Virus Genotype Distribution Research Articles

Molecular characterization of dengue viruses isolated from patients in Central Java, Indonesia.

Dengue is hyper-endemic in Indonesia. Purwokerto city in Central Java province is routinely ravaged by the disease. Despite the endemicity of dengue in this city, there is still no data on the virological aspects of dengue in the city. We conducted a molecular surveillance study of the circulating dengue viruses (DENV) in Purwokerto city to gain information on the virus origin, serotype and genotype distribution, and phylogenetic characteristics of DENV. A cross-sectional dengue molecular surveillance study was conducted in Purwokerto. Sera were collected from dengue-suspected patients attending three hospitals in the city. Diagnosis was performed using dengue NS1 antigen and IgG/IgM antibodies detection. DENV serotyping was performed using Simplexa Dengue real-time RT-PCR. Sequencing was conducted to obtain full-length DENV Envelope (E) gene sequences, which were then used in phylogenetic and genotypic analyses. Patients' clinical and demographic data were collected and analyzed. A total of 105 dengue-suspected patients' sera were collected, in which 80 (76.2%) were positive for IgM and/or IgG, and 57 (54.2%) were confirmed as dengue by NS1 antigen and/or DENV RNA detection using RT-PCR. Serotyping was successful for 47 isolates. All four serotypes circulated in the area with DENV-3 as the predominant serotype. Phylogenetic analyses grouped the isolates into Genotype I for DENV-1, Cosmopolitan genotype for DENV-2, and Genotype I and II for DENV-3 and -4, respectively. The analyses also revealed the close relatedness of Purwokerto isolates to other DENV strains from Indonesia and neighboring countries. We reveal the molecular and virological characteristics of DENV in Purwokerto, Banyumas regency, Central Java. The genotype and phylogenetic analyses indicate the endemicity of the circulating DENV in the city. Our serotype and genotype data provide references for future dengue molecular epidemiology studies and disease management in the region.

Hepatitis C virus genotype distribution in Southern China during 2015-2016

Objective To investigate the current distribution of hepatitis C virus (HCV) genotype in Southern China and to understand the HCV transmission and to infer its transmitting trend. Methods The HCV gene subtypes of 3 524 specimens from Southern China were detected and analyzed by polyonerase chain reaction (PCR)-fluorescence probe method or sequencing. The regular nested PCR and sequencing were used for the phylogenetic tree analysis when the fluorescence PCR inefficiently identifying virus isolates. Results Among 3 524 specimens, there were 2 922 cases from Guangdong, 78 cases from Fujian, 152 cases from Hainan and 372 cases from Guangxi. Genotype 1b comprised the majority (1 808/3 524, 51.3%), followed by genotype 6a (925/3 524, 26.2%), 2a (298/3 524, 8.46%), 3a (246/3 524, 6.98%), 3b (200/3 524, 5.68%) and 1a (27/3 524, 0.77%). In addition, 1 case was genotype 6e, 1 case was genotype 6q, 1 case was genotype 6r, 3 case were genotype 6w, 2 case were genotype 6xa, 2 case were genotype 6n, and 1 case was genotype 6 with unclassified subtype. The genotype 1b accounted for the majority in most areas of 21 cities and counties in Guangdong Province, followed by genotype 6a. But in some areas, the major genotype was genotype 6a, followed by 1b. Genotype 4, genotype 5 and genotype 7 were not found in this study. Conclusions In the past two years, genotype 1b and 6a are still the epidemic genotypes in Guangdong, Guangxi and Hainan provinces. However, genotype 6a has replaced 1b as the dominant one in some areas in Guangdong Province. The distributions of HCV genotypes do not change significantly in Guangxi and Fujian provinces. Key words: Southern China; Hepatitis C virus; PCR- fluorescent probe method; Genotype distribution; Phylogenetic tree

Characteristics of hepatitis C virus infection and genotype distribution among entry travelers at Tengchong Port

Objective To investigate the characteristics of epidemic and genotype/subtype distribution of hepatitis C virus (HCV) among entry travelers at Tengchong port, to provide references for HCV prophylaxis and treatment. Methods A total of 54 serum samples were collected from anti-HCV positive travelers at Tengchong port from June 2009 to June 2016. HCV NS5B gene was amplified using reverse transcription polyonerase chain reation (RT-PCR) and subsequently sequenced. Based on the obtained sequences and retrieved reference sequences, phylogenetic analysis was conducted to determine HCV genotype/subtype. Results HCV infection rate among entry travelers at Tengchong ports was 0.45%(54/12 059). Forty-five samples were successfully genotyped. Phylogenetically, HCV genotype 3b was revealed to be the predominant subtype (28.89%, 13/45) in this population, followed by genotype 6n (20.0%, 9/45), genotype 1b (17.78%, 8/45), genotype 3a (13.33%, 6/45), genotype 2a (11.11%, 5/45), genotype 1a (2.22%, 1/45) and genotype 6a (2.22%, 1/45). The major genotype in Myanmar travelers was genotype 6, while in Chinese population, genotype 1 predominated. Genotype 6 in the population showed close phylogenetic relationship with strains prevalent in China and Southeast Asia. Genotype 3 was closely clustered with strains prevalent in China. Conclusions The distribution of HCV genotypes among entry travelers at Tengchong port is impacted by HCV epidemic strains both in Yunnan province and neighboring regions. This population serves as a transmitting media which may influence the epidemiological characteristics of HCV in Tengchong and neighboring areas. Key words: Hepatitis C virus; Epidemiology, molecular; Entry travelers

Hepatitis C Virus (HCV) genotypes distribution among hepatocellular carcinoma patients in Southern Italy: a three year retrospective study

BackgroundHepatocellular carcinoma (HCC) is one of the major cause for cancer in the world. Aim of this case-control study was to investigate the distribution pattern of HCV genotypes among HCC patients and suggest whether infection with specific subtypes may be associated with an increased risk of progression to cancer.Methods152 HCC anti-HCV positive patients, fulfilling the criteria from the Barcelona 2000 EASL conference, and 568 patients HCV chronically infected but without HCC as control group were included in the study. Serum of each patient was evaluated for viral load estimation and genotyping.ResultsMales with HCC significantly showed to have quite 2 times higher risk of exposure to HCV infection (OR = 1.72; 95% CI = 1.15–2.58). Moreover, HCC was significantly associated with older age. In fact, > 50 years older patients showed to have a higher risk of developing HCC (OR = 17.4; 95% CI = 4.24 to 71.36) compared to younger patients.HCV RNA rate was significantly higher (83.7%) among HCC patients than in the control group (61.4%, p < 0.001) and the most prevalent genotype was 1b (68.0% in HCC vs 54.4% in the control group, p < 0.005). HCC patients significantly have a risk of exposure to HCV 1b infection almost 2 times greater than the control group (OR = 1.8; 95% CI = 1.11–2.82). The multivariate-adjusted OR (95% CI) of developing HCC for HCV 1b comparing to non-1b was 1.65 (1.16–2.33).ConclusionsOur study detected a significantly higher rate of HCV RNA positivity and a higher rate of HCV 1b infection in HCC patients, suggesting the strict association between subtype 1b infection and HCC. A prospective study with larger number of samples would be needed to confirm our results.

Evolution of the prevalence of hepatitis C virus infection and hepatitis C virus genotype distribution in human immunodeficiency virus-infected patients in Italy between 1997 and 2015

ObjectivesTo analyse the variation of hepatitis C virus (HCV) prevalence and genotype distribution and their determinants in people living with human immunodeficiency virus (HIV) who entered care between 1997 and 2015. MethodsHIV-infected patients enrolled in ICONA who were tested for HCV antibodies (HCV-Ab) were included. ResultsOverall 3407 of 12 135 (28.1%) were HCV-Ab+; and 735 of 12 135 (6.1%) were HBsAg+. Among patients whose HCV genotype was known, the most represented were genotypes 1 and 3. The prevalence of HCV infection decreased from 49.2% (2565/5217) during 1997–2002 to 10.2% (556/5466) during 2009–2015. The frequency of genotype 1a increased from 29.0% (264/911) to 43.0% (129/300), whereas genotype 3 decreased from 38.5% (351/911) to 27.0% (81/300). Independent predictors of HCV-Ab+ status were being female (adjusted OR (AOR) 1.23, 95% CI 1.04–1.50, p = 0.01), risk category (versus injecting drug users: men who have sex with men AOR 0.01, 95% CI 0.01–0.01, p <0.001; heterosexuals AOR 0.01, 95% CI 0.01–0.01, p <0.001; other/unknown AOR 0.02, 95% CI 0.01–0.02, p <0.001), being cared for in Central Italy (versus being cared for in Northern Italy: AOR 0.85, 95% CI 0.73–0.98, p <0.001), being Italian-born (AOR 1.44, 95% CI 1.16–1.80, p = 0.001) and being enrolled in less recent calendar years (versus 1997–2002: 2009–2015 AOR 0.23, 95% CI 0.19–0.27, p <0.001; 2003–2008 AOR 0.49, 95% CI 0.41–0.61, p <0.001). ConclusionsThe prevalence of HCV infection in HIV-infected patients entering into care in Italy significantly declined in more recent calendar years. After adjusting for risk factors and calendar years, HCV co-infection was more frequent in females and in those born in Italy.

Determination of hepatitis C virus genotype distribution in Adıyaman province

Amac: Hepatit C virus (HCV) enfeksiyonu Turkiye’de ve dunyada en onemli karaciger hastaliklarindan biridir. HCV yuksek duzeyde genetik heterojenite gostermektedir. Tum dunyada simdiye kadar alti major tipi ve cok sayida alt tipi tanimlanmistir. Dunyanin farkli bolgelerinde HCV genotipleri ve alt tiplerinin dagilimi degismektedir. Bu calismanin amaci Adiyaman ilinde kronik HCV enfeksiyonlu hastalarda HCV genotip dagilimini belirlemektir. Materyal ve Metod: Bu calismada kronik HCV enfeksiyonlu 71 (26 kadin, 45 erkek) hasta degerlendirildi. Viral genotipler dizi analizi (ABI Prism 310 Genetic Analyzer) ve HCV-RNA Real Time PCR genotipleme performans paneli (PHW 202, BBI Diagnostics) ile uretici firmanin onerilerine gore calisilarak belirlendi. Bulgular: 71 hastanin 51’inde (%71,83) genotip 1b gozlendi. HCV-RNA pozitif olan orneklerin geri kalaninda; 6 hastada genotip 1a (%8,45) ve 8’inde (%11,27) genotip 2b enfeksiyonu gosterildi. Geri kalan 6 ornegin 3’unde (%4,22) genotip 1 ve 3’unde (%4,22) genotip 3a olarak tespit edildi. Genotip ve ya alt tip dagilimi bakimindan kadin ve erkek cinsiyet yonunden istatistiksel olarak anlamli bir fark gozlenmedi. Sonuc: Sonuclarimiza gore genotip 1b Adiyaman ilinde baskin olarak saptandi. Ancak zamanla di g er genotiplerinde ortaya cikti g i gosterilmi s tir.

Prevalence of Cervical Infection and Genotype Distribution of Human Papilloma Virus Among Females in Da Nang, Vietnam.

The goal of the present study was to determine the prevalence and distribution of high-risk human papilloma virus (HPV) genotypes in women from two districts in and around Da Nang city, Vietnam. All participants were randomly selected, 200 from the Hai Chau district and 200 from the Son Tra district. The detection and genotyping of HPV were performed by real-time polymerase chain reaction (PCR) technique. Out of a total of 400 women, we found that 38 (9.5%) were infected with a high-risk HPV genotype, the most prevalent genotypes being 16, 18, 58 and 59. By assessment of the HPV findings in relation to sociodemographic characteristics, we found significant differences between the two study districts and between the age groups, as well as differences associated with occupation and the use of contraceptives. The proportion of high-risk genotypes other than 16 and 18 was relatively high, and since the HPV genotype distribution is known to vary greatly across populations, the information from this study can be used for planning of screening and vaccination programs in Da Nang.

Chronic hepatitis C virus infection in India: Regionaldemographics and distribution of viral genotypes.

Although chronic hepatitis C virus (HCV) infection affects millions of people in India, few studies have assessed host, viral, and disease characteristics of chronically infected patients at national and regional levels. Such information is critical to support large scale screening and treatment initiatives for chronic HCV infection in India. Patients with known chronic HCV infection making routine or for-cause visits to the participating study centers were enrolled in this observational study. Patients attended a single outpatient visit during which demographics and medical history were collected, a physical examination was performed, and blood and urine samples were collected for laboratory assessments. Samples were analyzed to determine HCV genotypes and subtypes, and genotypes of interferon lambda 3 (IFNL3) single nucleotide polymorphism. No therapeutic interventions were administered. We enrolled 500 patients at 19 centers, categorized into four geographic regions (North, South, East, and West). All patients self-identified as Indian, and most (66%) were male. Genotype 3 was the most common genotype overall (54%); however, its prevalence varied greatly by region, ranging from 34% in the South to 69% in the East. Genotypes 1 (24%) and 4 (6%) were the next most common, and HCV genotype could not be determined for 16% of patients. This prospective survey suggests that demographics, viral, and host factors in patients with chronic HCV infection are highly variable in India and pose significant challenges for the implementation of broad-scale screening and treatment initiatives.

Hepatitis B virus infection in blood donors in Argentina: prevalence of infection, genotype distribution and frequency of occult HBV infection.

This study describes the prevalence of HBV infection based on detection of HBsAg and HBV-DNA by NAT in 70,102 blood donors in Argentina (Córdoba province) and shows the viral genotype distribution and frequency of occult HBV infection (OBI) in this population. Forty-two donors were confirmed positive for HBV infection (0.06%), and four had OBI. Genotype F was the most prevalent (71.4%), followed by A (14.3%), C (7.1%) and D (7.1%). This is the first report of the prevalence of confirmed HBV infection and the high frequency of occult HBV infection in a blood bank in Argentina.

Incident Hepatitis C Virus Genotype Distribution and Multiple Infection in Australian Prisons.

Hepatitis C virus (HCV) is a highly diverse pathogen that is classified into seven distinct genotypes. Simultaneous or sequential reinfection with multiple HCV genotypes is recognized in high-risk populations, such as injecting drug users (IDUs). Multiple infection is of clinical concern as different genotypes have various sensitivities to current antiviral therapies. Therefore, a better understanding of the frequency of multiple infection and of the genotypes currently being transmitted is clinically relevant. An Australian cohort of IDUs (n = 123), identified with primary incident infection, was followed for multiple infection by regular HCV RNA testing between 2005 and 2013. A total of 354 samples were tested. Sequencing of primary incident infections revealed that genotype 3a was the most common circulating genotype, followed by genotype 1a. Examination of longitudinally collected samples identified complex patterns of multiple infection, including reinfection and superinfection. In those with multiple infection, there was no apparent evidence of homotypic immunity conferring protection against reinfection of the same subtype. This study revealed frequent multiple infection in a high-risk prisoner cohort, illustrating the complex nature of HCV infection and reinfection and highlighting the need for pan-genotypic antiviral therapies.

Hepatitis C Virus Genotype and Subtype Distribution in Patient Specimens Tested at the University of Texas Medical Branch, Galveston, Between January 2011 and November 2014.

Hepatitis C virus (HCV) genotype/subtype data are routinely generated in clinical laboratories to guide treatment. Genotype data can also inform genotype distribution and molecular epidemiology of HCV infections in patient populations and geographical regions that clinics/laboratories serve. The aim of this study was to determine the distribution of HCV genotypes/subtypes and their association with demographic characteristics among the patients that were routinely tested in the Molecular Diagnostics Laboratory at The University of Texas Medical Branch (UTMB) at Galveston. Among the 6573 patients tested between January 2011 and November 2014, the most frequent HCV genotype/subtype was 1a (65.3%), followed by 3a (11.5%), 1b (10.4%), and 2b (8.8%). Combined, genotype 4 and genotype 6 were found in less than 1% of this cohort. Approximately 1.3% of the patients presented multiple genotypes/subtypes. Factors independently associated with genotypes and subtypes were race/ethnicity, sex, and patient age.

Hepatitis C Virus Genotype Distribution in Kermanshah Province, Western Iran

&lt;p&gt;&lt;span style="font-size: 10.5pt; font-family: 'Times New Roman','serif'; mso-fareast-font-family: 宋体; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA; mso-bidi-font-size: 12.0pt;" lang="EN-US"&gt;Six major hepatitis C virus genotypes have been characterized, which vary in their geographical distribution. Knowledge of the distribution of various genotypes is essential for successful future research, treatment and control strategies. In this study, the distribution of HCV genotypes and their association with possible risk factors in a group of HCV infected patients from Kermanshah province of Iran was investigated. HCV viral load test by Real time- PCR method was used for diagnosis of infected cases. The genotypes of cases were revealed using Nested- and Multiplex-PCR and with direct sequencing results were confirmed. Risk factors were also recorded and a multivariate analysis was performed. Among 180 infected people, 138 (76.6%) with 3a genotype, 35 (19.4%) with 1a genotype, 3 (1.7%) with 1b genotype and 4 (2.2%) with 3a and 1b were determined. HCV was transmitted by different routes such as intravenous drug abuse (IVDA), tattooing, sexual, blood transfusion and other risk factors. IVDA and sex are the main risk factors in the men and women, respectively. However, 3a is the predominant genotype in the all groups. This study revealed that 3a is the most prevalent genotypes in Kermanshah province.&lt;/span&gt;&lt;/p&gt;

Global epidemiology of hepatitis C virus infection: An up-date of the distribution and circulation of hepatitis C virus genotypes.

AIMTo review Hepatitis C virus (HCV) prevalence and genotypes distribution worldwide.METHODSWe conducted a systematic study which represents one of the most comprehensive effort to quantify global HCV epidemiology, using the best available published data between 2000 and 2015 from 138 countries (about 90% of the global population), grouped in 20 geographical areas (with the exclusion of Oceania), as defined by the Global Burden of Diseases project (GBD). Countries for which we were unable to obtain HCV genotype prevalence data were excluded from calculations of regional proportions, although their populations were included in the total population size of each region when generating regional genotype prevalence estimates.RESULTSTotal global HCV prevalence is estimated at 2.5% (177.5 million of HCV infected adults), ranging from 2.9% in Africa and 1.3% in Americas, with a global viraemic rate of 67% (118.9 million of HCV RNA positive cases), varying from 64.4% in Asia to 74.8% in Australasia. HCV genotype 1 is the most prevalent worldwide (49.1%), followed by genotype 3 (17.9%), 4 (16.8%) and 2 (11.0%). Genotypes 5 and 6 are responsible for the remaining < 5%. While genotypes 1 and 3 are common worldwide, the largest proportion of genotypes 4 and 5 is in lower-income countries. Although HCV genotypes 1 and 3 infections are the most prevalent globally (67.0% if considered together), other genotypes are found more commonly in lower-income countries where still account for a significant proportion of HCV cases.CONCLUSIONA more precise knowledge of HCV genotype distribution will be helpful to best inform national healthcare models to improve access to new treatments.

Hepatitis C virus prevalence and genotype distribution in Pakistan: Comprehensive review of recent data.

Hepatitis C virus (HCV) is endemic in Pakistan and its burden is expected to increase in coming decades owing mainly to widespread use of unsafe medical procedures. The prevalence of HCV in Pakistan has previously been reviewed. However, the literature search conducted here revealed that at least 86 relevant studies have been produced since the publication of these systematic reviews. A revised updated analysis was therefore needed in order to integrate the fresh data. A systematic review of data published between 2010 and 2015 showed that HCV seroprevalence among the general adult Pakistani population is 6.8%, while active HCV infection was found in approximately 6% of the population. Studies included in this review have also shown extremely high HCV prevalence in rural and underdeveloped peri-urban areas (up to 25%), highlighting the need for an increased focus on this previously neglected socioeconomic stratum of the population. While a 2.45% seroprevalence among blood donors demands immediate measures to curtail the risk of transfusion transmitted HCV, a very high prevalence in patients attending hospitals with various non-liver disease related complaints (up to 30%) suggests a rise in the incidence of nosocomial HCV spread. HCV genotype 3a continues to be the most prevalent subtype infecting people in Pakistan (61.3%). However, recent years have witnessed an increase in the frequency of subtype 2a in certain geographical sub-regions within Pakistan. In Khyber Pakhtunkhwa and Sindh provinces, 2a was the second most prevalent genotype (17.3% and 11.3% respectively). While the changing frequency distribution of various genotypes demands an increased emphasis on research for novel therapeutic regimens, evidence of high nosocomial transmission calls for immediate measures aimed at ensuring safe medical practices.

Subtype distribution of hepatitis C virus in Jiangsu, China.

Hepatitis C virus (HCV) genotype distribution varied by regions and transmission modes. In this study, we investigated HCV genotype distribution in five cities of Jiangsu, China, all of which are located in the Yangtze River Delta Region. A total of 363 samples were collected during 2011-2012. C/E2 and NS5B fragments of HCV were amplified using a multiple RT-nested PCR strategy and subjected to sequencing. Phylogenetic analysis was performed for HCV genotyping. Among 106 PCR positive cases, HCV subtypes 1a (0.9%), 1b (61.3%), 2a (15.1%), 3a (4.7%), 3b (9.4%), 6a (6.6%), and 6n (1.9%) were detected. Together with our previous data, we found that HCV subtypes were more among injection drug users (IDUs) (nine) than among general population (GP) (six), and the most common subtype among GP was 1b (73.9%), followed by 2a (14.5%), while the top four common subtypes among IDUs were 3a, 1b, 3b, and 6a, with similar prevalence rates (24.4%, 22.7%, 20.9%, and 17.4%, respectively). There were nine HCV subtypes prevalent among IDUs in Jiangsu, more than those in Xinjiang, Hubei, Yunnan, Guangxi, Guangdong, and Hong Kong. The top four common subtypes among IDUs in Jiangsu covered all the two most common HCV subtypes (except 6n subtype) observed in six targeted provinces/region. These results suggested that Jiangsu may be an important gathering place for various HCV subtypes and the gathering may be involved in the large scale of population migration from other regions of China to Eastern China.

Hepatitis C virus genotype and subtype distribution in Chinese chronic hepatitis C patients: nationwide spread of HCV genotypes 3 and 6.

BackgroundHepatitis C virus (HCV) genotype and subtype are related to disease progression and response to antiviral therapy. Current HCV genotype and subtype distribution data, especially for genotypes 3 and 6, are limited in China. Our purpose was to investigate the current HCV genotype and subtype distributions in chronic hepatitis C patients in China.MethodsChronic hepatitis C patients (n = 1012) were enrolled, and demographic information and possible transmission risk factors were collected. Serum samples were subjected to reverse-transcription polymerase chain reaction, followed by direct DNA sequencing and phylogenetic analysis of the NS5B and core/E1 regions to determine HCV genotypes/subtypes. The geographical distributions of HCV genotypes/subtypes were analyzed. Demographic information and transmission risk factors were compared between different HCV genotypes/subtypes.ResultsFour genotypes and seven subtypes of HCV were detected in 970 patients. Subtypes 1b, 2a, 3a, 6a, 3b, 6n, and 1a were detected at frequencies of 71.96 %, 19.90 %, 3.20 %, 2.16 %, 1.96 %, 0.41 %, and 0.41 %, respectively. Genotypes 3 and 6 showed an increasingly wide geographic distribution over time. Patients with subtypes 1b and 2a were older than those with 3a, 3b, 6a, and 6n subtypes (p < 0.05 in all subtypes). More genotype 1 and 2 patients underwent blood transfusion than those with genotype 3 (all p < 0.05). More genotype 3 and 6 patients had a history of intravenous drug use than those with genotypes 1 and 2 (all p < 0.05).ConclusionsThough subtypes 1b and 2a are still the most prevalent HCV subtypes in China, genotype 3 and 6 HCV infections have already spread nationwide from southern and western China.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-015-0341-1) contains supplementary material, which is available to authorized users.

Pilot study of Torque Teno Virus genotypes distribution in different human tissues

Pilot study of Torque Teno Virus genotypes distribution in different human tissues

Nationwide prevalence of human papillomavirus infection and viral genotype distribution in 37 cities in China.

BackgroundType-specific high-risk HPV (hrHPV) infection is related to cervical carcinogenesis. The prevalence of hrHPV infection varies geographically, which might reflect the epidemiological characteristics of cervical cancer among different populations. To establish a foundation for HPV-based screening and vaccination programs in China, we investigated the most recent HPV prevalence and genotypic distributions in different female age groups and geographical regions in China.MethodsIn 2012, a total of 120,772 liquid-based cytological samples from women enrolled for population- or employee-based cervical screening in 37 Chinese cities were obtained by the Laboratory of Molecular Infectious Diseases of Guangzhou KingMed. A total of 111,131 samples were tested by Hybrid Capture II and the other 9,641 were genotyped using the Tellgenplex™ HPV DNA Assay.ResultsThe total positive rate for hrHPV was 21.07 %, which ranged from 18.42 % (Nanchang) to 31.94 % (Haikou) and varied by region. The regions of Nanchang, Changsha, Hangzhou, Chengdu, Fuzhou, Guangdong, and Guiyang could be considered the low prevalence regions. Age-specific prevalence showed a “two-peak” pattern, with the youngest age group (15–19 years) presenting the highest hrHPV infection rate (30.55 %), followed by a second peak for the 50–60-year-old group. Overall, the most prevalent genotypes were HPV16 (4.82 %) and HPV52 (4.52 %), followed by HPV58 (2.74 %). Two genotypes HPV6 (4.01 %) and HPV11 (2.29 %) were predominant in the low-risk HPV (lrHPV) type, while the mixed genotypes HPV16 + 52 and HPV52 + 58 were most common in women with multiple infections.ConclusionsThis study shows that HPV infection in China has increased to the level of an “HPV-heavy-burden” zone in certain regions, with prevalence varying significantly among different ages and regions. Data from this study represent the most current survey of the nationwide prevalence of HPV infection in China, and can serve as valuable reference to guide nationwide cervical cancer screening and HPV vaccination programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-0998-5) contains supplementary material, which is available to authorized users.

Virus Genotype Distribution and Virus Burden in Children and Adults Hospitalized for Norovirus Gastroenteritis, 2012-2014, Hong Kong.

We conducted a 2-year hospital-based study on norovirus gastroenteritis among children and adults between August 2012 and September 2014. A total of 1,146 norovirus cases were identified. Young children (aged ≤ 5 years) accounted for a majority (53.3%) of cases. Hospitalization incidence exhibited a U-shaped pattern with the highest rate in young children (1,475 per 100,000 person-years), followed by the elderly aged > 84 years (581 per 100,000 person-years). A subset (n = 395, 34.5%) of cases were selected for norovirus genotyping and noroviral load measurement. Non-GII.4 infections were more commonly observed in young children than in older adults (aged > 65 years) (20.5% versus 9.2%; p < 0.05). In young children, the median noroviral load of GII.4 and non-GII.4 cases was indistinguishably high (cycle threshold value, median [interquartile range]: 16.6 [15.2–19.3] versus 16.6 [14.9–21.6]; p = 0.45). Two age-specific non-GII.4 genotypes (GII.3 and GII.6) were identified among young children. These findings may have implications in norovirus vaccination strategy.

Molecular detection, genetic diversity and distribution of Sugarcane yellow leaf virus genotypes in China

A total of 332 sugarcane leaf samples were collected from seven provinces in China during 2010 to 2013. RT-PCR was performed using the YLS111/YLS462 primers to detect the causal pathogen Sugarcane yellow leaf virus (SCYLV) causing yellow leaf disease in sugarcane. The incidence of SCYLV infection ranged from 24 to 38 % depending on geographic areas. A new primer pair (P0-R3/P0-F2) was designed to prime the amplification of a 968-nucleotide (nt) fragment from SCYLV-positive samples. The fragment contained a partial 5′ untranslated region, the complete ORF0 encoding P0, and a partial ORF1. A phylogenetic analysis of 141 P0 fragment sequences (937 nt) worldwide showed that all SCYLV isolates were clustered into eight genotypes. The 107 SCYLV isolates collected in this study were classified into three genotypes (BRA, HAW, and CHN3), of which the BRA genotype (102/107) was the most prevalent and was detected in all evaluated locations. One isolate (1/107) of genotype HAW was found in Hainan province. Four isolates (4/107) of the genotype CHN3 were observed in Guangxi, Guizhou and Hainan provinces. These findings help understand the genotypic diversity and distribution of SCYLV isolates in China.