Lassa virus infection in Nigeria: clinical perspective overview

Lassa fever is a severe, often fatal, hemorrhagic fever caused by Lassa virus, an Arenavirus that can be transmitted to humans from asymptomatically infected multimammate rats. The speculation is that Lassa viral infection may affect between 2 to 3 million people each year in certain portions of the West African region, causing a mortality of about 10000 during the same period. Lassa fever is one of the endemic zoonosis in Nigeria with a high probability for nosocomial transmission due to several health care sector challenges. Although treatment is available for Lassa fever, early diagnosis is still difficult in almost all Nigerian health care institutions. The intention of this clinical overview is to: (1) summarize the pertinent literature for clinicians in primary, secondary, and tertiary health care centers; and (2) suggest a need to use the information from basic research and laboratory diagnosis to incorporate international best practices into public health and clinical practice guidelines.     

Molecular epidemiology of chicken anemia virus in Nigeria

Summary. Between February 2002 and May 2004, chicken anemia virus (CAV) was detected by PCR in organ samples from 14 flocks of poultry farms in Lagos, Ogun and Oyo States in Southwestern Nigeria. The farms reported low (<5%) to high mortalities (up to 100%) with various lesions at necropsy. The complete VP1 gene of 30 of these positive strains was sequenced. Strains that diverged by up to 4.4% on a nucleotide level differed only by up to 2.5% at the amino acid level (7 aa) as a result of clustered silent mutations. No amino acid substitutions specific for Nigerian strains were observed. Some birds had a CAV mixed infection. Genetic clustering of the VP1 gene did not correlate with differences in flock mortality but the co-infection of CAV with IBDV may be particularly lethal. This first molecular epidemiological study of CAV in Africa shows that the Nigerian strains cluster with viruses from very diverse geographic origins and were almost as diverse (4.4%) as all other strains combined (5.8%).     

The molecular epidemiology of Kokobera virus

We describe herein the molecular epidemiology and phylogeny of Kokobera (KOK) virus, a flavivirus found in Australia and Papua New Guinea. We sequenced a region encompassing the 200 nucleotides of the 3' terminus of the NS5 gene, and the first 300 nucleotides of the 3' untranslated region (UTR). The study included 25 isolates of the virus, including an isolate from PNG, and several recent isolates from the south-west of Western Australia (WA), where the virus had not previously been detected. We found that the KOK isolates clustered according to geographic location and time of isolation into three distinct topotypes: one covering Queensland and New South Wales; another represented by the single isolate from PNG; and a third covering the Northern Territory and WA. This latter group was further subdivided into northern and south-west isolates. This molecular epidemiology is significantly different from other Australian flaviviruses, such as Murray Valley encephalitis (MVE) and Kunjin (KUN) viruses, which exist as single genetic types across the entire Australian continent. However, it is similar to the molecular epidemiology of the alphavirus Ross River (RR) virus. This may be explained by the fact that MVE and KUN viruses are known to have birds as their main vertebrate hosts, whereas RR virus utilises macropods, which have also been implicated as the vertebrate host for KOK virus. In addition, the south-west isolates exhibited a degree of sequence heterogeneity, including one isolate that has a nine nucleotide deletion in the 3'UTR. This suggests that KOK virus has been in the south-west of WA for some time, and was not recently introduced.     

Hepatitis C virus molecular epidemiology in Uzbekistan

The aim of this study was to identify hepatitis C virus (HCV) genotypes and to estimate their prevalence in various risk groups and the regional distribution in Uzbekistan. Preliminary serological screening of 1,269 subjects revealed 6.5% anti-HCV-positive in a general population, 27.1% in patient groups, and 51.7% among intravenous drug users. HCV genotypes of 104 anti-HCV-positive subjects were determined using a PCR-genotyping system in core region, and the results were supported by nucleotide sequencing of the NS5B region. Genotype 1b identified in total 64.2%, was the most prevalent. The genotype 3a identified in 25.0% was the second one distributed. HCV genotypes 2a, 1a, 2b, and 3b were identified in 3.8%, 2.9%, 2.9%, and 1.0% of cases, respectively. The intravenous drug users were distinguished from other groups by having the highest prevalence of genotype 3a, i.e., 50.0%, higher than the 33.3% for genotype 1b in this group. Geographically, genotype 1b was common; genotype 3a was also found frequently in all three regions. Uncommon HCV genotypes (1a, 2a, 2b, and 3b) were found in comparatively greater variability in the western region. Molecular evolutionary analysis based on the NS5B region did not reveal specific clustering or indigenous strains among Uzbekistan HCV isolates. In summary, two main mechanisms of HCV infection distribution were observed in Uzbekistan: HCV 1b genotype infection is widespread through blood products, and HCV 3a genotype infection is spreading through the growing number of intravenous drug users.     

乙型肝炎分子流行病学研究进展

乙肝的分子流行病学是运用先进的分子生物学技术研究乙肝流行病学的诸多问题,能够进一步从分子水平阐明乙型肝炎病毒感染的病因、致病过程及发病机制,对于疾病早期诊断、传染性的评估、病情的预测、抗病毒药物疗效的观察、疾病发展进程的监测和乙肝感染自然史的研究等方面均有重要的指导意义.针对近几年乙肝分子流行病学研究的几个热点即乙型肝炎病毒的检测、基因分型、基因系统进化分析、基因变异、基因多态性的研究进展作一回顾.虽然近年来该领域的研究迅速增多,但多数仍处于探索阶段,乙肝病毒感染、清除等诸多机制的研究仍任重而道远.     

Phylogeography and molecular epidemiology of Papaya ringspot virus

Papaya ringspot virus (PRSV) is the most important virus affecting papaya and cucurbit plants in tropical and subtropical areas. PRSV isolates are divided into biotypes P and W: both the P and W types naturally infect plants in the family Cucurbitaceae, whereas the P type naturally infects papaya (Carica papaya). Understanding the origin and nature of the PRSV genetic diversity and evolution is critical for the implementation of control strategies based on cross-protection and the deployment of transgenic plants that show resistance to virus isolates highly similar to the transgene. The molecular epidemiology of PRSV was evaluated by analyzing the nucleotide sequence of the capsid protein (CP) and helper component-proteinase (HC-Pro) genes of isolates from around the world, including newly characterized ones from Colombia and Venezuela, using a relaxed molecular clock-based approach and a phylogeographic study. Our results confirm previous estimates on the origin of PRSV around 400 years ago and suggest distinct dispersion events from the Indian Peninsula to the rest of Asia, via Thailand, and subsequently to the Americas. A historical reconstruction of the P- and W-type characters in the phylogenetic study supports the need to revise the hypothesis that PRSV-P derives from PRSV-W since our results suggest that the ancestral state could be either of the two biotypes. Moreover, estimates of epidemic growth predict an increasing genetic diversity of the virus over time that has direct implications for control strategies of PRSV based on cross-protection and the use of transgenic plants.     

The molecular epidemiology of hepatitis E virus infection

Molecular characterization of various hepatitis E virus (HEV) strains circulating among humans and animals (particularly swine, deer and boars) in different countries has revealed substantial genetic heterogeneity. The distinctive four-genotype distribution worldwide of mammalian HEV and varying degrees of genetic relatedness among local strains suggest a long and complex evolution of HEV in different geographic regions. The population expansion likely experienced by mammalian HEV in the second half of the 20th century is consistent with an extensive genetic divergence of HEV strains and high prevalence of HEV infections in many parts of the world, including developed countries. The rate and mechanisms of human-to-human transmission and zoonotic transmission to humans vary geographically, thus contributing to the complexity of HEV molecular evolution.     

Laboratory-based surveillance and molecular epidemiology of influenza virus in Taiwan

A laboratory-based surveillance network of 11 clinical virological laboratories for influenza viruses was established in Taiwan under the coordination of the Center for Disease Control and Prevention (CDC), Taiwan. From October 2000 to March 2004, 3,244 influenza viruses were isolated, including 1,969 influenza A and 1,275 influenza B viruses. The influenza infections usually occurred frequently in winter in the northern hemisphere. However, the influenza seasonality in Taiwan was not clear during the four seasons under investigation. For example, the influenza A viruses peaked during the winters of 2001, 2002, and 2003. However, some isolated peaks were also found in the summer and fall (June to November) of 2001 and 2002. An unusual peak of influenza B also occurred in the summer of 2002 (June to August). Phylogenetic analysis shows that influenza A isolates from the same year were often grouped together. However, influenza B isolates from the year 2002 clustered into different groups, and the data indicate that both B/Victoria/2/87-like and B/Yamagata/16/88-like lineages of influenza B viruses were cocirculating. Sequence comparison of epidemic strains versus vaccine strains shows that many vaccine-like Taiwanese strains were circulating at least 2 years before the vaccine strains were introduced. No clear seasonality of influenza reports in Taiwan occurred in contrast to other more continental regions.     

Immunization of rabbits with Lassa virus

The parameters of humoral and cell-mediated immunity after inoculation of the infectious and inactivated antigen of Lassa virus to rabbits which are insusceptible to this infection were studied. Lassa virus antigen was demonstrated to induce synthesis of specific antibodies in rabbits the level of which was proportional to the dose of inoculation and the time of immunization. The results of leukocyte blastogenesis test and delayed type hypersensitivity test confirm the development of sensitization to inactivated Lassa virus in immune rabbits.     

Current molecular epidemiology and human parvovirus B19 infection

Viruses evolve gradually through replication. Therefore, isolates of a virus species can have different genome sequences, albeit slightly, if isolates are epidemiologically unrelated. The difference in virus genome involves difference in virus functions and clinical manifestations of virus infection. Molecular epidemiology of virus infection is a relatively new field directed at infection in humans but not other animals. Analyses are based on genomic differences between virus strains with advances in methodology related to DNA analyses, progress is being made. Classification of virus strains, tracing of transmission of a strain, analyses of outbreaks (including nosocomial infection), and analyses of pathogenesis of virus infection in humans (a natural host) are given attention in molecular epidemiological studies. Human parvovirus B19 is a common human pathogen associated with a wide variety of diseases, including erythema infectiosum, aplastic crisis, hydrops fetalis, and arthritis. B19 is not propagatable in conventional cell lines, hence, molecular cloning of B19 DNA directly from clinical materials has to be done. Events concerning B19 infection were analyzed based on the concept of molecular epidemiology and studies proved to be productive to better understand the pathogenesis of B19 infection.     

Changing molecular epidemiology of hepatitis C virus infection in Northeast Italy

To assess HCV genotype distribution and its determinants, 318 consecutive HCV RNA positive patients were examined. Subtype 1b infection was the most prevalent (35.5%), followed by subtype 1a (22%), 3a (21.4%) and 2 genotype (21.3%). Subtypes 1a, 1b and 3a had a comparable prevalence (30-35%) in the 0-15-, 16-30- and 31-45-year age groups. In subjects older than 45 years, genotype 2 prevalence increased, whereas subtype 1a and 3a infections decreased markedly. In this age group types 1b and 2 accounted for a prevalence of more than 90% in a comparable proportion. Genotype prevalence rates according to different risk factors were different statistically (P < 0.001): subtype 1a and 3a infections were predominant in injection drug users (42.9% and 37.7%, respectively), whereas community acquired infections and infections in patients with a history of transfusion were caused mainly by subtype 1b (38.5% and 66.6%, respectively). Logistic regression showed that age and injection drug use are independent determinants of genotype distribution.     

Reproduction of Lassa virus in different cell cultures

Sierra Leone strain of Lassa virus was growing to high titres of 10(5)-10(6) plaque forming units (PFU) per ml in Vero, L and swine kidney cell lines as well as in diploid human cells and primary human embryo kidney cells. As many as 80% of the cells became infected as demonstrated by the immunofluorescence (IF) technique. In BHK-21, CV-1, HeLa, FL, HEp-2 and dog kidney cell lines, the virus reproduced to lower titres (10(4)-10(5) PFU per ml), whereas in primary chick embryo fibroblasts it did not multiply at all. The virus formed plaques under agar overlay only in CV-1 and Vero cells.     

Pathogenesis of Lassa virus infection in guinea pigs.

A rodent model for human Lassa fever was developed which uses inbred (strain 13) and outbred (Hartley) guinea pigs. Strain 13 guinea pigs were uniformly susceptible to lethal infection by 2 or more PFU of Lassa virus strain Josiah. In contrast, no more than 30% of the Hartley guinea pigs died regardless of the virus dose. In lethally infected strain 13 guinea pigs, peak titers of virus (10(7) to 10(8) PFU) occurred in the spleen and lymph nodes at 8 to 9 days, in the salivary glands at 11 days, and in the lung at 14 to 16 days. Virus reached low titers (10(4) PFU) in the plasma and brain and intermediate titers in the liver, adrenal glands, kidney, pancreas, and heart. In moribund animals, the most consistent and severe histological lesion as an interstitial pneumonia. In contrast, the brain was only minimally involved. The immune response of lethally infected strain 13 guinea pigs, as measured by the indirect fluorescent antibody test, was detectable within 10 days of infection and was similar in timing and intensity to the fluorescent antibody test response of both lethally infected and surviving outbred animals. In contrast to the fluorescent antibody response, neutralizing antibody developed late in convalescence and was thus detected only in surviving outbred guinea pigs. The availability of a rodent model for human Lassa fever in uniformly susceptible strain 13 guinea pigs should facilitate detailed pathophysiological studies and efficacy testing of antiviral drugs, candidate vaccines, and immunotherapy regimens to develop control methods for this life-threatening disease in humans.     

Genetic heterogeneity and molecular epidemiology of GB virus C/hepatitis G virus in China

OBJECTIVE: The inter- and intrapatient genetic variation of GB virus C (GBV-C)/hepatitis G virus (HGV) was investigated to characterize the molecular epidemiologic profile of GBV-C/ HGV infection in China, an area endemic for viral hepatitis. The intrapatient variation of hepatitis C virus (HCV) from the same patients was compared to that of GBV-C/HGV. STUDY DESIGN/METHODS: GB virus C/HGV RNA was amplified by polymerase chain reaction in 88 patients with hepatitis C, hepatitis B or presumed non-A-E hepatitis from three cities in China. Five clones of the GBV-C/HGV NS3 region were sequenced from each GBV-C/HGV RNA-positive patient. The corresponding region of HCV was also sequenced from patients co-infected with HCV. Representative sequences of the GBV-C/HGV NS3 region from each patient and those of isolates from other continents were subjected to phylogenetic analyses. RESULTS: GB virus C/HGV was detected in 22 (25.25%) of 88 patients: 9 (21.4%) of 42 patients with presumed non-A-E hepatitis, 10 (27.7%) of 36 patients with hepatitis C, 3 (30.0%) in 10 patients with hepatitis B and C, and in none of 60 volunteer blood donors. The extent of nucleotide variation was less between Chinese isolates (2.4-17%; median, 10.4%) than between Chinese isolates and seven isolates from outside China (10.5-19.5%; median, 15.3%). Intrapatient sequence variation ranged from 0 to 1.75%, with a mean of 0.57 +/- 0.51%. Phylogenetic analysis grouped most Chinese isolates into four geographically specific clusters with a divergence of 10% to 16% from each other. The ratio of nonsynonymous to synonymous substitutions of GBV-C/HGV (Ka/Ks 0.019) was much lower than for HCV (0.071) in the same patients. CONCLUSION: Chinese isolates of GBV-C/HGV are genetically distinct. There are local strains as well as shared strains between different locales. The extent of amino acid sequence conservation suggests strong selection against nonsynonymous substitutions in the GBV-C/HGV genome.     

The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand

Dengue represents a major public health problem in Thailand, with all four viral serotypes co-circulating. Dengue virus serotype 4 (DENV-4) is the least frequently sampled serotype, although one that is often associated with hemorrhagic fever during secondary infection. To determine the evolutionary forces shaping the genetic diversity of DENV-4, and particularly whether its changing prevalence could be attributed to instances of adaptive evolution in the viral genome, we undertook a large-scale molecular epidemiological analysis of DENV-4 in Bangkok, Thailand, using both E gene and complete coding region sequences. This analysis revealed extensive genetic diversity within a single locality at a single time, including the discovery of a new and divergent genotype of DENV-4, as well as a pattern of continual lineage turnover. We also recorded the highest average rate of evolutionary change for this serotype, at 1.072 x 10(-3) nucleotide substitutions per site, per year. However, despite this abundant genetic variation, there was no evidence for adaptive evolution in any gene, codon, or lineage of DENV-4, with the highest rate of nonsynonymous substitution observed in NS2A. Consequently, the rapid turnover of DENV-4 lineages through time is most likely the consequence of a high rate of deleterious mutation in the viral genome coupled to seasonal fluctuations in the size of the vector population.     

Varicella seroprevalence and molecular epidemiology of varicella-zoster virus in Argentina, 2002

There is limited data on immunity against varicella-zoster virus (VZV) in adults in different parts of Argentina, and it is not known which VZV strains are circulating in Argentina. The objectives of this study were as follows: (i) to evaluate seroprevalence of varicella among adults, assessing the accuracy of clinical history and determining the sociodemographic factors associated with seropositivity; and (ii) to determine the VZV strains circulating in Argentina. A cross-sectional serological survey enrolling 2,807 women aged 15 to 49 years attending public health-care settings in four cities in Argentina (i.e., Buenos Aires, Salta, Mendoza, and Rosario) and one rural area was conducted from August to November 2002. Specimens for identification of VZV strains were obtained from vesicular lesions from 13 pediatric patients with varicella from different areas of the country. PCR amplification was used for genotyping. The overall seroprevalence of varicella antibodies was 98.5% (95% confidence interval, 98.0 to 98.9), ranging from 97.2% in central Buenos Aires to 99.3% in southern Buenos Aires and Salta. Varicella seroprevalence increased with age. Crowding and length of residence in the same place were associated with seropositivity. The positive predictive value of varicella history for immunity to varicella was 99.4%; however, the negative predictive value was 2.5%. The European genotype was identified in all viral specimens. In Argentina, seroprevalence in women more than 15 years old was high regardless of the area of residence. Negative or uncertain varicella history was not a good predictor of immunity. VZV genotype was stable in all areas of the country.