Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics

Phylodynamic approaches to studying avian influenza virus

Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.

Milestones to reach Hepatitis C Virus (HCV) elimination in Italy: From free-of-charge screening to regional roadmaps for an HCV-free nation

Although Italy has been on track for Hepatitis C Virus (HCV) elimination since 2019, it fell off track due to the decrease in the number of treated patients. HCV elimination in Italy will be possible if immediate action is taken. A health policy was implemented beginning in 2021, consisting of screening among key populations and birth cohorts (1969-1989), estimated to have a high prevalence of undiagnosed individuals. The active screening requires regional governance that manages the processes' complexity integrating a well-organized network between territory assistance and hospital to achieve an effective HCV care cascade. This document aims to support the regional decision-making process by defining paths for screening and linkage-to-care. Implementing active screening strategies beyond a risk-based approach is required as a General Practitioners' task. Simplified paths must be drawn for the key populations screening. The infrastructure built for COVID-19 vaccination could be used also for HCV screening. According to a multidisciplinary care delivery, screening should be supplemented with rapid linkage-to-care and treatment of newly diagnosed patients. The realization of the proactive screening during the first two years is vital because it will define the tracks for the whole HCV cost-effective screening of 1948-1988 birth cohorts in Italy.

High-Risk Injection-Related Practices Associated with anti-HCV Positivity among Young Adults Seeking Services in Three Small Cities in Wisconsin

BACKGROUND

Hepatitis C virus (HCV) infection has been increasing among people who inject drugs (PWID), younger than 30 years, and living in rural or suburban areas. We examined injection-related behaviors of young PWID to determine factors associated with HCV infection.

METHODS

From September 2013-May 2015, respondent-driven and snowball sampling were used in 3 suburban areas of Wisconsin to recruit PWID 18-29 years who reported injection drug use in the previous 12 months. Participants were tested for HCV antibody (anti-HCV) and reported injection-related behaviors/practices via self-administered computer-based survey. We calculated anti-HCV prevalence and assessed associated factors using multivariable logistic regression.

RESULTS

Forty-two percent (117/280) of participants were male, 83% (231/280) were white, and median age was 23 years. Overall HCV prevalence was 33%, but HCV prevalence among males was 39%. Adjusting for age, sex, race/ethnicity, education, relationship status, insurance status and income, anti-HCV positivity was associated with higher injection frequency (> 100 times in the past six months) (aOR = 3.07; 95% Confidence Interval (95% CI): 1.72-5.45), ever shared syringes (aOR = 5.15; 95% CI: 2.52-10.51), past week/last use receptive rinse water sharing (aOR = 1.88; 95% CI: 1.06-3.33), past week/last use receptive filter sharing (aOR = 3.25; 95% CI: 1.61-6.54), reusing syringes (aOR = 1.91, 95% CI: 1.08-3.37), history of overdose (aOR = 8.82; 95% CI: 2.26-3.95), and having ever injected another PWID (aOR = 8.82; 95%CI 3.94-19.76).

DISCUSSION

Anti-HCV positivity is associated with high-risk injection practices. Young PWID would benefit from access to evidence-based interventions that reduce their risk of infection, link those infected to HCV treatment, and provide education to reduce further transmission.

Phylodynamic analysis in the understanding of the current COVID-19 pandemic and its utility in vaccine and antiviral design and assessment

Over the last decades, the use of phylogenetic methods in the study of emerging infectious diseases has gained considerable traction in public health. Particularly, the integration of phylogenetic analyses with the understanding of the pathogen dynamics at the population level has provided powerful tools for epidemiological surveillance systems. In the same way, the development of statistical methods and theory, as well as improvement of computational efficiency for evolutionary analysis, has expanded the use of these tools for vaccine and antiviral development. Today with the Coronavirus Disease 2019 (COVID-19), this seems to be critical. In this article, we discuss how the application of phylodynamic analysis can improve the understanding of current pandemic dynamics as well as the design, selection, and evaluation of vaccine candidates and antivirals.

Genome-wide comparison of coronaviruses derived from veterinary animals: A canine and feline perspective

Feline- and canine-derived coronaviruses (FCoVs and CCoVs) are widespread among dog and cat populations. This study was to understand the route of disease origin and viral transmission in veterinary animals and in human through comparative pan-genomic analysis of coronavirus sequences, especially retrieved from genomes of FCoV and CCoV. Average nucleotide identity based on complete genomes might clustered CoV strains according to their infected host, with an exception of type II of CCoV (accession number KC175339) that was clustered closely to virulent FCoVs. In contrast, the hierarchical clustering based on gene repertories retrieved from pan-genome analysis might divided the examined coronaviruses into host-independent clusters, and formed obviously the cluster of Alphacoronaviruses into sub-clusters of feline-canine, only feline, feline-canine-human coronavirus. Also, functional analysis of genomic subsets might help to divide FCoV and CCoV pan-genomes into (i) clusters of core genes encoding spike, membrane, nucleocapsid proteins, and ORF1ab polyprotein; (ii) clusters of core-like genes encoding nonstructural proteins; (iii) clusters of accessory genes encoding the ORF1A; and (iv) two singleton genes encoding nonstructural protein and polyprotein 1ab. Seven clusters of gene repertories were categorized as common to the FCoV and/or CCoV genomes including pantropic and high virulent strains, illustrating that distinct core-like genes/accessory genes concerning to their pathogenicity should be exploited in further biotype analysis of new isolate. In conclusion, the phylogenomic analyses have allowed the identification of trends in the viral genomic data, especially in developing a specific control measures against coronavirus disease, such as the selection of good markers for differentiating new species from common and/or pantropic isolates.

Innovative procedures for micro-elimination of HCV infection in persons who use drugs

People who use drugs are a key population in global HCV control. We evaluated the efficacy of an innovative model to eliminate HCV infection in a high-risk population of PWUD in a service for substance use disorder (SUD). Between January 2018 and December 2018, we conducted a prospective, interventional, before and after study, based on audits performed by Infectious Diseases physicians in a SUD facility in Piedimonte Matese, in southern Italy, to improve the knowledge about HCV infection; a shared protocol for screening and linkage to care of patients was implemented. The pre-intervention period was defined as January-December 2017 and the post-intervention period as January-December 2018. The subjects followed up at SUD facility in the pre-intervention and post-intervention periods were 318 and 275, respectively. Compared with the pre-intervention period, the number of anti-HCV-positive subjects tested for HCV RNA was higher in the post-intervention period (91% vs 27%, P < .0001), as was the number who started directly acting antivirals (DAAs). Of the 18 HCV RNA-positive subjects in the pre-intervention period, only 3 (16.6%) started DAA, a percentage decisively lower than that observed after the start of the programme, 63 (84%) of 75 subjects (P < .0001), and all obtained SVR. The data were similar for people who inject drugs (PWID) and non-PWID sub-populations. The use of our innovative model with close interaction between the Infectious Disease Unit and the SUD facility determined a significant increase in HCV RNA testing, linkage to care and the start of DAA in the PWUD population.

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into account. To address these issues, we developed two phylogenetic methods based on virus sequence data: 1) to generally detect if significant transmission heterogeneity is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring. We derive inference procedures to estimate model parameters, including the amount of transmission heterogeneity, in a sampled epidemic. We show that it is possible to detect transmission heterogeneity under a wide range of simulated situations, including incomplete sampling, varying levels of heterogeneity, and including within-host genetic diversity. When evaluating real HIV-1 data from different epidemic scenarios, we found a lower level of transmission heterogeneity in slowly spreading situations and a higher level of heterogeneity in data that included a rapid outbreak, while R0 and Sackin's index (overall tree shape statistic) were similar in the two scenarios, suggesting that our new method is able to detect transmission heterogeneity in real data. We then show by simulations that targeted prevention, where we pinpoint high-level spread using a coalescence measurement, is efficient when sequence data are collected in an ongoing surveillance system. Such phylogeny-guided prevention is efficient under both single-step contact tracing as well as iterative contact tracing as compared to random intervention.

Nanomedicine as a future therapeutic approach for Hepatitis C virus

Hepatitis C virus (HCV) is not easily cleared from the human body and in most cases turned into chronic infection. This chronicity is a major cause of liver damage, cirrhosis and hepatocellular carcinoma. Therefore, immediate detection and treatment of HCV guarantees eradication of the virus and prevention of chronicity complications. Since discovery of HCV in 1989, several emerging treatments were developed such as polyethylene glycol(PEG)-ylated interferon/ribavirin, direct acting antivirals and host targeting antivirals. Despite the progress in anti-HCV therapy, there is still a pressing need of new approaches for affordable and effective drug delivery systems using nanomedicine. In this review, the contribution of nanoparticles as a promising delivery system for HCV immunizing, diagnostic and therapeutic agents are discussed.

Medical complications of opioid use disorder in pregnancy

Women with opioid use disorder are at increased risk of other medical complications of pregnancy. Providing care for such complex patients requires the ability to 1) acknowledge addiction as a chronic disease, 2) incorporate the altered physiology of pregnancy, and 3) devise a treatment plan that can effectively manage acute conditions. A basic tenet of care is rooted in experience, rather than evidence, but includes stabilization of opiate use disorder (OUD) as a primary goal of management of other medical complications of pregnancy. Proceeding with treatment for other medical conditions will be suboptimal without stabilization of the underlying chronic disease process. This chapter outlines some associated medical complications of OUD both in general and some of which are unique to pregnancy: infectious diseases, soft tissue infections, endocarditis, cholestasis of pregnancy, and overdose.

Mouse Models for Studying HCV Vaccines and Therapeutic Antibodies

In spite of the immense progress in hepatitis C virus (HCV) research, efforts to prevent infection, such as generating a vaccine, have not yet been successful. The high price tag associated with current treatment options for chronic infection and the spike in new infections concurrent with growing opioid abuse are strong motivators for developing effective immunization and understanding neutralizing antibodies' role in preventing infection. Humanized mice-both human liver chimeras as well as genetically humanized models-are important platforms for testing both possible vaccine candidates as well as antibody-based therapies. This chapter details the variety of ways humanized mouse technology can be employed in pursuit of learning how HCV infection can be prevented.

Contextualizing Canada's hepatitis C virus epidemic

In 2016, Canada signed on to the World Health Organization (WHO) 2030 hepatitis C virus (HCV) disease elimination targets. Most of Canada's HCV disease burden is among five disproportionately affected population groups: 1) Baby boomers, who are at increased risk of dying from decompensated cirrhosis and hepatocellular carcinoma and for whom one-time screening should be recommended to identify those undiagnosed; 2) People who inject drugs (PWID), whose mortality risks include HCV infection, HCV acquisition risks and co-morbid conditions. While HCV infection in PWID can be effectively cured with direct-acting antivirals, premature deaths from acquisition risks, now exacerbated by Canada's opioid crisis, will need to be addressed to achieve the full benefits of curative treatment. PWID require syndemic-based solutions (harm reduction, addictions and mental health support, and management of co-infections, including HIV); 3) Indigenous populations who will require wellness-based health promotion, prevention, care and treatment designed by Indigenous people to address their underlying health disparities; 4) Immigrants who will require culturally designed and linguistically appropriate services to enhance screening and engagement into care; and (5) For those incarcerated because of drug-related crimes, decriminalization and better access to harm reduction could help reduce the impact of HCV infections and premature mortality. A comprehensive prevention, care and treatment framework is needed for Canada's vulnerable populations, including those co-infected with HIV, if we are to achieve the WHO HCV elimination targets by 2030. The aim of this review is to describe the HCV epidemic in the Canadian context.

China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis

A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China-the country with the third highest tuberculosis burden-we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population.

Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series

Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. Aggregated data such as incidence time series are often not sufficiently informative to estimate k. Incorporating phylogenetic analysis can help to estimate k concurrently with other epidemiological parameters. We have developed an inference framework that uses particle Markov Chain Monte Carlo to estimate k and other epidemiological parameters using both incidence time series and the pathogen phylogeny. Using the framework to fit a modified compartmental transmission model that includes the parameter k to simulated data, we found that more accurate and less biased estimates of the reproductive number were obtained by combining epidemiological and phylogenetic analyses. However, k was most accurately estimated using pathogen phylogeny alone. Accurately estimating k was necessary for unbiased estimates of the reproductive number, but it did not affect the accuracy of reporting probability and epidemic start date estimates. We further demonstrated that inference was possible in the presence of phylogenetic uncertainty by sampling from the posterior distribution of phylogenies. Finally, we used the inference framework to estimate transmission parameters from epidemiological and genetic data collected during a poliovirus outbreak. Despite the large degree of phylogenetic uncertainty, we demonstrated that incorporating phylogenetic data in parameter inference improved the accuracy and precision of estimates.

For a program of eradication of hepatitis C in the populations at risk (drug users and convicts)

Injection drugs are the greater source for HCV infection. About 60% of drug users and about 20-30% of convicts are infected with HCV. HCV infection is often associated with behavioral disorders and drug use. At present, few subjects with HCV belonging to risk groups have been treated with Direct-Acting Antivirals (DAAs). SerDs and prisons should implement the screening for HCV. HCV populations at risk can be successfully treated with DAAs. The primary objective of the linkage to care is the holistic and integrated treatment, and the prevention of reinfections is a priority and essential part of the treatment goals. The removal of the barriers to treatment is a primary goal of the linkage-to-care models and integrated systems; the main action to be undertaken for the linkage to care of the HCV population at risk are screening, referral, treatment and prevention of reinfection. All HCV RNA+ patients may be eligible for treatment, and those with the clinical criteria for starting treatment should be treated with DAAs. All patients should receive a structured harm-reduction program (with skill training). The prevention of the infection is of paramount importance in the linkage to care of the HCV population at risk and is an element which should always be associated with the drug treatment. (www.actabiomedica.it)

"Hep C, where art thou": What are the remaining (fundable) questions in hepatitis C virus research?

Hepatitis C virus (HCV) has dominated the field of hepatology for the past 25 years, and its cure in the majority of treated patients is one of the greatest achievements in all of medicine. However, the latter has led to the belief by some that HCV research should be shelved for other, more pressing areas. The mission for HCV eradication is far from accomplished. As a historical reference, we should consider that disease elimination has required vaccination with all previously controlled infections including smallpox and polio and that simple, effective treatment is not sufficient in most infections to lead to substantial control. Syphilis is the best example, for which a single dose of penicillin (which literally costs pennies and that we have had since 1945) is curative in early stages. Not only have we not eradicated syphilis, rates of infection have increased in many places within the United States in recent years. Most HCV-infected subjects are unaware of their infection, remaining at risk for transmission to others and disease progression, including cirrhosis and hepatocellular carcinoma. In the era of highly effective direct-acting antivirals (DAAs), many questions pertaining to HCV remain, but they are more complex and difficult to answer. Here, I provide my perspective on some of these salient issues: the residual risk for disease progression after sustained virologic response, the optimal approach to current DAA failures, the impact of targeting people who inject drugs with DAAs, vaccine prospects, and application of neutralizing HCV glycoprotein antibodies. (Hepatology 2017;65:341-349).

Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects

OBJECTIVE

Although our understanding of viral transmission among people who inject drugs (PWID) has improved, we still know little about when and how many times each injector transmits HIV throughout the duration of infection. We describe HIV dynamics in PWID to evaluate which preventive strategies can be efficient.

DESIGN

Due to the notably scarce interventions, HIV-1 spread explosively in Russia and Ukraine in 1990s. By studying this epidemic between 1995 and 2005, we characterized naturally occurring transmission dynamics of HIV among PWID.

METHOD

We combined publicly available HIV pol and env sequences with prevalence estimates from Russia and Ukraine under an evolutionary epidemiology framework to characterize HIV transmissibility between PWID. We then constructed compartmental models to simulate HIV spread among PWID.

RESULTS

In the absence of interventions, each injector transmits on average to 10 others. Half of the transmissions take place within 1 month after primary infection, suggesting that the epidemic will expand even after blocking all the post-first month transmissions. Primary prevention can realistically target the first month of infection, and we show that it is very efficient to control the spread of HIV-1 in PWID. Treating acutely infected on top of primary prevention is notably effective.

CONCLUSION

As a large proportion of transmissions among PWID occur within 1 month after infection, reducing and delaying transmissions through scale-up of harm reduction programmes should always form the backbone of HIV control strategies in PWID. Growing PWID populations in the developing world, where primary prevention is scarce, constitutes a public health time bomb.

Epidemiology of hepatitis C in Greece

Hepatitis C is a global health issue and constitutes a major cause of chronic liver disease worldwide. In this article, a comprehensive literature search was conducted for the prevalence of hepatitis C virus (HCV) infection in Greece, since data on the HCV prevalence, viremia and genotypes are important for developing strategies to manage or eliminate HCV infection. In addition, the pattern of HCV infection was analyzed according to the geographic region and the risk factors. These differences reflect not only distinct epidemiological characteristics among populations, but also differences on the strategy of data acquisition and quantification. Although there are not enough data, the estimation of the current prevalence of Hepatitis C in Greece ranges from 0.5% to 2%. The most important risk factors for HCV infection include blood product transfusion, intravenous drug use, chronic hemodialysis, organ transplantation, occupational exposure, sexual transmission, and vertical transmission. Because of lack of vaccine or effective post-exposure prophylaxis for HCV, the main focus of prevention is to recognize and control these risk factors. HCV infection in Greece is closely associated with the development of chronic liver disease, cirrhosis, and primary hepatocellular carcinoma. As far as the genotype distribution is concerned genotype 1 estimated to be 45%-47% and it constitutes the prevalent genotype in Greece, followed by genotype 3.

A Smartphone Application Supporting Recovery from Heroin Addiction: Perspectives of Patients and Providers in China, Taiwan, and the USA

Smartphone-based interventions are increasingly used to support self-monitoring, self-management, and treatment and medication compliance in order to improve overall functioning and well-being. In attempting to develop a smartphone application (S-Health) that assists heroin-dependent patients in recovery, a series of focus groups (72 patients, 22 providers) were conducted in China, Taiwan, and the USA to obtain their perspectives on its acceptance and potential adoption. Data were analyzed according to the Diffusion of Innovation (DOI) theory of characteristics important to the adoption of innovation. Important to Relative Advantage, USA participants cited S-Health's potential ability to overcome logistical barriers, while those in China and Taiwan valued its potential to supplement currently limited services. In terms of Compatibility, participants across sites reported recovery needs and goals that such an application could be helpful in supporting; however, its utility during strong craving was questioned in China and Taiwan. Important factors relevant to Complexity included concerns about smartphone access and familiarity, individualization of content, and particularly in China and Taiwan, participants wanted assurance of privacy and security. The study results suggest a general acceptance, but also indicate cultural variations in access to therapeutic and other social support systems, legal repercussions of substance use, societal perceptions of addiction, and the role of family and other social support in recovery. Taking these factors into consideration is likely to increase diffusion as well as effectiveness of these smartphone-based interventions.

Trends in the Mechanistic and Dynamic Modeling of Infectious Diseases

The dynamics of infectious disease epidemics are driven by interactions between individuals with differing disease status (e.g., susceptible, infected, immune). Mechanistic models that capture the dynamics of such “dependent happenings” are a fundamental tool of infectious disease epidemiology. Recent methodological advances combined with access to new data sources and computational power have resulted in an explosion in the use of dynamic models in the analysis of emerging and established infectious diseases. Increasing use of models to inform practical public health decision making has challenged the field to develop new methods to exploit available data and appropriately characterize the uncertainty in the results. Here, we discuss recent advances and areas of active research in the mechanistic and dynamic modeling of infectious disease. We highlight how a growing emphasis on data and inference, novel forecasting methods, and increasing access to “big data” are changing the field of infectious disease dynamics. We showcase the application of these methods in phylodynamic research, which combines mechanistic models with rich sources of molecular data to tie genetic data to population-level disease dynamics. As dynamics and mechanistic modeling methods mature and are increasingly tied to principled statistical approaches, the historic separation between the infectious disease dynamics and “traditional” epidemiologic methods is beginning to erode; this presents new opportunities for cross pollination between fields and novel applications.

The application of HIV molecular epidemiology to public health

HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.

Risk Factors Associated with HCV Among Opioid-Dependent Patients in a Multisite Study

We examined risk factors associated with hepatitis C virus (HCV) infection among opioid-dependent patients enrolled into medication-assisted therapy (buprenorphine or methadone) to determine factors affecting chronic infection. Patients (N = 1039) were randomized as part of a larger, multisite clinical trial sponsored by the National Drug Abuse Treatment Clinical Trials Network assessing liver function. HCV status was first assessed with an antibody screen; if positive, then current infection was determined with an antigen screen testing for detectable virus. Patients were classified as HCV negative, HCV positive but have cleared the virus, or as having chronic HCV. Logistic regression analysis was used to examine demographic and behavioral correlates of the three groups. Thirty-four percent of patients were classified with chronic infection and 14% had evidence of prior infection with apparent clearing of the virus. Chronic infection was associated with recent injection drug use and cocaine use. Chronic HCV infection was also associated with being older and Hispanic. Age, ethnicity, and current drug use increase the likelihood of being chronically infected with HCV. Strategies targeting high risk subgroups can aid in preventing further disease escalation.

Integrating molecular epidemiology and social network analysis to study infectious diseases: Towards a socio-molecular era for public health

The number of public health applications for molecular epidemiology and social network analysis has increased rapidly since the improvement in computational capacities and the development of new sequencing techniques. Currently, molecular epidemiology methods are used in a variety of settings: from infectious disease surveillance systems to the description of disease transmission pathways. The latter are of great epidemiological importance as they let us describe how a virus spreads in a community, make predictions for the further epidemic developments, and plan preventive interventions. Social network methods are used to understand how infections spread through communities and what the risk factors for this are, as well as in improved contact tracing and message-dissemination interventions. Research is needed on how to combine molecular and social network data as both include essential, but not fully sufficient information on infection transmission pathways. The main differences between the two data sources are that, firstly, social network data include uninfected individuals unlike the molecular data sampled only from infected network members. Thus, social network data include more detailed picture of a network and can improve inferences made from molecular data. Secondly, network data refer to the current state and interactions within the social network, while molecular data refer to the time points when transmissions happened, which might have happened years before the sampling date. As of today, there have been attempts to combine and compare the data obtained from the two sources. Even though there is no consensus on whether and how social and genetic data complement each other, this research might significantly improve our understanding of how viruses spread through communities.

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We summarise and analyse the roles of molecular evolution studies in molecular epidemiology of infectious diseases.

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We review how social network and molecular sequence data have been integrated in the past.

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We show how integrating social network and molecular evolution approaches may change the study of infectious diseases.

Molecular characterization of HCV in a Swedish county over 8 years (2002-2009) reveals distinct transmission patterns

Background

Hepatitis C virus (HCV) is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county). The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission.

Methods

Molecular analyses of serum samples from 91% (N=557) of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp) was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL) was used to analyze trends over time.

Results

The most prevalent subtypes were 1a (38%) and 3a (34%). Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs). Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered), while the 1a sequences formed smaller clusters (19% of the sequences clustered), possibly suggesting different epidemics.

Conclusion

We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.

ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics

Background

The digitization of health-related information through electronic health records (EHR) and electronic healthcare reimbursement claims and the continued growth of self-reported health information through social media provides both tremendous opportunities and challenges in developing effective biosurveillance tools. With novel emerging infectious diseases being reported across different parts of the world, there is a need to build systems that can track, monitor and report such events in a timely manner. Further, it is also important to identify susceptible geographic regions and populations where emerging diseases may have a significant impact.

Methods

In this paper, we present an overview of Oak Ridge Biosurveillance Toolkit (ORBiT), which we have developed specifically to address data analytic challenges in the realm of public health surveillance. In particular, ORBiT provides an extensible environment to pull together diverse, large-scale datasets and analyze them to identify spatial and temporal patterns for various biosurveillance-related tasks.

Results

We demonstrate the utility of ORBiT in automatically extracting a small number of spatial and temporal patterns during the 2009-2010 pandemic H1N1 flu season using claims data. These patterns provide quantitative insights into the dynamics of how the pandemic flu spread across different parts of the country. We discovered that the claims data exhibits multi-scale patterns from which we could identify a small number of states in the United States (US) that act as "bridge regions" contributing to one or more specific influenza spread patterns. Similar to previous studies, the patterns show that the south-eastern regions of the US were widely affected by the H1N1 flu pandemic. Several of these south-eastern states act as bridge regions, which connect the north-east and central US in terms of flu occurrences.

Conclusions

These quantitative insights show how the claims data combined with novel analytical techniques can provide important information to decision makers when an epidemic spreads throughout the country. Taken together ORBiT provides a scalable and extensible platform for public health surveillance.

Current knowledge and future perspectives on acute hepatitis C infection

Acute hepatitis C virus (HCV) infections are frequently seen worldwide in certain risk groups, with an annual incidence rate varying between 0.08% and 66%. Although this incidence is substantial, a delayed diagnosis during chronic infection is most often made in the absence of clinical symptoms in the acute phase of the infection. Currently used methods to diagnose acute HCV infection are IgG antibody seroconversion and repeated HCV RNA measurements, although no definitive diagnostic test is currently available. Progress in the field of adaptive and innate immune responses has aided both advances in the field of HCV vaccine development and a more basic understanding of viral persistence. The rapid changes in the treatment of chronic HCV infection will affect therapeutic regimens for acute HCV infection in the coming years, leading to shorter treatment courses and pegylated interferon-free modalities. This review gives an overview of the current knowledge and uncertainties, together with some future perspectives on acute hepatitis C epidemiology, virology, immunology, and treatment.

Tactics and strategies for managing Ebola outbreaks and the salience of immunization

We present a stochastic transmission chain simulation model for Ebola viral disease (EVD) in West Africa, with the salutary result that the virus may be more controllable than previously suspected. The ongoing tactics to detect cases as rapidly as possible and isolate individuals as safely as practicable is essential to saving lives in the current outbreaks in Guinea, Liberia, and Sierra Leone. Equally important are educational campaigns that reduce contact rates between susceptible and infectious individuals in the community once an outbreak occurs. However, due to the relatively low R 0 of Ebola (around 1.5 to 2.5 next generation cases are produced per current generation case in naïve populations), rapid isolation of infectious individuals proves to be highly efficacious in containing outbreaks in new areas, while vaccination programs, even with low efficacy vaccines, can be decisive in curbing future outbreaks in areas where the Ebola virus is maintained in reservoir populations.

Molecular epidemiology, phylogeny and evolution of the filarial nematode Wuchereria bancrofti

Wuchereria bancrofti (Wb) is the most widely distributed of the three nematodes known to cause lymphatic filariasis (LF), the other two being Brugia malayi and Brugia timori. Current tools available to monitor LF are limited to diagnostic tests targeting DNA repeats, filarial antigens, and anti-filarial antibodies. While these tools are useful for detection and surveillance, elimination programs have yet to take full advantage of molecular typing for inferring infection history, strain fingerprinting, and evolution. To date, molecular typing approaches have included whole mitochondrial genomes, genotyping, targeted sequencing, and random amplified polymorphic DNA (RAPDs). These studies have revealed much about Wb biology. For example, in one study in Papua New Guinea researchers identified 5 major strains that were widespread and many minor strains some of which exhibit geographic stratification. Genome data, while rare, has been utilized to reconstruct evolutionary relationships among taxa of the Onchocercidae (the clade of filarial nematodes) and identify gene synteny. Their phylogeny reveals that speciation from the common ancestor of both B. malayi and Wb occurred around 5-6 millions years ago with shared ancestry to other filarial nematodes as recent as 15 million years ago. These discoveries hold promise for gene discovery and identifying drug targets in species that are more amenable to in vivo experiments. Continued technological developments in whole genome sequencing and data analysis will likely replace many other forms of molecular typing, multiplying the amount of data available on population structure, genetic diversity, and phylogenetics. Once widely available, the addition of population genetic data from genomic studies should hasten the elimination of LF parasites like Wb. Infectious disease control programs have benefited greatly from population genetics data and recently from population genomics data. However, while there is currently a surplus of data for diseases like malaria and HIV, there is a scarcity of this data for filarial nematodes. With the falling cost of genome sequencing, research on filarial nematodes could benefit from the addition of population genetics statistics and phylogenetics especially in dealing with elimination programs. A comprehensive review focusing on population genetics of filarial nematode does not yet exist. Here our goal is to provide a current overview of the molecular epidemiology of W. bancrofti (Wb) the primary causative agent of LF. We begin by reviewing studies utilizing molecular typing techniques with specific focus on genomic and population datasets. Next, we used whole mitochondrial genome data to construct a phylogeny and examine the evolutionary history of the Onchocercidae. Then, we provide a perspective to aid in understanding how population genetic techniques translate to modern epidemiology. Finally, we introduce the concept of genomic epidemiology and provide some examples that will aid in future studies of Wb.

Genomic analysis of emerging pathogens: methods, application and future trends

The number of emerging infectious diseases is increasing. Characterizing novel or re-emerging infections is aided by the availability of pathogen genomes. In this review, we evaluate methods that exploit pathogen sequences and the contribution of genomic analysis to understand the epidemiology of recently emerged infectious diseases.

Transitioning to highly effective therapies for the treatment of chronic hepatitis C virus infection: a policy statement and implementation guideline

Chronic hepatitis C virus (HCV) infection increases all-cause mortality, rates of cirrhosis, hepatocellular carcinoma, liver transplantation and overall health care utilization. Morbidity and mortality disproportionately affect individuals born between 1945 and 1975. The recent development of well-tolerated and highly effective therapies for chronic HCV infection represents a unique opportunity to dramatically reduce rates of HCV-related complications and their costs. Critical to the introduction of such therapies will be well-designed provincial programming to ensure immediate treatment access to individuals at highest risk for complication, and well-defined strategies to address the global treatment needs of traditionally high-risk and marginalized populations. HCV practitioners in New Brunswick created a provincial strategy that stratifies treatment according to those at highest need, measures clinical impact, and creates evaluation strategies to demonstrate the significant direct and indirect cost savings anticipated with curative treatments.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.

The changing epidemiology of hepatitis C virus infection in the United States: National Health and Nutrition Examination Survey 2001 through 2010

BACKGROUND & AIMS

In light of the dramatically changing hepatitis C therapeutic landscape, knowledge of the current burden of HCV infection in the general population of the United States is critical.

METHODS

The National Health and Nutrition Examination survey collects nationally representative data on HCV infection in the civilian population of the United States. Data from 2001 to 2010 were combined for this study. HCV testing was completed in 38,025 participants.

RESULTS

The prevalence of anti-HCV in the United Sates decreased from 1.9% (95% CI 1.5%-2.5%) in 2001-2002 to 1.3% (95% CI 0.9%-1.8%) in 2005-2006, and remained stable up to 2010. About 67% of all infected persons were positive for HCV RNA, indicating 2.3 million people with chronic HCV infection, of whom 68% have genotype 1. Seventy percent of infected persons were born between 1945 and 1965, with prevalence of 3.5% (95% CI 2.2%-4.8%). The stable rate since 2006 is mostly related to prevalent cases and foreign born persons migrating into US. Other important risk factors include less education and low economic status. Race, HIV status, number of sexual partners, and blood transfusions are no longer associated with HCV infection.

CONCLUSIONS

As of 2010, approximately 2.3 million persons were chronically infected with Hepatitis C in the US. Most of those infected are prevalent, rather than incident cases. The prevalence of HCV was on the decline, but has stabilized since 2006. Future studies should explore reasons for no decline in HCV prevalence since 2006.

Evidence that hepatitis C virus genome partly controls infection outcome

Infection by hepatitis C virus (HCV) leads to one of two outcomes; either the infection resolves within approximately 6 months or the virus can persist indefinitely. Host genetics are known to affect the likelihood of clearance or persistence. By contrast, the importance of the virus genotype in determining infection outcome is unknown, as quantifying this effect traditionally requires well-characterized transmission networks, which are rare. Extending phylogenetic approaches previously developed to estimate the virus control over set-point viral load in HIV-1 infections, we simulate inheritance of a binary trait along a phylogenetic tree, use this data to quantify how infection outcomes cluster and ascertain the effect of virus genotype on these. We apply our method to the Hepatitis C Incidence and Transmission Study in prisons (HITS-p) data set from Australia, as this cohort prospectively identified incident cases including viraemic subjects who ultimately clear the virus, thus providing us with a unique collection of sequences from clearing infections. We detect significant correlations between infection outcome and virus distance in the phylogeny for viruses of Genotype 1, with estimates lying at around 67%. No statistically significant estimates were obtained for viruses of Genotype 3a.

Discovery of ledipasvir (GS-5885): a potent, once-daily oral NS5A inhibitor for the treatment of hepatitis C virus infection

A new class of highly potent NS5A inhibitors with an unsymmetric benzimidazole-difluorofluorene-imidazole core and distal [2.2.1]azabicyclic ring system was discovered. Optimization of antiviral potency and pharmacokinetics led to the identification of 39 (ledipasvir, GS-5885). Compound 39 (GT1a replicon EC50 = 31 pM) has an extended plasma half-life of 37-45 h in healthy volunteers and produces a rapid >3 log viral load reduction in monotherapy at oral doses of 3 mg or greater with once-daily dosing in genotype 1a HCV-infected patients. 39 has been shown to be safe and efficacious, with SVR12 rates up to 100% when used in combination with direct-acting antivirals having complementary mechanisms.

Addicts with chronic hepatitis C: Difficult to reach, manage or treat?

AIM: To assess the acceptance, safety and efficacy of care and treatment for chronic hepatitis C (CHC) in drug addicts.

METHODS: We designed a multidisciplinary, phase IV prospective cohort study. All illicit drug users (IDUs) visited a Territorial Addiction Service (SerT) in the District of Brescia, and hepatitis C antibody (HCVAb) testing positive were offered as part of a standardised hepatologic visit in our Gastroenterology Unit. Patients with confirmed CHC and without medical contraindications were administered peginterferon alfa-2b 1.5 μg/kg per week plus ribavirin (800-1400 mg/d) for 16-48 wk. All IDUs were unselected because of ongoing addiction and read and signed an informed consent form. Virologic responses at weeks 4 and 12 of therapy, at the end of treatment and 24 wk after the end of treatment were the main measures of efficacy. Adherence was estimated according to the 80/80/80 criteria.

RESULTS: From November 2007 to December 2009, 162 HCVAb+ IDUs were identified. Sixty-seven patients (41% of the initial cohort) completed the diagnostic procedure, and CHC was diagnosed in 54 (33% of the total). Forty-nine patients were offered therapy, and 39 agreed (80% of acceptance rate). The prevalent HCV genotype was type 1, and the HCV RNA baseline level was over 5.6 log/mL in 61% of cases. Five patients dropped out, two because of severe adverse events (SAEs) and three without medical need. Twenty-three and 14 patients achieved end of treatment responses (ETRs; 59%) and sustained virologic responses (SVRs; 36%), respectively. Thirty-one patients were fully compliant with the study protocol (80% adherence). The prevalence of host and viral characteristics negatively affecting the treatment response was high: age over 40 years (54%), male gender (85%), overweight body type (36%), previous unsuccessful antiviral therapy (21%), HCV genotype and viral load (60% and 62%, respectively), earlier contact with HBV (40%) and steatosis and fibrosis (44% and 17%, respectively). In a univariate analysis, alcohol intake was associated with a non-response (P = 0.0018, 95%CI: 0.0058-0.4565).

CONCLUSION: Drug addicts with CHC can be successfully treated in a multidisciplinary setting using standard antiviral combination therapy, despite several “difficult to reach, manage and treat” characteristics.

Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam

Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches—often referred to as phylodynamic methods—have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies.

Phylogenetic analysis of HCV-4d in Turkey: the curious case of Kayseri province

In Turkey, genotype 1, especially type 1b virus, causes approximately 90% of these infections, while types 2, 3, and 4 exist, albeit in low prevalences and are due to relatively recent and limited introductions. Two recent reports from Kayseri, a relatively large city in Central Anatolia, indicated unusually high prevalence for type 4 infections in the province reaching a 35% among patients admitted to hospitals for treatment of chronic hepatitis C. In this study, the origin, the demographic history, and the dynamic of the epidemic of unusual HCV genotype 4d in Turkey by using Bayesian coalescent-based method were investigated. A gene flow migration approach was also used to describe the synchronous geographical dispersal and genetic diversification of this unusual genotype in Kayseri province. The Turkish clade had a tMRCA of 44 years corresponding to the year 1967 and seems to have a different origin being completely segregated from the European one. Gene flow migration analysis indicated that Kayseri province appeared to be the epicenter of HCV-4d epidemic, exporting the infections. The demographic history of HCV-4d showed that the epidemic started in 1970s year then following a slow exponential growth until 1980s. The Turkish monophyletic clade suggests a segregate circulation of the epidemic in this region mostly due to unsafe parenteral medical procedures (with drug addiction playing a relatively negligible role).

Global control of hepatitis C: where challenge meets opportunity

We are entering an important new chapter in the story of hepatitis C virus (HCV) infection. There are clear challenges and opportunities. On the one hand, new HCV infections are still occurring, and an estimated 185 million people are or have previously been infected worldwide. Most HCV-infected persons are unaware of their status yet are at risk for life-threatening diseases such as cirrhosis and hepatocellular carcinoma (HCC), whose incidences are predicted to rise in the coming decade. On the other hand, new HCV infections can be prevented, and those that have already occurred can be detected and treated--viral eradication is even possible. How the story ends will largely be determined by the extent to which these rapidly advancing opportunities overcome the growing challenges and by the vigor of the public health response.

Global control of hepatitis C: where challenge meets opportunity

We are entering an important new chapter in the story of hepatitis C virus (HCV) infection. There are clear challenges and opportunities. On the one hand, new HCV infections are still occurring, and an estimated 185 million people are or have previously been infected worldwide. Most HCV-infected persons are unaware of their status yet are at risk for life-threatening diseases such as cirrhosis and hepatocellular carcinoma (HCC), whose incidences are predicted to rise in the coming decade. On the other hand, new HCV infections can be prevented, and those that have already occurred can be detected and treated--viral eradication is even possible. How the story ends will largely be determined by the extent to which these rapidly advancing opportunities overcome the growing challenges and by the vigor of the public health response.