Chlorine resistance of poliovirus isolants recovered from drinking water.

Poliovirus 1 isolants were recovered from finished drinking water produced by a modern, well-operated water treatment plant. These waters contained free chlorine residuals in excess of 1 mg/liter. The chlorine inactivation of purified high-titer preparations of two such isolants was compared with the inactivation behavior of two stock strains of poliovirus 1, LSc and Mahoney. The surviving fraction of virus derived from the two natural isolants was shown to be orders of magnitude greater than that of the standard strains. These results raise the question whether indirect drinking water standards based on free chlorine residuals are adequate public health measures, or whether direct standards based on virus determinations might be necessary.     

Bioaccumulation and depuration of enteroviruses by the soft-shelled clam, Mya arenaria.

Low levels of feces-associated natural virus, simulating virus numbers estimated to exist in moderately polluted shellfish-growing waters, were used to evaluate the effectiveness of depuration as a virus depletion procedure in soft-shell clams. Depuration effectiveness depended upon the numbers of virus bioaccumulated and whether virus was solids associated. Virus uptake was greatest when viruses were solids associated and pollution levels were equivalent or greater than those likely to be found in grossly polluted growing waters. Virtually all bioaccumulated feces-associated natural virus was deposited within either the hepatopancreas or siphon tissues. Viruses usually were eliminated within a 24- to 48-h depuration period. Dependence upon depuration of clams to elimate health hazards of virus etiology involved a risk factor not measureable in the study. The greatest reduction of health risks would come from the routine depuration of clams harvested from growing waters of good sanitary quality.     

Diagnosis of Amyloidosis and Differentiation from Chronic,Idiopathic Enterocolitis in Rhesus (Macaca mulatta) and Pig-Tailed (M. nemestrina) Macaques

Amyloidosis is a progressive and ultimately fatal disease in which amyloid, an insoluble fibrillar protein, is deposited inappropriately in multiple organs, eventually leading to organ dysfunction. Although this condition commonly affects macaques, there is currently no reliable method of early diagnosis. Changes in clinical pathology parameters have been associated with amyloidosis but occur in late stages of disease, are nonspecific, and resemble those seen in chronic, idiopathic enterocolitis. A review of animal records revealed that amyloidosis was almost always diagnosed postmortem, with prevalences of 15% and 25% in our rhesus and pig-tailed macaque colonies, respectively. As a noninvasive, high-throughput diagnostic approach to improve antemortem diagnosis of amyloidosis in macaques, we evaluated serum amyloid A (SAA), an acute-phase protein and the precursor to amyloid. Using necropsy records and ELISA analysis of banked serum, we found that SAA is significantly elevated in both rhesus and pig-tailed macaques with amyloid compared with those with chronic enterocolitis and healthy controls. At necropsy, 92% of rhesus and 83% of pig-tailed had amyloid deposition in either the intestines or liver. Minimally invasive biopsy techniques including endoscopy of the small intestine, mucosal biopsy of the colon, and ultrasound-guided trucut biopsy of the liver were used to differentiate macaques in our colonies with similar clinical presentations as either having amyloidosis or chronic, idiopathic enterocolitis. Our data suggest that SAA can serve as an effective noninvasive screening tool for amyloidosis and that minimally invasive biopsies can be used to confirm this diagnosis.Abbreviations: SAA, serum amyloid AAmyloidosis is a pathologic condition that occurs spontaneously in humans, mammals, birds, and reptiles.⁴⁷ Secondary systemic amyloidosis, also referred to as reactive amyloidosis, is the most common form described in domestic animals.⁴⁶ It is a progressive disease in which an insoluble fibrillar protein consisting of β pleated sheets, amyloid, is deposited inappropriately in multiple organs, eventually leading to dysfunction.^40,46 Secondary amyloidosis is most often the result of chronic infections or inflammatory disease. In humans, it occurs with a wide variety of conditions including inflammatory bowel disease,³ osteoarthritis including rheumatoid and juvenile forms,^20,25 chronic infections such as tuberculosis, and hereditary disease such as familial Mediterranean fever.⁴³ Similarly, in nonhuman primates, the disease has been described with several conditions of chronic infection or inflammation including bacterial enterocolitis,^4,19,30,37 chronic indwelling catheters,⁹ parasitism,^2,4 respiratory disease,^30,37 trauma,³⁷ and rheumatoid arthritis.⁶Despite reported prevalences as high as 30% in rhesus (Macaca mulatta)⁴ and 47% in pig-tailed macaques (Macaca nemestrina),¹⁹ amyloidosis remains a challenge to diagnose. The current diagnostic ‘gold standard’ in macaques is histopathology of the affected organ;¹⁹ however, amyloid can be deposited in tissues for as long as 3 y before the development of clinical signs.¹⁶ Histologic diagnoses of amyloidosis typically are confirmed with Congo red staining, in which amyloid proteins appear apple-green and birefringent under polarized light. In addition, electron microscopy can detect the fibrillar amyloid proteins in tissues, and other histologic stains including methyl violet, sulphonated Alcian blue, and thioflavin S and T can be used but are less specific than is Congo red.³³ Although changes in clinical pathology parameters such as decreases in serum albumin and total protein have been associated with amyloidosis,^19,29 they are often nonspecific and resemble those seen in the frequently comorbid conditions chronic anorexia and chronic, idiopathic enterocolitis. Furthermore, imaging techniques such as abdominal X-ray and ultrasonography have been shown to be nondiagnostic in macaques with amyloidosis.¹⁹ Consequently, at our institution and in other macaque colonies, diagnosis of amyloidosis is often made at necropsy.The current standard of diagnosis in humans is biopsy with histopathology of affected organs, but unlike in nonhuman primates, minimally invasive tissue sampling has been extensively explored.¹⁷ Aspiration or biopsy of the subcutaneous abdominal fat pad has currently replaced many biopsy techniques as the preliminary diagnostic, with reported sensitivities ranging from 66% to 92%.^{5,24,28,39,44} Rectal biopsy was previously the preferred minimally invasive approach and is now often used adjunctively when subcutaneous abdominal fat is negative for amyloid but the clinical suspicion for amyloidosis remains high.^5,17 Additional tissue biopsy sites with limited morbidity such as skin, gingiva, and stomach have been reported with lesser sensitivities.^5,34,39,44 In contrast, limited information is published on the usefulness of minimally invasive biopsy techniques for diagnosing amyloidosis in macaques. One report found endoscopic biopsy of the stomach and colon to be of limited utility in diagnosing amyloidosis in a colony of pig-tailed macaques.¹⁹ Similarly, a single publication reported colonoscopy to be noninformative and labor-intensive in a colony of rhesus macaques.¹⁵ Retrospective studies of macaque colonies have shown a predilection for amyloid deposition in the intestines and liver,^4,30,38 suggesting that endoscopic or percutaneous biopsy of these tissues may reliably provide definitive antemortem diagnosis for amyloidosis.In addition to biopsy, identification of the relevant amyloid precursor protein within the blood is an integral part of the diagnosis of amyloidosis in human patients¹⁷ and holds promise as a screening tool in macaque colonies because of its high throughput potential in comparison to biopsy. Serum amyloid A (SAA), an acute-phase protein, can be found circulating in the blood and is the precursor for amyloid formation and deposition in secondary systemic amyloidosis. Specifically, when elevated SAA persists in the bloodstream, it ultimately progresses to amyloid deposition in tissues.^13,45 Profound elevations in SAA occur in the bloodstream as a result of acute inflammation, but these elevations are transient as SAA then is rapidly degraded and removed from the peripheral circulation.^7,45 Although the exact role of chronic inflammation and SAA in the pathogenesis of secondary, systemic amyloidosis is not well understood, SAA is pathologically persistently elevated in human patients with chronic inflammatory disease that develop secondary systemic amyloidosis. In contrast, serum SAA remains at normal lower levels in human patients without amyloidosis but ongoing chronic inflammatory disease.^13,14,26 Furthermore, quantification of SAA is more effective than are organ function tests as a prognostic measure of amyloid disease and is routinely used to monitor disease progression and response to treatment in humans.¹⁴ In rhesus and pig-tailed macaques, SAA is elevated in subjects with amyloidosis as compared with those that are clinically normal.^8,19 The ability to distinguish between healthy animals and those with subclinical amyloidosis would be clinically useful. Human studies indicate that establishing a diagnosis of secondary amyloidosis in its early stages followed by prompt treatment of the inciting chronic inflammatory process can arrest the progression of amyloidosis and can even result in disease remission in some cases.^{21,23,31,32,36} Of equal interest would be the ability to distinguish amyloidosis from chronic, idiopathic enterocolitis, a common disease among macaque colonies^12,35 that has considerable clinical overlap with the late stages of amyloidosis but different therapeutic options and prognosis than does systemic amyloidosis. Although there is no definitive treatment for amyloidosis in humans or macaques, recent human case reports suggest that antiinflammatory therapy with newer targeted monocolonal antibody medications, such as IL6 receptor antagonists, can successfully reverse the disease. This outcome has been demonstrated in several cases by both the reduction of circulating SAA to normal levels and by the histologic disappearance of amyloid proteins in biopsies of affected tissues.^{21,23,31,32,36} Accurate antemortem diagnosis of amyloidosis in macaques potentially would support further investigations into the novel application of these drugs for the treatment of amyloidosis in both human and macaque patients.We hypothesize that SAA, in addition to being a useful screening method for identifying animals with amyloidosis, can be used to distinguish between macaques with this disease and those with chronic, idiopathic enterocolitis. We further hypothesize that, in agreement with retrospective studies from macaques at other institutions, the intestines and liver will be commonly affected in amyloidotic macaques in our own colonies and that minimally invasive biopsy of these tissues can provide definitive, antemortem diagnosis of amyloidosis.     

Optimal Semelparity

Semelparous organisms have a simple life cycle characterized by immediate death after reproduction. We assume that semelparous life histories can be separated into a juvenile non-reproductive period followed by an adult period during which reproduction is possible. We derive formulae for the optimal age and size at reproduction and for the optimal size of the offspring (e.g., seeds). Our main contribution is to determine the conditions under which the optimal size of the offspring does not depend on the optimal size at reproduction and vice versa.     

HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion

HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.     

Hand,Foot, and Mouth Disease in China: Modeling Epidemic Dynamics of Enterovirus Serotypes and Implications for Vaccination

Background

Hand, foot, and mouth disease (HFMD) is a common childhood illness caused by serotypes of the Enterovirus A species in the genus Enterovirus of the Picornaviridae family. The disease has had a substantial burden throughout East and Southeast Asia over the past 15 y. China reported 9 million cases of HFMD between 2008 and 2013, with the two serotypes Enterovirus A71 (EV-A71) and Coxsackievirus A16 (CV-A16) being responsible for the majority of these cases. Three recent phase 3 clinical trials showed that inactivated monovalent EV-A71 vaccines manufactured in China were highly efficacious against HFMD associated with EV-A71, but offered no protection against HFMD caused by CV-A16. To better inform vaccination policy, we used mathematical models to evaluate the effect of prospective vaccination against EV-A71-associated HFMD and the potential risk of serotype replacement by CV-A16. We also extended the model to address the co-circulation, and implications for vaccination, of additional non-EV-A71, non-CV-A16 serotypes of enterovirus.

Methods and Findings

Weekly reports of HFMD incidence from 31 provinces in Mainland China from 1 January 2009 to 31 December 2013 were used to fit multi-serotype time series susceptible–infected–recovered (TSIR) epidemic models. We obtained good model fit for the two-serotype TSIR with cross-protection, capturing the seasonality and geographic heterogeneity of province-level transmission, with strong correlation between the observed and simulated epidemic series. The national estimate of the basic reproduction number, R ₀, weighted by provincial population size, was 26.63 for EV-A71 (interquartile range [IQR]: 23.14, 30.40) and 27.13 for CV-A16 (IQR: 23.15, 31.34), with considerable variation between provinces (however, predictions about the overall impact of vaccination were robust to this variation). EV-A71 incidence was projected to decrease monotonically with higher coverage rates of EV-A71 vaccination. Across provinces, CV-A16 incidence in the post-EV-A71-vaccination period remained either comparable to or only slightly increased from levels prior to vaccination. The duration and strength of cross-protection following infection with EV-A71 or CV-A16 was estimated to be 9.95 wk (95% confidence interval [CI]: 3.31, 23.40) in 68% of the population (95% CI: 37%, 96%). Our predictions are limited by the necessarily short and under-sampled time series and the possible circulation of unidentified serotypes, but, nonetheless, sensitivity analyses indicate that our results are robust in predicting that the vaccine should drastically reduce incidence of EV-A71 without a substantial competitive release of CV-A16.

Conclusions

The ability of our models to capture the observed epidemic cycles suggests that herd immunity is driving the epidemic dynamics caused by the multiple serotypes of enterovirus. Our results predict that the EV-A71 and CV-A16 serotypes provide a temporary immunizing effect against each other. Achieving high coverage rates of EV-A71 vaccination would be necessary to eliminate the ongoing transmission of EV-A71, but serotype replacement by CV-A16 following EV-A71 vaccination is likely to be transient and minor compared to the corresponding reduction in the burden of EV-A71-associated HFMD. Therefore, a mass EV-A71 vaccination program of infants and young children should provide significant benefits in terms of a reduction in overall HFMD burden.     

Negative selection on BRCA1 susceptibility alleles sheds light on the population genetics of late-onset diseases and aging theory

The magnitude of negative selection on alleles involved in age-specific mortality decreases with age. This is the foundation of the evolutionary theory of senescence. Because of this decrease in negative selection with age, and because of the absence of reproduction after menopause, alleles involved in women's late-onset diseases are generally considered evolutionarily neutral. Recently, genetic and epidemiological data on alleles involved in late onset-diseases have become available. It is therefore timely to estimate selection on these alleles. Here, we estimate selection on BRCA1 alleles leading to susceptibility to late-onset breast and ovarian cancer. For this, we integrate estimates of the risk of developing a cancer for BRCA1-carriers into population genetics frameworks, and calculate selection coefficients on BRCA1 alleles for different demographic scenarios varying across the extent of human demography. We then explore the magnitude of negative selection on alleles leading to a diverse range of risk patterns, to capture a variety of late-onset diseases. We show that BRCA1 alleles may have been under significant negative selection during human history. Although the mean age of onset of the disease is long after menopause, variance in age of onset means that there are always enough cases occurring before the end of reproductive life to compromise the selective value of women carrying a susceptibility allele in BRCA1. This seems to be the case for an extended range of risk of onset functions varying both in mean and variance. This finding may explain the distribution of BRCA1 alleles' frequency, and also why alleles for many late-onset diseases, like certain familial forms of cancer, coronary artery diseases and Alzheimer dementia, are typically recent and rare. Finally, we discuss why the two most popular evolutionary theories of aging, mutation accumulation and antagonistic pleiotropy, may underestimate the effect of selection on survival at old ages.