Andrew Aronsohn

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

ABSTRACT Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection.

Hepatitis C virus (HCV) and human pegivirus (HPgV), formerly GBV-C, are the only known human viruses in the Hepacivirus and Pegivirus genera, respectively, of the family Flaviviridae. We present the discovery of a second pegivirus, provisionally designated human pegivirus 2 (HPgV-2), by next-generation sequencing of plasma from an HCV-infected patient with multiple bloodborne exposures who died from sepsis of unknown etiology. HPgV-2 is highly divergent, situated on a deep phylogenetic branch in a clade that includes rodent and bat pegiviruses, with which it shares <32% amino acid identity. Molecular and serological tools were developed and validated for high-throughput screening of plasma samples, and a panel of 3 independent serological markers strongly correlated antibody responses with viral RNA positivity (99.9% negative predictive value). Discovery of 11 additional RNA-positive samples from a total of 2440 screened (0.45%) revealed 93–94% nucleotide identity between HPgV-2 strains. All 12 HPgV-2 RNA-positive cases were identified in individuals also testing positive for HCV RNA (12 of 983; 1.22%), including 2 samples co-infected with HIV, but HPgV-2 RNA was not detected in non-HCV-infected individuals (p<0.0001), including those singly infected by HIV (p = 0.0075) or HBV (p = 0.0077), nor in volunteer blood donors (p = 0.0082). Nine of the 12 (75%) HPgV-2 RNA positive samples were reactive for antibodies to viral serologic markers, whereas only 28 of 2,429 (1.15%) HPgV-2 RNA negative samples were seropositive. Longitudinal sampling in two individuals revealed that active HPgV-2 infection can persist in blood for at least 7 weeks, despite the presence of virus-specific antibodies. One individual harboring both HPgV-2 and HCV RNA was found to be seronegative for both viruses, suggesting a high likelihood of simultaneous acquisition of HCV and HPgV-2 infection from an acute co-transmission event. Taken together, our results indicate that HPgV-2 is a novel bloodborne infectious virus of humans and likely transmitted via the parenteral route.

Long-term outcomes after treatment with interferon and ribavirin in HCV patients.

Hepatitis C is a leading indication for transplantation and a common cause of liver-related death worldwide. Treatment for hepatitis C has evolved from interferon therapy alone, which yielded relatively poor response rates compared with the currently recommended and more effective combination of pegylated interferon and ribavirin. Factors such as hepatitis C viral genotype, pretreatment viral load, race, renal function, degree of hepatic fibrosis, and comorbid conditions such as HIV coinfection have clinical importance in that they influence viral kinetics, which play a large role in determining a sustained response to therapy or virologic “cure.” However, the goal of therapy is to reduce liver-related morbidity and mortality by decreasing rates of progression or improvement of fibrosis, reducing risk of hepatocellular carcinoma, improving posttransplant graft and patient survival, and resolving or improving some of the extrahepatic manifestations of hepatitis C. Studies generally infer long-term success from the more tangible goal of sustained viral suppression; however, increasing data suggest that effective therapy does result in decreased morbidity and mortality. Given the heterogeneity of patients who are infected with hepatitis C, treatment decisions should be specifically tailored to each individual patient on the basis of their predisposing conditions and anticipated clinical outcomes.

Herbal hepatoxicity from Chinese skullcap: A case report

The use of herbal supplements has increased considerably over the last decade. We report a case of an elderly woman who began taking Move Free Advanced for arthritis, which in addition to glucosamine and chondroitin, contained two herbal ingredients, Chinese skullcap and Black Catechu. Our patient presented with significant cholestasis and hepatitis which significantly improved after discontinuation of the supplement. Since neither the patient nor the treating physician recognized this supplement as a potential hepatotoxin, she resumed taking the supplement and again suffered from considerable hepatotoxicity. Liver biopsy at that time was consistent with acute drug induced liver injury. She, once again, recovered after discontinuation of the supplement. Review of the literature confirms that Chinese skullcap has been implicated as a possible hepatotoxic agent which was demonstrated in this case.

Decision making in liver transplantation—Limited application of the liver donor risk index

The liver donor risk index (LDRI), originally developed in 2006 by Feng et al. and since modified, is a method of evaluating liver grafts from deceased donors through the determination of the relative risk of graft failure after transplantation. Online and paper surveys about attitudes and practices regarding decision making in liver transplantation and the role of the LDRI were sent to liver transplant physicians. One hundred forty‐seven of 401 eligible respondents (37%) returned partial or complete surveys. The majority of the respondents were male (116/134 or 87%) and practiced in academic medical centers (128/138 or 93%). Transplant coordinators initially contacted the candidate with an offer in 81% of the programs. Eighty‐eight of 143 respondents (62%) reported that they were very familiar with the LDRI, but the vast majority (114/137 or 83%) rarely or never discussed the concept of the LDRI with their patients. A majority of the respondents (96/132 or 73%) believed that the LDRI does not adequately describe a livers relative risk of graft failure and that there are factors making the LDRI potentially misleading (122/138 or 88%). Nevertheless, 60 of 130 respondents (46%) believed that the LDRI would increase/improve shared decision making. The LDRI has not been widely adopted because of concerns that (1) it does not accurately reflect posttransplant survival, (2) it excludes relevant donor and recipient factors, and (3) it is too complicated for candidates to grasp. There is a need to improve it or to develop other decision‐making tools to help promote shared decision making. There is also great diversity in how liver offers are made to ambulatory candidates and in how transplant programs address a candidates refusal. Research is needed to determine evidence‐based best practice. Liver Transpl 20:831‐837, 2014.

Interferon-combination strategies for the treatment of chronic hepatitis C.

Direct acting antiviral agents have revolutionized hepatitis C (HCV) therapy. Many agents that are either currently available or undergoing investigation offer higher rates of sustained virologic response, reduced toxicity and shorter duration of therapy when compared to traditional treatment consisting of pegylated interferon and ribavirin. Although interferon free therapy may be a preferred option, some patients may still require an interferon based regimen to ensure efficacy. In this review, we discuss therapeutic strategies which utilize various combinations of protease inhibitors, NS5A inhibitors, nucleotide polymerase inhibitors and non-nucleoside polymerase inhibitors along with pegylated interferon in the treatment of chronic HCV.

Hepatobiliary manifestations of critically ill and postoperative patients.

Liver dysfunction is common in both the critically ill and postoperative patient. Metabolic derangements secondary to sepsis, poor hepatic perfusion, total parenteral nutrition, in addition to hemodynamic and anesthetic-induced changes that occur during surgery, can cause liver damage ranging from small self-limited abnormalities in liver chemistries to acute liver failure. Early recognition, supportive care, and effective treatment of the underlying disease process are crucial steps in managing liver disease in a critically ill patient.

The benefit of paracentesis on hospitalized adults with cirrhosis and ascites.

The aim of this study is to assess paracentesis utilization and outcomes in hospitalized adults with cirrhosis and ascites.

Overcoming Injustice: A Roadmap to Improve Access to HCV Therapy for Our Medicaid Patients

Arecent survey of state Medicaid programs by the Senate Finance Committee revealed that of 68 million Medicaid enrollees in 44 states, nearly 700,000 are positive for the hepatitis C virus (HCV). The advent of new direct-acting antivirals (DAAs) has not just given these patients treatment without the devastating side effects of interferon; it has given them the promise of a cure. However, as 88% of states have established and now implemented restrictive prior authorization policies regarding new DAAs in clear violation of federal mandate, the promise of a cure is one that the Medicaid system is not fulfilling. As such, it has been left to doctors and advocates to stand up for the rights of these individuals in a fight not unlike that faced in the early years of the human immunodeficiency virus crisis. We have seen that change is possible. What we are urging is that greater change will come from providers’ willingness to serve as advocates. It is important to note that coverage for outpatient prescription drugs within a Medicaid plan is not a requirement by federal or state mandate. Rather, it is a decision left entirely to each state. However, despite being optional, every state has chosen to participate in the Medicaid Drug Rebate Program and is therefore de facto bound and accountable to the regulations set forth in the Social Security Act, title XIX. Hence, while prior authorization requirements are neither forbidden nor uncommon in state Medicaid plans, they should comply with federal regulations. As it stands now, with more than 40 states having not only instituted restrictive prior authorization policies but also continuing those violations in direct defiance of Medicaid’s November 2015 Medicaid Drug Rebate Program Notice, the joint Medicaid system shows a grave weakness in that it does very little to recognize and reprimand the blatant noncompliance of state partners. This perspectives piece addresses the common question of both doctors and advocates: What can I do right now to make a change? It so happens that we are not alone, not without cause, and not without a roadmap. There are at least 10 states to which we can look for guidance in achieving greater access and the elimination of restrictions (see Table 1). Recent successes toward improved access to DAAs include advocacy-driven demand letters, four class action lawsuits, related investigations initiated by the state attorney general toward private insurers, challenges to state prison systems, and recommendations by drug utilization review boards. The arguments used in the above successes, some of which we review below, include one or more of three basic arguments: failure to provide care that is medically necessary, failure to provide care with reasonable promptness, and failure to provide comparable care.

Overcoming injustice: A roadmap to improve access to hepatitis C virus therapy for our medicaid patients

Arecent survey of state Medicaid programs by the Senate Finance Committee revealed that of 68 million Medicaid enrollees in 44 states, nearly 700,000 are positive for the hepatitis C virus (HCV). The advent of new direct-acting antivirals (DAAs) has not just given these patients treatment without the devastating side effects of interferon; it has given them the promise of a cure. However, as 88% of states have established and now implemented restrictive prior authorization policies regarding new DAAs in clear violation of federal mandate, the promise of a cure is one that the Medicaid system is not fulfilling. As such, it has been left to doctors and advocates to stand up for the rights of these individuals in a fight not unlike that faced in the early years of the human immunodeficiency virus crisis. We have seen that change is possible. What we are urging is that greater change will come from providers’ willingness to serve as advocates. It is important to note that coverage for outpatient prescription drugs within a Medicaid plan is not a requirement by federal or state mandate. Rather, it is a decision left entirely to each state. However, despite being optional, every state has chosen to participate in the Medicaid Drug Rebate Program and is therefore de facto bound and accountable to the regulations set forth in the Social Security Act, title XIX. Hence, while prior authorization requirements are neither forbidden nor uncommon in state Medicaid plans, they should comply with federal regulations. As it stands now, with more than 40 states having not only instituted restrictive prior authorization policies but also continuing those violations in direct defiance of Medicaid’s November 2015 Medicaid Drug Rebate Program Notice, the joint Medicaid system shows a grave weakness in that it does very little to recognize and reprimand the blatant noncompliance of state partners. This perspectives piece addresses the common question of both doctors and advocates: What can I do right now to make a change? It so happens that we are not alone, not without cause, and not without a roadmap. There are at least 10 states to which we can look for guidance in achieving greater access and the elimination of restrictions (see Table 1). Recent successes toward improved access to DAAs include advocacy-driven demand letters, four class action lawsuits, related investigations initiated by the state attorney general toward private insurers, challenges to state prison systems, and recommendations by drug utilization review boards. The arguments used in the above successes, some of which we review below, include one or more of three basic arguments: failure to provide care that is medically necessary, failure to provide care with reasonable promptness, and failure to provide comparable care.