phages, hepatitis A virus, poliovirus, and rotavirus in seawater and seawater-sediment mixtures. Samples of each matrix were seeded with mixed populations of the viruses and incubated at 5 and 25°C for 60 days. F+ coliphages were inactivated faster than three enteric viruses in seawater at 25°C. In seawater-sediment mixture at 5 and 25°C or at 5°C in seawater, their survival was comparable to those enteric viruses that died off rapidly. In contrast, B. fragilis phages survived comparable to or better than enteric viruses in all conditions. Except for HAV, greater percentages of total detectable viruses were distributed in sediment over time. The effect of sediment on survival of viruses differed among viruses. Survival rates were significantly greater at 5°C than at 25° for all five viruses.

Sediment transport modeling review―current and future developments

Abstract: With the rapid developments in numerical methods for fluid mechanics,computational modeling has become an attractive tool for studying flow/sediment transport and associated pollutant fate processes in such different environments as rivers,lakes,and coastal areas,over the past three decades,a large number of computational hydrodynamic/sediment transport models have been developedThe article traces the devel-opmental stages of current representative(1D,2D,and 3D)models and describes their main features,strengths,and limitations,and is intended as a first guide to readers interested in immersing themselves in modeling and at the same time sets the stage for discussing current limitations and future needsThe article provided model formulation,the spatial and temporal characteristics,the coupling/linkage of the hydrodynamic and sediment components,the model capabilities to handle unsteady flows,bed load and suspended load,sediment exchange processes,type of sediment(cohesive versus cohesion-less),and multi-fractional sediment transportSome examples of the different model applications are summarized,the reader can use these case studies as a reference guide for model setup,calibration,and verificationThe authors also attempt to provide an insight for model users about model choice,problem and way to improve model input and calibrationThe article discussed model limitations such as simulating complex turbulent flows,sediment entrainment,multi-fractional transport rates,the treatment of the dispersion and diffusion coefficients,soil contributions from the bank or the hill slopes and floodplains,coupling between flow and sediment processes,and highlighted the future research needs for improving available hydrodynamic/sediment transport modelsAt last,the two-phase flow approach to formulate models of sediment-flow interaction and other cross-cutting issues are discussed and reviewed

Breaking beta: deconstructing the parasite transmission function

Abstract: Transmission is a fundamental step in the life cycle of every parasite but it is also one of the most challenging processes to model and quantify. In most host–parasite models, the transmission process is encapsulated by a single parameter b. Many different biological processes and interactions, acting on both hosts and infectious organisms, are subsumed in this single term. There are, however, at least two undesirable consequences of this high level of abstraction. First, nonlinearities and heterogeneities that can be critical to the dynamic behaviour of infections are poorly represented; second, estimating the transmission coefficient b from field data is often very difficult. In this paper,we present a conceptual model,which breaks the transmission process into its component parts. This deconstruction enables us to identify circumstances that generate nonlinearities in transmission, with potential implications for emergent transmission behaviour at individual and population scales. Such behaviour cannot be explained by the traditional linear transmission frameworks. The deconstruction also provides a clearer link to the empirical estimation of key components of transmission and enables the construction of flexible models that produce a unified understanding of the spread of both micro- and macro-parasite infectious disease agents. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.