C. Y. William Tong

Evolutionary Genetics of Human Enterovirus 71: Origin, Population Dynamics, Natural Selection, and Seasonal Periodicity of the VP1 Gene

ABSTRACT Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.

Molecular Epidemiology of Human Enterovirus 71 in the United Kingdom from 1998 to 2006

ABSTRACT The last decade witnessed a significant increase in epidemic activity of human enterovirus 71 (EV71) in the Western Pacific Region (WPR). In most European countries, this risk is unrecognized despite occasional cases of severe disease and two severe outbreaks in Eastern Europe 30 years ago. In this study we report the first examination of the molecular epidemiology of EV71 in the United Kingdom from 1998 to 2006. Genomic regions encoding the 1D coat protein (VP1) and 3D polymerase (Pol) from 32 EV71 isolates associated with neurological or cutaneous manifestations were sequenced. Phylogenetic analyses of VP1 and 3D Pol sequences identified genotype C as the dominant strain. Several United Kingdom isolates had genetic linkages with predated C1 or C2 strains from Europe and the WPR. Recombination events were not detected between United Kingdom strains. However, a previously published Taiwanese strain was identified as an intergenotypic recombinant. EV71 genotype C appears to have continuous circulation in the United Kingdom from 1998 to 2006 with repeated introductions of new strains replacing previous strains. It is necessary to continuously monitor the molecular evolution and recombination events of EV71.

Antiviral therapy for polyomavirus-associated nephropathy after renal transplantation

Polyomavirus-associated nephropathy (PVAN) has recently emerged as an important cause of allograft failure following renal transplantation. The BK virus is the most important polyomavirus associated with this condition. The mainstay of therapy for PVAN is a prompt immunosuppressive dose reduction in conjunction with careful monitoring for BK viraemia. A number of antiviral agents have been tried to help to reduce BK viral replication. So far, there has been only a single randomized controlled study on the use of one of these agents. Pooled data from various small case series did not show significant differences in outcome. Prospective randomized studies with a standardized protocol are urgently required.

Early hepatitis B virological rebound on entecavir through selection of lamivudine-associated mutations

G109A in the reverse transcriptase region, and I13V, L33I, L63P and V77I in the protease region. The last HAART regimen before transplantation, discontinued pre-operatively, was lamivudine 150 mg twice a day, tenofovir 300 mg once daily and fosampre-navir 1400 mg twice a day. Immunosuppression was initially achieved with cyclosporin (300 mg twice a day) and steroids, and then maintained with cyclosporin only. On the third post-operative day, HAART was resumed with emtricitabine 200 mg, tenofovir 300 mg once daily and a subcutaneous (sc) injection of enfuvirtide 90 mg twice a day. At 3 months after transplantation, the CD4þ T cell count and HIV RNA level were 263 cells/mm 3 (20%) and ,50 copies/mL, respectively, while HCV RNA was 4.09 log 10 copies/mL (Cobas Ampliprep/Cobas TaqMan HCV Test Roche Diagnostics). After 9 months, because of a further increase in HCV RNA levels (6.09 log 10 copies/mL) and of macro-and micronodular cirrhosis revealed by transjugular liver biopsy, the patient started anti-HCV treatment with pegylated interferon (PEG-IFN) alfa 2b (180 mg sc once a week) and riba-virin (1200 mg twice a day). Cyclosporin was administered twice daily and its dosage was adjusted individually to match target trough levels of 75– 125 mg/L. Four weeks later, because he had ongoing injection site reactions and complained of injection fatigue due to enfuvirtide and PEG-IFN, the patient switched from enfuvirtide to raltegravir (400 mg twice a day). Four weeks later, HIV RNA was still ,50 copies/mL, while the CD4þ T cell count had increased from 162 (18%) to 336 (23%). Self-reported therapeutic adherence was apparently optimal. No other potentially interacting drugs were administered. Cyclosporin levels were monitored at regular intervals during outpatient visits (Figure 1). Moreover, at week 4 and week 8 raltegravir concentrations were also measured by a validated HPLC method 7 before the morning dose and 3 h later and showed drug levels to be 60 and 5165 ng/mL at week 4, and 119 and 3386 ng/mL at week 8, respectively. No specific toxicity related to antiretroviral and immunosuppressive therapies was recorded. No administration of factor VIII for treatment of haemophilia A was requested. After 18 months of follow-up post-transplantation, the patient is alive and HIV RNA levels are undetectable. In our patient, a raltegravir-based regimen was chosen in order to avoid the potential deleterious effect of PIs on cyclos-porin. A new NNRTI-based regimen was excluded because etra-virine is a substrate for, and inhibitor …