Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-30 (of 30 Records) |
Query Trace: Khudyakov YE[original query] |
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Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon.
Lara J , Tavis JE , Donlin MJ , Lee WM , Yuan HJ , Pearlman BL , Vaughan G , Forbi JC , Xia GL , Khudyakov YE . In Silico Biol 2011 11 213-24 Machine-learning methods in the form of Bayesian networks (BN), linear projection (LP) and self-organizing tree (SOT) models were used to explore association among polymorphic sites within the HVR1 and NS5a regions of the HCV genome, host demographic factors (ethnicity, gender and age) and response to the combined interferon (IFN) and ribavirin (RBV) therapy. The BN models predicted therapy outcomes, gender and ethnicity with accuracy of 90%, 90% and 88.9%, respectively. The LP and SOT models strongly confirmed associations of the HVR1 and NS5A structures with response to therapy and demographic host factors identified by BN. The data indicate host specificity of HCV evolution and suggest the application of these models to predict outcomes of IFN/RBV therapy. |
Recent and occult hepatitis B virus infections among blood donors in the United States
Ramachandran S , Groves JA , Xia GL , Saa P , Notari EP , Drobeniuc J , Poe A , Khudyakov N , Schillie SF , Murphy TV , Kamili S , Teo CG , Dodd RY , Khudyakov YE , Stramer SL . Transfusion 2018 59 (2) 601-611 BACKGROUND: Characteristics of US blood donors with recent (RBI) or occult (OBI) hepatitis B virus (HBV) infection are not well defined. METHODS: Donors with RBI and OBI were identified by nucleic acid and serologic testing among 34.4 million donations during 2009-2015. Consenting donors were interviewed and their HBV S-gene sequenced. RESULTS: The overall rate of HBV-infected donors was 7.95 per 100,000; of these, 0.35 per 100,000 and 1.70 per 100,000 were RBI and OBI, respectively. RBI (n = 120) and OBI (n = 583) donors constituted 26% of all HBV-infected (n = 2735) donors. Detection of HBV DNA in 92% of OBI donors required individual donation nucleic acid testing. Donors with OBI compared to RBI were older (mean age, 48 vs 39 years; p < 0.0001) with lower median viral loads (9 vs. 529 IU/mL; p < 0.0001). A higher proportion of OBI than RBI donors were born or resided in an endemic country (39% vs. 5%; p = 0.0078). Seventy-seven percent of all RBI and OBI donors had multiple sex partners, an HBV-risk factor. Of 40 RBI and 10 OBI donors whose S gene was sequenced, 33 (83%) and 6 (60%), respectively, carried HBV subgenotype A2; 18 (55%) and 2 (33%), respectively, shared an identical sequence. Infection with 1 or more putative HBV-immune-escape mutants was identified in 5 (50%) of OBI but no RBI donors. CONCLUSION: RBI and OBI continue to be identified at low rates, confirming the importance of comprehensive HBV DNA screening of US blood donations. HBV-infected donors require referral for care and evaluation and contact tracing; their HBV strains may provide important information on emergent genotypes. |
Molecular epidemiology of hepatitis B virus infection in Tanzania.
Forbi JC , Dillon M , Purdy MA , Drammeh BS , Tejada-Strop A , McGovern D , Xia GL , Lin Y , Ganova-Raeva LM , Campo DS , Thai H , Vaughan G , Haule D , Kutaga RP , Basavaraju SV , Kamili S , Khudyakov YE . J Gen Virol 2017 98 (5) 1048-1057 Despite the significant public health problems associated with hepatitis B virus (HBV) in sub-Saharan Africa, many countries in this region do not have systematic HBV surveillance or genetic information on HBV circulating locally. Here, we report on the genetic characterization of 772 HBV strains from Tanzania. Phylogenetic analysis of the S-gene sequences showed prevalence of HBV genotype A (HBV/A, n=671, 86.9 %), followed by genotypes D (HBV/D, n=95, 12.3 %) and E (HBV/E, n=6, 0.8 %). All HBV/A sequences were further classified into subtype A1, while the HBV/D sequences were assigned to a new cluster. Among the Tanzanian sequences, 84 % of HBV/A1 and 94 % of HBV/D were unique. The Tanzanian and global HBV/A1 sequences were compared and were completely intermixed in the phylogenetic tree, with the Tanzanian sequences frequently generating long terminal branches, indicating a long history of HBV/A1 infections in the country. The time to the most recent common ancestor was estimated to be 188 years ago [95 % highest posterior density (HPD): 132 to 265 years] for HBV/A1 and 127 years ago (95 % HPD: 79 to 192 years) for HBV/D. The Bayesian skyline plot showed that the number of transmissions 'exploded' exponentially between 1960-1970 for HBV/A1 and 1970-1990 for HBV/D, with the effective population of HBV/A1 having expanded twice as much as that of HBV/D. The data suggest that Tanzania is at least a part of the geographic origin of the HBV/A1 subtype. A recent increase in the transmission rate and significant HBV genetic diversity should be taken into consideration when devising public health interventions to control HBV infections in Tanzania. |
Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana.
Forbi JC , Layden JE , Phillips RO , Mora N , Xia GL , Campo DS , Purdy MA , Dimitrova ZE , Owusu DO , Punkova LT , Skums P , Owusu-Ofori S , Sarfo FS , Vaughan G , Roh H , Opare-Sem OK , Cooper RS , Khudyakov YE . PLoS One 2015 10 (12) e0145530 Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genetic composition of HCV populations in many countries of the region. Using conventional and next-generation sequencing (NGS), we identified and genetically characterized 65 HCV strains circulating among HCV-positive blood donors in Kumasi, Ghana. Phylogenetic analysis using consensus sequences derived from 3 genomic regions of the HCV genome, 5'-untranslated region, hypervariable region 1 (HVR1) and NS5B gene, consistently classified the HCV variants (n = 65) into genotypes 1 (HCV-1, 15%) and genotype 2 (HCV-2, 85%). The Ghanaian and West African HCV-2 NS5B sequences were found completely intermixed in the phylogenetic tree, indicating a substantial genetic heterogeneity of HCV-2 in Ghana. Analysis of HVR1 sequences from intra-host HCV variants obtained by NGS showed that three donors were infected with >1 HCV strain, including infections with 2 genotypes. Two other donors share an HCV strain, indicating HCV transmission between them. The HCV-2 strain sampled from one donor was replaced with another HCV-2 strain after only 2 months of observation, indicating rapid strain switching. Bayesian analysis estimated that the HCV-2 strains in Ghana were expanding since the 16th century. The blood donors in Kumasi, Ghana, are infected with a very heterogeneous HCV population of HCV-1 and HCV-2, with HCV-2 being prevalent. The detection of three cases of co- or super-infections and transmission linkage between 2 cases suggests frequent opportunities for HCV exposure among the blood donors and is consistent with the reported high HCV prevalence. The conditions for effective HCV-2 transmission existed for ~ 3-4 centuries, indicating a long epidemic history of HCV-2 in Ghana. |
A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa.
Purdy MA , Forbi JC , Sue A , Layden JE , Switzer WM , Opare-Sem OK , Phillips RO , Khudyakov YE . J Gen Virol 2015 96 (8) 2157-2164 Hepatitis C virus (HCV) is classified into 7 genotypes based on genetic diversity and most genotypes have been found in Africa. Infections with HCV genotype 2 (HCV2) are most prevalent in West Africa, and it was suggested that HCV2 originated in West Africa. To better understand the evolutionary epidemiology of HCV2 in Africa, we examined new NS5b sequences of HCV2 strains obtained from Cote d'Ivoire, Ghana and Nigeria sequenced in this laboratory with those available from West, North and Central Africa. Bayesian phylogeographic analysis using a discrete trait model showed that Ghana is the most likely geographic region for origin of HCV2. Spread of HCV2 from Ghana does not appear to be through diffusion to adjacent countries along the coast. Rather, it was transmitted from Ghana to many distant countries in Africa, suggesting that certain routes of geographic dissemination were historically more efficient than mere proximity and that the HCV2 epidemic history in West Africa is extremely complex. |
High frequency of active HCV infection among seropositive cases in west Africa and evidence for multiple transmission pathways.
Layden JE , Phillips RO , Owusu-Ofori S , Sarfo FS , Kliethermes S , Mora N , Owusu D , Nelson K , Opare-Sem O , Dugas L , Luke A , Shoham D , Forbi JC , Khudyakov YE , Cooper RS . Clin Infect Dis 2014 60 (7) 1033-41 BACKGROUND: Sub-Saharan Africa (SSA) has among the highest global Hepatitis C Virus (HCV) prevalence estimates. However, reports suggesting high rates of serologic false positives and low levels of viremia have led to uncertainty regarding the burden of active infection in this region. Additionally, little is known about the predominant transmission risk factors in SSA. METHODS: We prospectively recalled 363 past blood donors (180 who were rapid screen assay (RSA) positive and 183 that were RSA negative at time of donation) to identify the level of active infection and risk factors for infection at a teaching hospital in Kumasi, Ghana. Participants had repeat blood testing and were administered a questionnaire on risk factors. RESULTS: The frequency of HCV active infection ranged from 74.4% to 88% depending on the criteria used to define serologically positive cases. Individuals with active disease had biochemical evidence of liver inflammation and median viral loads of 5.7 log copies/ml. Individuals from the northern and upper regions of Ghana had greater risks of infection compared to participants from other areas. Additional risk factors included traditional circumcision, home birth, tribal scarring and HBV co-infection. CONCLUSIONS: Viremic infection was common among serologically confirmed cases. Attention to testing algorithms is needed to define the true HCV burden in SSA. These data also suggest that several transmission modes are likely contributing to the current HCV epidemic in Ghana, and the distribution of these practices may result in substantial regional variation in prevalence. |
Outbreak of hepatitis A in the USA associated with frozen pomegranate arils imported from Turkey: an epidemiological case study.
Collier MG , Khudyakov YE , Selvage D , Adams-Cameron M , Epson E , Cronquist A , Jervis RH , Lamba K , Kimura AC , Sowadsky R , Hassan R , Park SY , Garza E , Elliott AJ , Rotstein DS , Beal J , Kuntz T , Lance SE , Dreisch R , Wise ME , Nelson NP , Suryaprasad A , Drobeniuc J , Holmberg SD , Xu F . Lancet Infect Dis 2014 14 (10) 976-81 BACKGROUND: In May, 2013, an outbreak of symptomatic hepatitis A virus infections occurred in the USA. Federal, state, and local public health officials investigated the cause of the outbreak and instituted actions to control its spread. We investigated the source of the outbreak and assessed the public health measures used. METHODS: We interviewed patients, obtained their shopping information, and did genetic analysis of hepatitis A virus recovered from patients' serum and stool samples. We tested products for the virus and traced supply chains. FINDINGS: Of 165 patients identified from ten states, 69 (42%) were admitted to hospital, two developed fulminant hepatitis, and one needed a liver transplant; none died. Illness onset occurred from March 31 to Aug 12, 2013. The median age of patients was 47 years (IQR 35-58) and 91 (55%) were women. 153 patients (93%) reported consuming product B from retailer A. 40 patients (24%) had product B in their freezers, and 113 (68%) bought it according to data from retailer A. Hepatitis A virus genotype IB, uncommon in the Americas, was recovered from specimens from 117 people with hepatitis A virus illness. Pomegranate arils that were imported from Turkey-where genotype IB is common-were identified in product B. No hepatitis A virus was detected in product B. INTERPRETATION: Imported frozen pomegranate arils were identified as the vehicle early in the investigation by combining epidemiology-with data from several sources-genetic analysis of patient samples, and product tracing. Product B was removed from store shelves, the public were warned not to eat product B, product recalls took place, and postexposure prophylaxis with both hepatitis A virus vaccine and immunoglobulin was provided. Our findings show that modern public health actions can help rapidly detect and control hepatitis A virus illness caused by imported food. Our findings show that postexposure prophylaxis can successfully prevent hepatitis A illness when a specific product is identified. Imported food products combined with waning immunity in some adult populations might make this type of intervention necessary in the future. |
Recent population expansions of hepatitis B virus in the United States.
Ramachandran S , Purdy MA , Xia GL , Campo DS , Dimitrova ZE , Teshale EH , Teo CG , Khudyakov YE . J Virol 2014 88 (24) 13971-80 The recent epidemic history of hepatitis B virus (HBV) infections in the United States is complex, as indicated by current disparity in HBV genotype distribution between acute and chronic hepatitis B cases and rapid decline in hepatitis B incidence since the 1990s. We report temporal changes in genetic composition of the HBV population using whole-genome sequences (n=179) from acute hepatitis B cases (n=1206) identified through the Sentinel County Surveillance for Acute Hepatitis (1998-2006). HBV belonged mainly to subtypes A2 (75%) and D3 (18%), with times of their most recent common ancestors being, respectively, 1979 and 1987, respectively. A2 underwent rapid population expansions in ca. 1995 and ca. 2002, coinciding with transient rises in acute hepatitis B notification rates among adults; D3 underwent expansion in ca. 1998. A2 strains from cases identified after 2002, compared to those before 2002, tended to cluster phylogenetically, indicating selective expansion of specific strains, and were significantly reduced in genetic diversity (p = 0.001) and frequency of drug-resistance mutations (p = 0.001). The expansion of genetically close HBV A2 strains was associated with risk of infection among male homosexuals (p = 0.03). Incident HBV strains circulating in the US were recent in origin, and restricted in genetic diversity. Disparate transmission dynamics among phylogenetic lineages affected the genetic composition of HBV populations and their capacity to maintain drug-resistance mutations. The tendency of selectively expanding HBV strains to be transmitted among male homosexuals highlights the need to improve hepatitis B vaccination coverage among at-risk adults. IMPORTANCE: Hepatitis B virus (HBV) remains an important cause of acute and chronic liver disease globally, and in the United States. Genetic analysis of HBV whole genomes from cases of acute hepatitis B identified from 1998-2006 in the United States showed dominance of genotype A2 (75%), followed by D3 (18%). Strains of both subtypes were recent in origin and underwent rapid population expansions from 1995-2000, indicating increase in transmission rate for certain HBV strains during a period of decline in the reported incidence of acute hepatitis B in the US. HBV A2 strains from a particular cluster that experienced the most recent population expansion were more commonly detected among men who have sex with men. Vaccination needs to be stepped up to protect persons who remain at risk of HBV infection. |
Genetic history of hepatitis C virus in Pakistan.
Ur Rehman I , Vaughan G , Purdy MA , Xia GL , Forbi JC , Rossi LM , Butt S , Idrees M , Khudyakov YE . Infect Genet Evol 2014 27 318-24 Hepatitis C virus (HCV) genotype 3a accounts for approximately 80% of HCV infections in Pakistan, where approximately 10 million people are HCV-infected. Here, we report analysis of the genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan. Phylogenetic analyses showed that Pakistani genotype 3a variants were as genetically diverse as global variants, with extensive intermixing. Bayesian estimates showed that the most recent ancestor for genotype 3a in Pakistan was last extant in approximately 1896-1914 C.E. (range: 1851-1932). This genotype experienced a population expansion starting from approximately 1905 to approximately 1970 after which the effective population leveled. Death/birth models suggest that HCV 3a has reached saturating diversity with decreasing turnover rate and positive extinction. Taken together, these observations are consistent with a long and complex history of HCV 3a infection in Pakistan. |
Genetic host specificity of hepatitis E virus.
Lara J , Purdy MA , Khudyakov YE . Infect Genet Evol 2014 24 127-39 Hepatitis E virus (HEV) causes epidemic and sporadic cases of hepatitis worldwide. HEV genotypes 3 (HEV3) and 4 (HEV4) infect humans and animals, with swine being the primary reservoir. The relevance of HEV genetic diversity to host adaptation is poorly understood. We employed a Bayesian network (BN) analysis of HEV3 and HEV4 to detect epistatic connectivity among protein sites and its association with the host specificity in each genotype. The data imply coevolution among approximately 70% of polymorphic sites from all HEV proteins and association of numerous coevolving sites with adaptation to swine or humans. BN models for individual proteins and domains of the nonstructural polyprotein detected the host origin of HEV strains with accuracy of 74%-93% and 63%-87%, respectively. These findings, taken together with lack of phylogenetic association to host, suggest that the HEV host specificity is a heritable and convergent phenotypic trait achievable through variety of genetic pathways (abundance), and explain a broad host range for HEV3 and HEV4. |
Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire.
Forbi JC , Campo DS , Purdy MA , Dimitrova ZE , Skums P , Xia GL , Punkova LT , Ganova-Raeva LM , Vaughan G , Ben-Ayed Y , Switzer WM , Khudyakov YE . J Med Virol 2014 86 (5) 765-71 Hepatitis C virus (HCV) infection presents an important, but underappreciated public health problem in Africa. In Cote d'Ivoire, very little is known about the molecular dynamics of HCV infection. Plasma samples (n = 608) from pregnant women collected in 1995 from Cote d'Ivoire were analyzed in this study. Only 18 specimens ( approximately 3%) were found to be HCV PCR-positive. Phylogenetic analysis of the HCV NS5b sequences showed that the HCV variants belong to genotype 1 (HCV1) (n = 12, 67%) and genotype 2 (HCV2) (n = 6, 33%), with a maximum genetic diversity among HCV variants in each genotype being 20.7% and 24.0%, respectively. Although all HCV2 variants were genetically distant from each other, six HCV1 variants formed two tight sub-clusters belonging to HCV1a and HCV1b. Analysis of molecular variance (AMOVA) showed that the genetic structure of HCV isolates from West Africa with Cote d'Ivoire included were significantly different from Central African strains (P = 0.0001). Examination of intra-host viral populations using next-generation sequencing of the HCV HVR1 showed a significant variation in intra-host genetic diversity among infected individuals, with some strains composed of sub-populations as distant from each other as viral populations from different hosts. Collectively, the results indicate a complex HCV evolution in Cote d'Ivoire, similar to the rest of West Africa, and suggest a unique HCV epidemic history in the country. |
Full-length genome characterization and genetic relatedness analysis of hepatitis A virus outbreak strains associated with acute liver failure among children.
Vaughan G , Forbi JC , Xia GL , Fonseca-Ford M , Vazquez R , Khudyakov YE , Montiel S , Waterman S , Alpuche C , Goncalves Rossi LM , Luna N . J Med Virol 2014 86 (2) 202-8 Clinical infection by hepatitis A virus (HAV) is generally self-limited but in some cases can progress to liver failure. Here, an HAV outbreak investigation among children with acute liver failure in a highly endemic country is presented. In addition, a sensitive method for HAV whole genome amplification and sequencing suitable for analysis of clinical samples is described. In this setting, two fatal cases attributed to acute liver failure and two asymptomatic cases living in the same household were identified. In a second household, one HAV case was observed with jaundice which resolved spontaneously. Partial molecular characterization showed that both households were infected by HAV subtype IA; however, the infecting strains in the two households were different. The HAV outbreak strains recovered from all cases grouped together within cluster IA1, which contains closely related HAV strains from the United States commonly associated with international travelers. Full-genome HAV sequences obtained from the household with the acute liver failure cases were related (genetic distances ranging from 0.01% to 0.04%), indicating a common-source infection. Interestingly, the strain recovered from the asymptomatic household contact was nearly identical to the strain causing acute liver failure. The whole genome sequence from the case in the second household was distinctly different from the strains associated with acute liver failure. Thus, infection with almost identical HAV strains resulted in drastically different clinical outcomes. |
Genetic relatedness among hepatitis A virus strains associated with food-borne outbreaks
Vaughan G , Xia G , Forbi JC , Purdy MA , Rossi LM , Spradling PR , Khudyakov YE . PLoS One 2013 8 (11) e74546 The genetic characterization of hepatitis A virus (HAV) strains is commonly accomplished by sequencing subgenomic regions, such as the VP1/P2B junction. HAV genome is not extensively variable, thus presenting opportunity for sharing sequences of subgenomic regions among genetically unrelated isolates. The degree of misrepresentation of phylogenetic relationships by subgenomic regions is especially important for tracking transmissions. Here, we analyzed whole-genome (WG) sequences of 101 HAV strains identified from 4 major multi-state, food-borne outbreaks of hepatitis A in the Unites States and from 14 non-outbreak-related HAV strains that shared identical VP1/P2B sequences with the outbreak strains. Although HAV strains with an identical VP1/P2B sequence were specific to each outbreak, WG were different, with genetic diversity reaching 0.31% (mean 0.09%). Evaluation of different subgenomic regions did not identify any other section of the HAV genome that could accurately represent phylogenetic relationships observed using WG sequences. The identification of 2-3 dominant HAV strains in 3 out of 4 outbreaks indicates contamination of the implicated food items with a heterogeneous HAV population. However, analysis of intra-host HAV variants from eight patients involved in one outbreak showed that only a single sequence variant established infection in each patient. Four non-outbreak strains were found closely related to strains from 2 outbreaks, whereas ten were genetically different from the outbreak strains. Thus, accurate tracking of HAV strains can be accomplished using HAV WG sequences, while short subgenomic regions are useful for identification of transmissions only among cases with known epidemiological association. |
Hepatitis A virus: host interactions, molecular epidemiology and evolution.
Vaughan G , Goncalves Rossi LM , Forbi JC , de Paula VS , Purdy MA , Xia G , Khudyakov YE . Infect Genet Evol 2013 21 227-43 Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions. |
Hepatitis B virus transmissions associated with a portable dental clinic, West Virginia, 2009
Radcliffe RA , Bixler D , Moorman A , Hogan VA , Greenfield VS , Gaviria DM , Patel PR , Schaefer MK , Collins AS , Khudyakov YE , Drobeniuc J , Gooch BF , Cleveland JL . J Am Dent Assoc 2013 144 (10) 1110-8 BACKGROUND: Although hepatitis B virus (HBV) transmission in dental settings is rare, in 2009 a cluster of acute HBV infections was reported among attendees of a two-day portable dental clinic in West Virginia. METHODS: The authors conducted a retrospective investigation by using treatment records and volunteer logs, interviews of patients and volunteers with acute HBV infection as well as of other clinic volunteers, and molecular sequencing of the virus from those acutely infected. RESULTS: The clinic was held under the auspices of a charitable organization in a gymnasium staffed by 750 volunteers, including dental care providers who treated 1,137 adults. Five acute HBV infections-involving three patients and two volunteers-were identified by the local and state health departments. Of four viral isolates available for testing, all were genotype D. Three case patients underwent extractions; one received restorations and one a dental prophylaxis. None shared a treatment provider with any of the others. One case volunteer worked in maintenance; the other directed patients from triage to the treatment waiting area. Case patients reported no behavioral risk factors for HBV infection. The investigation revealed numerous infection control breaches. CONCLUSIONS: Transmission of HBV to three patients and two volunteers is likely to have occurred at a portable dental clinic. Specific breaches in infection control could not be linked to these HBV transmissions. PRACTICAL IMPLICATIONS: All dental settings should adhere to recommended infection control practices, including oversight; training in prevention of bloodborne pathogens transmission; receipt of HBV vaccination for staff who may come into contact with blood or body fluids; use of appropriate personal protective equipment, sterilization and disinfection procedures; and use of measures, such as high-volume suction, to minimize the spread of blood. |
Disparate distribution of hepatitis B virus genotypes in four sub-Saharan African countries.
Forbi JC , Ben-Ayed Y , Xia GL , Vaughan G , Drobeniuc J , Switzer WM , Khudyakov YE . J Clin Virol 2013 58 (1) 59-66 BACKGROUND: Hepatitis B virus (HBV) places a substantial health burden on Africa. Here, we investigated genetic diversity of HBV variants circulating in 4 countries of sub-Saharan Africa using archived samples. In total, 1492 plasma samples were tested from HIV-infected individuals and pregnant women, among which 143 (9.6%) were PCR-positive for HBV DNA (Cote d'Ivoire, 70/608 [11.5%]; Ghana, 13/444 [2.9%]; Cameroon, 33/303 [10.9%]; and Uganda, 27/137 [19.7%]). STUDY DESIGN/RESULTS: Phylogenetic analysis of the S-gene sequences identified HBV genotypes E (HBV/E, n=96) and A (HBV/A, n=47) distributed as follows: 87% of HBV/E and 13% of HBV/A in Cote d'Ivoire; 100% of HBV/E in Ghana; 67% of HBV/E and 33% of HBV/A in Cameroon; and 100% of HBV/A in Uganda. The average and maximal nucleotide distances among HBV/E sequences were 1.9% and 6.4%, respectively, suggesting a greater genetic diversity for this genotype than previously reported (p<0.001). HBV/A strains were classified into subgenotypes HBV/A1, HBV/A2 and HBV/A3. In Uganda, 93% of HBV/A strains belonged to HBV/A1 whereas HBV/A3 was the only subgenotype of HBV/A found in Cameroon. In Cote d'Ivoire, HBV/A strains were classified as HBV/A1 (11.1%), HBV/A2 (33.3%) and HBV/A3 (55.6%). Phylogeographic analysis of the sequences available from Africa supported earlier suggestions on the origin of HBV/A1, HBV/A2 and HBV/A3 in East, South and West/Central Africa, respectively. Using predicted amino acid sequences, hepatitis B surface antigen (HBsAg) was classified into serotype ayw4 in 93% of HBV/E strains and adw2 in 68% of HBV/A strains. Also, 7.7% of the sequences carried substitutions in HBsAg associated with immune escape. CONCLUSIONS: The observations of pan-African and global dissemination of HBV/A1 and HBV/A2, and the circulation of HBV/E and HBV/A3 almost exclusively in West and Central Africa suggest a more recent increase in prevalence in Africa of HBV/E and HBV/A3 compared to HBV/A1 and HBV/A2. The broad genetic heterogeneity of HBsAg detected here may impact the efficacy of prevention and control efforts in sub-Saharan Africa. |
Application of mass spectrometry to molecular diagnostics of viral infections
Ganova-Raeva LM , Khudyakov YE . Expert Rev Mol Diagn 2013 13 (4) 377-88 Mass spectrometry (MS) has found numerous applications in life sciences. It has high accuracy, sensitivity and wide dynamic range in addition to medium- to high-throughput capabilities. These features make MS a superior platform for analysis of various biomolecules including proteins, lipids, nucleic acids and carbohydrates. Until recently, MS was applied for protein detection and characterization. During the last decade, however, MS has successfully been used for molecular diagnostics of microbial and viral infections with the most notable applications being identification of pathogens, genomic sequencing, mutation detection, DNA methylation analysis, tracking of transmissions, and characterization of genetic heterogeneity. These new developments vastly expand the MS application from experimental research to public health and clinical fields. Matching of molecular techniques with specific requirements of the major MS platforms has produced powerful technologies for molecular diagnostics, which will further benefit from coupling with computational tools for extracting clinical information from MS-derived data. |
Detection of hepatitis C virus transmission by use of DNA mass spectrometry.
Ganova-Raeva LM , Dimitrova ZE , Campo DS , Yulin L , Ramachandran S , Xia GL , Honisch C , Cantor CR , Khudyakov YE . J Infect Dis 2013 207 (6) 999-1006 The molecular detection of transmission of rapidly mutating pathogens such as hepatitis C virus (HCV) is commonly achieved by assessing the genetic relatedness of strains among infected patients. We describe the development of a novel mass spectrometry (MS)-based approach to identification of HCV transmissions. MS was used to detect products of base-specific cleavage of RNA molecules obtained from HCV PCR fragments. The MS-peak profiles (MSPs) were found to reflect variation in the HCV genomic sequence and the intra-host composition of the HCV population. Serum specimens (n=60) originating from case-patients of 14 epidemiologically confirmed outbreaks and unrelated controls (n=25) were tested. Neighbor-joining trees constructed using MSP-based Hamming distances showed 100% accuracy, and linkage networks constructed using a threshold established from the Hamming distances between epidemiologically unrelated cases showed 100% sensitivity and 99.93% specificity in transmission detection. The MS approach is rapid, robust, reproducible and cost-effective, and applicable to investigating transmissions of other pathogens. |
Investigation of hepatitis B virus and human immunodeficiency virus transmission among severely mentally ill residents at a long term care facility
Jasuja S , Thompson ND , Peters PJ , Khudyakov YE , Patel MT , Linchangco P , Thai HT , Switzer WM , Shankar A , Heneine W , Hu DJ , Moorman AC , Gerber SI . PLoS One 2012 7 (8) e43252 BACKGROUND: A high prevalence of hepatitis B virus (HBV) and human immunodeficiency virus (HIV) infections have been reported among persons with severe mental illness. In October, 2009, the Cook County Department of Public Health (CCDPH) initiated an investigation following notification of a cluster of HBV infections among mentally ill residents at a long term care facility (LTCF). METHODS: LTCF staff were interviewed and resident medical records were reviewed. Residents were offered testing for HBV, HCV, and HIV. Serum specimens from residents diagnosed with HBV or HIV infection were sent to the Centers for Disease Control and Prevention (CDC) for analysis. RESULTS: Eleven newly diagnosed HBV infections were identified among mentally ill residents at the LTCF. Of these 11 infections, 4 serum specimens were available for complete HBV genome sequencing; all 4 genomes were found to be closely related. Four newly diagnosed HIV infections were identified within this same population. Upon molecular analysis, 2 of 4 HIV sequences from these new infections were found to be nearly identical and formed a tight phylogenetic cluster. CONCLUSIONS: HBV and HIV transmission was identified among mentally ill residents of this LTCF. Continued efforts are needed to prevent bloodborne pathogen transmission among mentally ill residents in LTCFs. |
Results from a large-scale epidemiologic look-back investigation of improperly reprocessed endoscopy equipment
Holodniy M , Oda G , Schirmer PL , Lucero CA , Khudyakov YE , Xia G , Lin Y , Valdiserri R , Duncan WE , Davey VJ , Cross GM . Infect Control Hosp Epidemiol 2012 33 (7) 649-56 OBJECTIVE: To determine whether improper high-level disinfection practices during endoscopy procedures resulted in bloodborne viral infection transmission. DESIGN: Retrospective cohort study. SETTING: Four Veterans Affairs medical centers (VAMCs). PATIENTS: Veterans who underwent colonoscopy and laryngoscopy (ear, nose, and throat [ENT]) procedures from 2003 to 2009. METHODS: Patients were identified through electronic health record searches and serotested for human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV). Newly discovered case patients were linked to a potential source with known identical infection, whose procedure occurred no more than 1 day prior to the case patient's procedure. Viral genetic testing was performed for case/proximate pairs to determine relatedness. RESULTS: Of 10,737 veterans who underwent endoscopy at 4 VAMCs, 9,879 patients agreed to viral testing. Of these, 90 patients were newly diagnosed with 1 or more viral bloodborne pathogens (BBPs). There were no case/proximate pairings found for patients with either HIV or HBV; 24 HCV case/proximate pairings were found, of which 7 case patients and 8 proximate patients had sufficient viral load for further genetic testing. Only 2 of these cases, both of whom underwent laryngoscopy, and their 4 proximates agreed to further testing. None of the 4 remaining proximate patients who underwent colonoscopy agreed to further testing. Mean genetic distance between the 2 case patients and 4 proximate patients ranged from 13.5% to 19.1%. CONCLUSIONS: Our investigation revealed that exposure to improperly reprocessed ENT endoscopes did not result in viral transmission in those patients who had viral genetic analysis performed. Any potential transmission of BBPs from colonoscopy remains unknown. |
Health care-associated hepatitis C virus infections attributed to narcotic diversion
Hellinger WC , Bacalis LP , Kay RS , Thompson ND , Xia GL , Lin Y , Khudyakov YE , Perz JF . Ann Intern Med 2012 156 (7) 477-82 BACKGROUND: Three cases of genetically related hepatitis C virus (HCV) infection that were unattributable to infection control breaches were identified at a health care facility. OBJECTIVE: To investigate HCV transmission from an HCV-infected health care worker to patients through drug diversion. DESIGN: Cluster and look-back investigations. SETTING: Acute care hospital and affiliated multispecialty clinic. PATIENTS: Inpatients and outpatients during the period of HCV transmission. MEASUREMENTS: Employee work and narcotic dispensing records, blood testing for HCV antibody and RNA, and sequencing of the NS5B gene and the hypervariable region 1 of the E2 gene. RESULTS: 21 employees were recorded as being at work or as retrieving a narcotic from an automated dispensing cabinet in an area where a narcotic was administered to each of the 3 case patients; all employees provided blood samples for HCV testing. One employee was infected with HCV that had more than 95% NS5B sequence homology with the HCV strains of the 3 case patients. Quasi-species analysis showed close genetic relatedness with variants from each of the case patients and more than 97.9% nucleotide identity. The employee acknowledged parenteral opiate diversion. An investigation identified 6132 patients at risk for exposure to HCV because of the drug diversion. Of the 3929 living patients, 3444 (87.7%) were screened for infection. Two additional cases of genetically related HCV infection attributable to the employee were identified. LIMITATION: Of the living patients at risk for HCV exposure, 12.3% were not tested. CONCLUSION: Five cases of HCV infection occurring over 3 to 4 years were attributed to drug diversion by an HCV-infected health care worker. Studies of drug diversion and assessments of strategies to prevent narcotics tampering in all health care settings are needed. PRIMARY FUNDING SOURCE: None. |
The hepatitis E virus polyproline region is involved in viral adaptation.
Purdy MA , Lara J , Khudyakov YE . PLoS One 2012 7 (4) e35974 Genomes of hepatitis E virus (HEV), rubivirus and cutthroat virus (CTV) contain a region of high proline density and low amino acid (aa) complexity, named the polyproline region (PPR). In HEV genotypes 1, 3 and 4, it is the only region within the non-structural open reading frame (ORF1) with positive selection (4-10 codons with dN/dS>1). This region has the highest density of sites with homoplasy values >0.5. Genotypes 3 and 4 show approximately 3-fold increase in homoplastic density (HD) in the PPR compared to any other region in ORF1, genotype 1 does not exhibit significant HD (p<0.0001). PPR sequence divergence was found to be 2-fold greater for HEV genotypes 3 and 4 than for genotype 1. The data suggest the PPR plays an important role in host-range adaptation. Although the PPR appears to be hypervariable and homoplastic, it retains as much phylogenetic signal as any other similar sized region in the ORF1, indicating that convergent evolution operates within the major HEV phylogenetic lineages. Analyses of sequence-based secondary structure and the tertiary structure identify PPR as an intrinsically disordered region (IDR), implicating its role in regulation of replication. The identified propensity for the disorder-to-order state transitions indicates the PPR is involved in protein-protein interactions. Furthermore, the PPR of all four HEV genotypes contains seven putative linear binding motifs for ligands involved in the regulation of a wide number of cellular signaling processes. Structure-based analysis of possible molecular functions of these motifs showed the PPR is prone to bind a wide variety of ligands. Collectively, these data suggest a role for the PPR in HEV adaptation. Particularly as an IDR, the PPR likely contributes to fine tuning of viral replication through protein-protein interactions and should be considered as a target for development of novel anti-viral drugs. |
Epidemic history of hepatitis C virus infection in two remote communities in Nigeria, West Africa.
Forbi JC , Purdy MA , Campo DS , Vaughan G , Dimitrova ZE , Ganova-Raeva LM , Xia GL , Khudyakov YE . J Gen Virol 2012 93 1410-1421 We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15% of the population had serological or molecular markers of HCV infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV infected residents showed that HCV variants belonged to genotype 1 (n=51; 85%) and genotype 2 (n=9; 15%). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n=43) and genotype 2 (n=6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200-300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the last 3 centuries. |
Human and porcine hepatitis e viruses, southeastern Bolivia
Purdy MA , Dell'amico MC , Gonzales JL , Segundo H , Tolari F , Mazzei M , Bartoloni A , Khudyakov YE . Emerg Infect Dis 2012 18 (2) 339-40 TO THE EDITOR: Hepatitis E virus (HEV) genotypes 3 and 4 are considered to be primarily zoonotic (1). However, recent data indicate that both genotypes can be transmitted among humans through other routes (2,3). Observations of genetic distinctiveness between swine and human HEV strains circulating within the same region argue against exclusivity of zoonotic transmission (4). A recent report presented a remarkable example of such distinction between genotype 3 isolates in rural communities in southeastern Bolivia (5). |
Evaluation of intra-host variants of the entire hepatitis B virus genome.
Ramachandran S , Zhai X , Thai H , Campo DS , Xia G , Ganova-Raeva LM , Drobeniuc J , Khudyakov YE . PLoS One 2011 6 (9) e25232 Genetic analysis of hepatitis B virus (HBV) frequently involves study of intra-host variants, identification of which is commonly achieved using short regions of the HBV genome. However, the use of short sequences significantly limits evaluation of genetic relatedness among HBV strains. Although analysis of HBV complete genomes using genetic cloning has been developed, its application is highly labor intensive and practiced only infrequently. We describe here a novel approach to whole genome (WG) HBV quasispecies analysis based on end-point, limiting-dilution real-time PCR (EPLD-PCR) for amplification of single HBV genome variants, and their subsequent sequencing. EPLD-PCR was used to analyze WG quasispecies from serum samples of patients (n = 38) infected with HBV genotypes A, B, C, D, E and G. Phylogenetic analysis of the EPLD-isolated HBV-WG quasispecies showed the presence of mixed genotypes, recombinant variants and sub-populations of the virus. A critical observation was that HBV-WG consensus sequences obtained by direct sequencing of PCR fragments without EPLD are genetically close, but not always identical to the major HBV variants in the intra-host population, thus indicating that consensus sequences should be judiciously used in genetic analysis. Sequence-based studies of HBV WG quasispecies should afford a more accurate assessment of HBV evolution in various clinical and epidemiological settings. |
The molecular epidemiology of hepatitis E virus infection.
Purdy MA , Khudyakov YE . Virus Res 2011 161 (1) 31-9 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. |
Temporal variations in the hepatitis C virus intrahost population during chronic infection.
Ramachandran S , Campo DS , Dimitrova ZE , Xia GL , Purdy MA , Khudyakov YE . J Virol 2011 85 (13) 6369-80 The hepatitis C virus (HCV) intra-host evolution holds keys to understanding mechanisms responsible for establishment of chronic infections and development of a vaccine and therapeutics. In this study, intra-host variants of two variable HCV genomic regions, HVR1 and NS5A, were sequenced from four treatment-naive chronically infected patients who were followed up from the acute stage for 9-18 years. Median joining network analysis indicated that majority of the HCV intra-host variants were observed only at certain time-points, but some variants were detectable at more than one time-point. In all patients, these variants were found organized into communities or subpopulations. We hypothesize that HCV intra-host evolution is defined by 2 processes: incremental changes within communities through random mutation, and alternations between coexisting communities. The HCV population was observed to incrementally evolve within a single community during the first approximately 3 years of infection followed by dispersion into several subpopulations. Two patients demonstrated this pattern of dispersion for the rest of the observation period, while HCV variants in the other two patients converged into another single subpopulation after approximately 9-12 years of dispersion. The final subpopulation in these two patients was under purifying selection. Intra-host HCV evolution in all four patients was characterized by a consistent increase in negative selection over time, suggesting the increasing HCV adaptation to the host late in infection. The data suggest specific staging of the intra-host HCV evolution. |
Evolutionary history and population dynamics of hepatitis E virus
Purdy MA , Khudyakov YE . PLoS One 2010 5 (12) e14376 BACKGROUND: Hepatitis E virus (HEV) is an enterically transmitted hepatropic virus. It segregates as four genotypes. All genotypes infect humans while only genotypes 3 and 4 also infect several animal species. It has been suggested that hepatitis E is zoonotic, but no study has analyzed the evolutionary history of HEV. We present here an analysis of the evolutionary history of HEV. METHODS AND FINDINGS: The times to the most recent common ancestors for all four genotypes of HEV were calculated using BEAST to conduct a Bayesian analysis of HEV. The population dynamics for genotypes 1, 3 and 4 were analyzed using skyline plots. Bayesian analysis showed that the most recent common ancestor for modern HEV existed between 536 and 1344 years ago. The progenitor of HEV appears to have given rise to anthropotropic and enzootic forms of HEV, which evolved into genotypes 1 and 2 and genotypes 3 and 4, respectively. Population dynamics suggest that genotypes 1, 3 and 4 experienced a population expansion during the 20(th) century. Genotype 1 has increased in infected population size approximately 30-35 years ago. Genotype 3 and 4 have experienced an increase in population size starting late in the 19(th) century until ca.1940-45, with genotype 3 having undergone additional rapid expansion until ca.1960. The effective population size for both genotype 3 and 4 rapidly declined to pre-expansion levels starting in ca.1990. Genotype 4 was further examined as Chinese and Japanese sequences, which exhibited different population dynamics, suggesting that this genotype experienced different evolutionary history in these two countries. CONCLUSIONS: HEV appears to have evolved through a series of steps, in which the ancestors of HEV may have adapted to a succession of animal hosts leading to humans. Analysis of the population dynamics of HEV suggests a substantial temporal variation in the rate of transmission among HEV genotypes in different geographic regions late in the 20(th) Century. |
Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria
Forbi JC , Vaughan G , Purdy MA , Campo DS , Xia GL , Ganova-Raeva LM , Ramachandran S , Thai H , Khudyakov YE . PLoS One 2010 5 (7) e11615 BACKGROUND: In Nigeria, hepatitis B virus (HBV) infection has reached hyperendemic levels and its nature and origin have been described as a puzzle. In this study, we investigated the molecular epidemiology and epidemic history of HBV infection in two semi-isolated rural communities in North/Central Nigeria. It was expected that only a few, if any, HBV strains could have been introduced and effectively transmitted among these residents, reflecting limited contacts of these communities with the general population in the country. METHODS AND FINDINGS: Despite remoteness and isolation, approximately 11% of the entire population in these communities was HBV-DNA seropositive. Analyses of the S-gene sequences obtained from 55 HBV-seropositive individuals showed the circulation of 37 distinct HBV variants. These HBV isolates belong predominantly to genotype E (HBV/E) (n=53, 96.4%), with only 2 classified as sub-genotype A3 (HBV/A3). Phylogenetic analysis showed extensive intermixing between HBV/E variants identified in these communities and different countries in Africa. Quasispecies analysis of 22 HBV/E strains using end-point limiting-dilution real-time PCR, sequencing and median joining networks showed extensive intra-host heterogeneity and inter-host variant sharing. To investigate events that resulted in such remarkable HBV/E diversity, HBV full-size genome sequences were obtained from 47 HBV/E infected persons and P gene was subjected to Bayesian coalescent analysis. The time to the most recent common ancestor (tMRCA) for these HBV/E variants was estimated to be year 1952 (95% highest posterior density (95% HPD): 1927-1970). Using additional HBV/E sequences from other African countries, the tMRCA was estimated to be year 1948 (95% HPD: 1924-1966), indicating that HBV/E in these remote communities has a similar time of origin with multiple HBV/E variants broadly circulating in West/Central Africa. Phylogenetic analysis and statistical neutrality tests suggested rapid HBV/E population expansion. Additionally, skyline plot analysis showed an increase in the size of the HBV/E-infected population over the last approximately 30-40 years. CONCLUSIONS: Our data suggest a massive introduction and relatively recent HBV/E expansion in the human population in Africa. Collectively, these data show a significant shift in the HBV/E epidemic dynamics in Africa over the last century. |
Hepatitis C virus infections from unsafe injection practices at an endoscopy clinic in Las Vegas, Nevada, 2007-2008
Fischer GE , Schaefer MK , Labus BJ , Sands L , Rowley P , Azzam IA , Armour P , Khudyakov YE , Lin Y , Xia G , Patel PR , Perz JF , Holmberg SD . Clin Infect Dis 2010 51 (3) 267-73 BACKGROUND: In January 2008, 3 persons with acute hepatitis C who all underwent endoscopy at a single facility in Nevada were identified. METHOD: We reviewed clinical and laboratory data from initially detected cases of acute hepatitis C and reviewed infection control practices at the clinic where case patients underwent endoscopy. Persons who underwent procedures on days when the case patients underwent endoscopy were tested for hepatitis C virus (HCV) infection and other bloodborne pathogens. Quasispecies analysis determined the relatedness of HCV in persons infected. RESULTS: In addition to the 3 initial cases, 5 additional cases of clinic-acquired HCV infection were identified from 2 procedure dates included in this initial field investigation. Quasispecies analysis revealed 2 distinct clusters of clinic-acquired HCV infections and a source patient related to each cluster, suggesting separate transmission events. Of 49 HCV-susceptible persons whose procedures followed that of the source patient on 25 July 2007, 1 (2%) was HCV infected. Among 38 HCV-susceptible persons whose procedures followed that of another source patient on 21 September 2007, 7 (18%) were HCV infected. Reuse of syringes on single patients in conjunction with use of single-use propofol vials for multiple patients was observed during normal clinic operations. CONCLUSION: Patient-to-patient transmission of HCV likely resulted from contamination of single-use medication vials that were used for multiple patients during anesthesia administration. The resulting public health notification of approximately 50,000 persons was the largest of its kind in United States health care. This investigation highlighted breaches in aseptic technique, deficiencies in oversight of outpatient settings, and difficulties in detecting and investigating such outbreaks. |
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