SummaryHumans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli—ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus—and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations.

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D espite decades of research, the processes that govern liver development and regeneration are only partially understood. A good understanding of the mechanisms that play a role in these processes is important because it may lead to new treatments of human liver diseases. Several in vivo experimental conditions have been used to study liver regeneration and repair and the interaction of different cell types in these processes. These include partial hepatectomy, administration of toxic compounds, or a combination of both, and transgenic expression of certain proteins. 1,2 In contrast to in vitro experiments, these approaches raise fewer questions concerning the influence of artificial matrices on the function and behavior of hepatocytes and other liver cell types.Although these procedures have generated useful information on rodent liver regeneration, stem cell activation, and other processes, extrapolating these findings to the Abbreviations: uPA, urokinase plasminogen activator; HBV, hepatitis B virus; HCV, hepatitis C virus; HBsAg, hepatitis B surface antigen; HBeAg, hepatitis B e antigen; PAS, periodic-acid-Schiff. From the

Hepatitis C virus (HCV) is a major cause of chronic liver disease, frequently progressing to cirrhosis and increased risk of hepatocellular carcinoma. Current therapies are inadequate and progress in the field has been hampered by the lack of efficient HCV culture systems. By using a recently described HCV genotype 2a infectious clone that replicates and produces infectious virus in cell culture (HCVcc), we report here that HCVcc strain FL-J6͞JFH can establish long-term infections in chimpanzees and in mice containing human liver grafts. Importantly, virus recovered from these animals was highly infectious in cell culture, demonstrating efficient ex vivo culture of HCV. The improved infectivity of animal-derived HCV correlated with virions of a lower average buoyant density than HCVcc, suggesting that physical association with low-density factors influences viral infectivity. These results greatly extend the utility of the HCVcc genetic system to allow the complete in vitro and in vivo dissection of the HCV life cycle.animal model ͉ pathogenesis ͉ reverse genetics ͉ viral hepatitis A major limitation in hepatitis C virus (HCV) research has been the lack of virus culture systems. After identification of the viral genome in 1989 (1), early efforts focused on understanding the structure and function of individual viral gene products. HCV is an enveloped, positive-strand RNA virus classified in the family Flaviviridae (2). The 9.6-kb ssRNA genome encodes three structural (virion-associated) and seven nonstructural (intracellular) genes within a single ORF.The first functional cDNA clones of HCV were constructed in 1997, allowing chimpanzees to be infected after intrahepatic transfection with recombinant viral RNA (3, 4). Unfortunately, these infectious genomes failed to replicate in cell culture. By engineering HCV replicons to express a drug-selectable gene, it became possible to select for HCV RNA replication in cell culture (5). However, efficient replication required cell cultureadaptive mutations in the viral RNA (6). Moreover, only the intracellular aspects of HCV replication were modeled by these systems. For unknown reasons, cell culture-adaptive mutations can inhibit virion production in culture (T. Pietschmann and R. Bartenschlager, personal communication) and attenuate RNA infectivity in vivo (7).Recent progress in the field has come from the identification of JFH-1, a genotype 2a subgenomic replicon that does not require adaptive mutations for efficient RNA replication in culture (8). Based on this sequence, we constructed a chimeric JFH-1 genome containing the core to nonstructural protein 2 (NS2) region of HCV strain J6. This genome, FL-J6͞JFH, replicated and produced high levels of infectious virus in cell culture (HCVcc) (9), allowing us to study new aspects of the viral life cycle in tissue culture (9, 10). Similarly, full-length JFH-1 clones produced HCVcc, albeit with delayed kinetics of virus release (11, 12). HCVcc strain JFH-1 was able to transiently infect a chimpanzee, although replication le...

Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) E2 envelope glycoprotein has been implicated in virus neutralization and persistence. We deleted HVR1 from JFH1-based HCV recombinants expressing Core/E1/E2/p7/NS2 of genotypes 1 to 6, previously found to grow efficiently in human hepatoma Huh7.5 cells. The 2a ⌬HVR1 , 5a ⌬HVR1 , and 6a ⌬HVR1 Core-NS2 recombinants retained viability in Huh7.5 cells, whereas 1a ⌬HVR1 , 1b ⌬HVR1 , 2b ⌬HVR1 , 3a ⌬HVR1 , and 4a ⌬HVR1 recombinants were severely attenuated. However, except for recombinant 4a ⌬HVR1 , viruses eventually spread, and reverse genetics studies revealed adaptive envelope mutations that rescued the infectivity of 1a ⌬HVR1 , 1b ⌬HVR1 , 2b ⌬HVR1 , and 3a ⌬HVR1 recombinants. Thus, HVR1 might have distinct functional roles for different HCV isolates. Ultracentrifugation studies showed that deletion of HVR1 did not alter HCV RNA density distribution, whereas infectious particle density changed from a range of 1.0 to 1.1 g/ml to a single peak at ϳ1.1 g/ml, suggesting that HVR1 was critical for low-density HCV particle infectivity. Using chronic-phase HCV patient sera, we found three distinct neutralization profiles for the original viruses with these genotypes. In contrast, all HVR1-deleted viruses were highly sensitive with similar neutralization profiles. In vivo relevance for the role of HVR1 in protecting HCV from neutralization was demonstrated by ex vivo neutralization of 2a and 2a ⌬HVR1 produced in human liver chimeric mice. Due to the high density and neutralization susceptibility of HVR1-deleted viruses, we investigated whether a correlation existed between density and neutralization susceptibility for the original viruses with genotypes 1 to 6. Only the 2a virus displayed such a correlation. Our findings indicate that HVR1 of HCV shields important conserved neutralization epitopes with implications for viral persistence, immunotherapy, and vaccine development.

Background. Few studies have prospectively assessed viral etiologies of acute respiratory infections in community-based elderly individuals. We assessed viral respiratory pathogens in individuals ≥65 years with influenza-like illness (ILI).Methods. Multiplex reverse-transcriptase polymerase chain reaction identified viral pathogens in nasal/throat swabs from 556 episodes of moderate-to-severe ILI, defined as ILI with pneumonia, hospitalization, or maximum daily influenza symptom severity score (ISS) >2. Cases were selected from a randomized trial of an adjuvanted vs nonadjuvanted influenza vaccine conducted in elderly adults from 15 countries.Results. Respiratory syncytial virus (RSV) was detected in 7.4% (41/556) moderate-to-severe ILI episodes in elderly adults. Most (39/41) were single infections. There was a significant association between country and RSV detection (P = .004). RSV prevalence was 7.1% (2/28) in ILI with pneumonia, 12.5% (8/64) in ILI with hospitalization, and 6.7% (32/480) in ILI with maximum ISS > 2. Any virus was detected in 320/556 (57.6%) ILI episodes: influenza A (104/556, 18.7%), rhinovirus/enterovirus (82/556, 14.7%), coronavirus and human metapneumovirus (each 32/556, 5.6%).Conclusions. This first global study providing data on RSV disease in ≥65 year-olds confirms that RSV is an important respiratory pathogen in the elderly. Preventative measures such as vaccination could decrease severe respiratory illnesses and complications in the elderly.

Production of infectious hepatitis C virus in cell culture has become possible because of the unique properties of the JFH1 isolate. However, virus titers are rather low, limiting the utility of this system. Here we describe the generation of cell culture-adapted JFH1 variants yielding higher titers of infectious particles and enhanced spread of infection in cultured cells. Sequence analysis of adapted genomes revealed a complex pattern of mutations that differed in two independent experiments. Adaptive mutations were observed both in the structural and in the nonstructural regions, with the latter having the highest impact on enhancement of virus titers. The major adaptive mutation was identified in NS5A, and it enhanced titers of three intergenotypic chimeras consisting of the structural region of a genotype 1a, 1b, or 3a isolate and the remainder of the JFH1 isolate. The mutation resides at the P3 position of the NS5A-B cleavage site and slows down processing, implying that subtle differences in replication complex formation appear to determine the efficiency of virus formation. Highly adapted JFH1 viruses carrying six mutations established a robust infection in uPA-transgenic SCID mice xenografted with human hepatocytes. However, the mutation in NS5A which enhanced virus titers in cell culture the most had reverted to wild type in nearly half of the viral genomes isolated from these animals at 15 weeks postinoculation. These results argue for some level of impaired fitness of this mutant in vivo.The hepatitis C virus (HCV) is an enveloped virus of the genus Hepacivirus within the family Flaviviridae (52). HCV isolates can be classified into six major genotypes that differ in their nucleotide sequence by 30 to 35%, and within these genotypes, several subtypes can be defined (47). Viral infection most often becomes persistent and causes acute and chronic liver disease (22,46). At present, more than 170 million people suffer from chronic hepatitis C (44). Current treatment consists of a combination of polyethylene glycol-conjugated alpha interferon and ribavirin (44), but success rates are limited and the outcome of therapy is very dependent on the genotype of the infecting virus (13).The genome of HCV is a linear, single-stranded RNA molecule of positive polarity with a size of ϳ9.6 kb, and it is flanked at the 5Ј and 3Ј ends by noncoding regions (NCRs). Both NCRs play an important role in the initiation of RNA synthesis by the viral RNA-dependent RNA polymerase (RdRp) NS5B (16,18,27). The RNA genome carries a long open reading frame of about 3,000 amino acids (aa) that is coand posttranslationally cleaved by cellular and viral proteases into the structural proteins core, E1, and E2, followed by p7 and the nonstructural (NS) proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B (3). Expression of the polyprotein is initiated at an internal ribosome entry site, comprising most of the 5Ј NCR and the 5Ј-proximal core coding region (41). The core protein forms the viral nucleocapsid, which is surrounded by the lipid envel...

Human liver chimeric mice can be infected with HEV of different genotypes. This small animal model will be a valuable tool for the study of HEV infection and the evaluation of novel antiviral molecules.