The current hepatitis C virus prevalence in China may have resulted mainly from an officially encouraged plasma campaign in the 1990s: a coalescence inference with genetic sequences

Distribution pattern, molecular transmission networks, and phylodynamic of hepatitis C virus in China

In China, few molecular epidemiological data on hepatitis C virus (HCV) are available and all previous studies were limited by small sample sizes or specific population characteristics. Here, we report characterization of the epidemic history and transmission dynamics of HCV strains in China. We included HCV sequences of individuals belonging to three HCV surveillance programs: 1) patients diagnosed with HIV infection at the Beijing HIV laboratory network, most of whom were people who inject drugs and former paid blood donors, 2) men who have sex with men, and 3) the general population. We also used publicly available HCV sequences sampled in China in our study. In total, we obtained 1,603 Ns5b and 865 C/E2 sequences from 1,811 individuals. The most common HCV strains were subtypes 1b (29.1%), 3b (25.5%) and 3a (15.1%). In transmission network analysis, factors independently associated with clustering included the region (OR: 0.37, 95% CI: 0.19-0.71), infection subtype (OR: 0.23, 95% CI: 0.1-0.52), and sampling period (OR: 0.43, 95% CI: 0.27-0.68). The history of the major HCV subtypes was complex, which coincided with some important sociomedical events in China. Of note, five of eight HCV subtype (1a, 1b, 2a, 3a, and 3b), which constituted 81.8% HCV strains genotyped in our study, showed a tendency towards decline in the effective population size during the past decade until present, which is a good omen for the goal of eliminating HCV by 2030 in China.

Growth history of hepatitis C virus among HIV/HCV co-infected patients in Guizhou Province

Background: The evolutionary and epidemiological history and the regional differences of various hepatitis C virus (HCV) genotypes are complex. Our aim was to better understand the molecular epidemiology and evolutionary dynamics of HCV among HIV/HCV co-infected individuals in Guizhou Province. This information could contribute to improve HCV prevention and control strategies in Guizhou and surrounding provinces. Methods: The HCV RNA was extracted from the serum of HIV/HCV co-infected patients, and reverse transcription/nested PCR was performed to amplify nucleotide sequences of the C-E1 region. Then, the successfully amplified sequences were selected for phylogenetic analysis. The available C-E1 region reference sequences from the surrounding provinces of Guizhou (Guangxi, Yunnan, Hunan, and Sichuan) were retrieved in GenBank, and the evolutionary analysis by Bayesian Markov chain Monte Carlo (MCMC) algorithm was performed using BEAST software to reconstruct a phylogeographic tree in order to explore their migration patterns. Finally, the epidemiological history of HCV in the Guizhou region was retraced by reconstructing Bayesian skyline plots (BSPs) after excluding sequences from surrounding provinces. Results: Among 186 HIV/HCV co-infected patients, the C-E1 region sequence was successfully amplified in 177 cases. Phylogenetic analysis classified these sequences into six subtypes: 1a, 1b, 3a, 3b, 6a, and 6n. Among them, subtype 6a was the most dominant strain (n = 70), followed by 3b (n = 55), 1b (n = 31), 3a (n = 11), 1a (n = 8), and 6n (n = 2). By reconstructing the phylogeographic tree, we estimated that the 6a strain in Guizhou mainly originated from Yunnan and Guangxi, while the 3b strain emerged due to transmission from the IDU network in Yunnan. Subtypes 1b, 3a, 3b, and 6a, as the major subtypes of HCV in HIV/HCV co-infected individuals in Guizhou, emerged and later grew more rapidly than the national average. Notably, BSPs of the currently prevalent HCV predominant strain subtype 6a in Guizhou have shown a rapid population growth since 2004. Although the growth rate slowed down around 2010, this growth has continued to date. Conclusion: Overall, despite the improvement and implementation of a series of HCV prevention and control policies and measures, a delayed growth pattern may indicate a unique history of the spread of 6a in Guizhou. Its trend as the dominant strain in Guizhou in recent years may continue to increase slowly over subsequent years.

The distribution of hepatitis C virus infection in Shanghai, China: a time-spatial study

BACKGROUND

Shanghai, as a pilot city of China to achieve the goal of eliminating hepatitis C, its strategy of allocating medical resources is a pressing problem to be solved. This study aims to infer the time-spatial clustering patterns of HCV-infected cases, and grasp the dynamic genotype distribution of HCV, thereby inform elimination strategies of HCV with efficacy and efficiency.

METHODS

Reported HCV cases including their demographic information in Shanghai city from 2005 to 2018 were released from the National Infectious Disease Reporting Information System, population data at community scale, geographical layers of hospitals, communities and districts were gathered from former research. Blood samples of HCV-infected individuals were collected during 2014-2018 from 24 sentinel hospitals, HCV-antibody test, qualitative nucleic acid test and NS5B/5'UTR gene amplification were performed accordingly to determine the genotypes of the specimen. Furthermore, global and local spatial self-correlation analysis of both acute and chronic HCV infections were conducted at community scale year by year, then time-spatial clusters of acute and chronic HCV infections and HCV genotype distribution of specimen collected from sentinel hospitals by districts were mapped by using Arcmap10.1.

RESULTS

A total of 2631 acute HCV cases and 15,063 chronic HCV cases were reported in Shanghai from 2005 to 2018, with a peak in 2010 and 2017, respectively. The mean age of chronic HCV patients was 49.70 ± 14.55 years, 3.34 ± 0.32 years older than the acute (t = 10.55, P-value < 0.01). The spatial distribution of acute HCV infection formed one primary cluster (Relative Risk = 2.71), and the chronic formed one primary cluster and three secondary clusters with Relative Risk ranged from 1.94 to 14.42, meanwhile, an overlap of 34 communities between acute and chronic HCV clusters were found with time period spans varied from 6 to 12 years. Genotype 1 (N = 257, 49.71%) was the most prevalent HCV genotype in Shanghai, genotype 3 infections have increased in recent years. Baoshan district presented cluster of acute HCV and the highest proportion of genotype 2, Pudong new area was the cluster of chronic HCV and occupied the highest proportion of genotype 3.

CONCLUSIONS

Despite the low prevalence of HCV infection, it is still needed to push forward the elimination process in Shanghai, as there is a certain amount of HCV infected people waiting to be treated. The time-spatial clustering patterns and the dynamic of HCV genotype distribution together indicated a changing constitution of different transmission routes of HCV infection, thus, a focused strategy may be needed for high-risk population related to genotype 3 infection like drug users, in addition to an enforcement of the existing measures of preventing the iatrogenic and hematogenic transmission of HCV.

The inference of HIV-1 transmission direction between HIV-1 positive couples based on the sequences of HIV-1 quasi-species

Background

To infer transmission direction of a HIV transmission chain is helpful not only in legal jurisdiction but also in precise intervention to prevent HIV spread. Recently, the direction of transmission is inferred by whether paraphyletic-monophyletic (PM) or a combination of paraphyletic and polyphyletic (PP) topologies is observed or not between the sequences of source and recipient in the phylogenetic tree. However, paraphyly between them often declines over time and may disappear between spouses due to bidirectional transmission after primary infection. In this study, our aim is to test the reliability of inferring HIV transmission direction between epidemiologically linked HIV-1 positive couples using whether or not paraphyly is observed in phylogenetic tree.

Methods

HIV quasi-species were sequenced using PCR product clones, and then Bayesian analysis of molecular sequences with MCMC was employed to construct phylogenetic relationship of env, gag, pol gene fragments of HIV-1 positive couples using BEAST software.

Results

Our results showed that all sequences of seven couples except pol sequences of couple 12 and 13 form their own monophyletic cluster in phylogenetic tree including the closest control sequences from GenBank or other studies on local samples, which are supported by significant Bayesian posterior probabilities more than 0.9932. Of seven couples, paraphyly is only observed in phylogenetic tree constructed with env and pol gene sequences of three couples and gag gene sequences of four couples. Paraphyly is not observed in half of HIV positive couples. Pol sequences of couple 13 is separated by Blast selected controls; pol sequences of couple 12 in phylogenetic tree is supported by a lower Bayesian posterior value.

Conclusion

Paraphyly relationship between sequences of donator and recipient is only observed among partial HIV-1 positive couples with epidemiological link. Phylogenetic relationship is not always the same when various gene regions of HIV are used to conduct phylogenetic analysis. The combination of phylogenetic analysis based on various gene regions of HIV and enough epidemiology investigation is essential when inferring transmission direction of HIV in a transmission chain or in one couple. However, while observed paraphyly can be used to infer transmission direction in HIV-1 positive couple, no observed paraphyly cannot deny it.

Complicated HCV subtype expansion among drug users in Guangdong province, China

Guangdong Province is one of the most developed and populous provinces in southern China. The subtype situation of hepatitis C virus (HCV) in Guangdong remains unknown. The aim of this study was to investigate and estimate the HCV subtypes in drug users (DU) using a city-based sampling strategy to better understand the characteristics of HCV transmission in Guangdong. Archived plasma samples (n = 1074) from DU who were anti-HCV positive in 2014 were selected randomly from 20 cities in Guangdong Province. Subtypes were determined based on core and/or E1 sequences using phylogenetic analysis. The distributions of HCV subtypes in DU and different regions were analyzed. A total of 8 genotypes were identified. The three main HCV subtypes in DU in Guangdong were 6a (63.0%), 3a (15.2%), and 3b (11.8%). Significant differences were discovered among different registered residency and regions but not among genders, marital status, education level, or drug use patterns. HCV subtype 3b was significantly higher in Guangdong residents than in non-Guangdong residents. In contrast, HCV subtype 6a was significantly lower in Guangdong residents than in non-Guangdong residents. Subtype 1b in eastern Guangdong (eastern) was significantly lower, while 6a was significantly higher when compared with other regions. Subtype 3a in the Pearl River Delta (PRD) region was significantly higher, while 3b was significantly lower when compared with other regions. In western Guangdong, HCV subtype 3a was significantly lower when compared with other regions. Additionally, in northern Guangdong subtypes 1b and 3b were significantly higher, while 6a was significantly lower when compared with other regions. Our study revealed the diversity and distribution of HCV subtypes in DU in nearly all the cities in Guangdong. The results provide essential information that will allow the establishment of specific intervention strategies that may help prevent HCV transmission.

Genotype distribution of hepatitis C virus in 952 cases from 2014 to 2016 in Hunan Province, China

INTRODUCTION

Few large-scale investigations on genotype (GT) distribution of hepatitis C virus (HCV) in Hunan Province, China, are reported.

MATERIAL AND METHODS

We recruited all of the 952 patients in the census register of Hunan Province who were first diagnosed with HCV infection in the Second Xiangya Hospital, Central South University in 2014-2016. HCV genotypes were surveyed. The genotype distribution pattern was compared with those of the neighboring regions in China.

RESULTS

Among the 952 patients, genotype 1 (GT1) (69.9%) was the most common HCV genotype, followed by GT6 (19.0%), GT3 (8.4%), and GT2 (2.6%). GT4 and GT5 were not found. One case had mixed infection of GT3 and GT6. Predominance of GT1 HCV was more evident in the patients aged ≥ 40 years than in those aged < 40 years (79.5% vs. 47.9%, χ2 = 95.993, p < 0.001). HCV genotype distribution had gender difference (χ2 = 44.695, p < 0.001), with GT3 and GT6 more prevalent in males than in females (36.2% vs. 18.2%, χ2 = 39.088, p < 0.001) while GT1 more prevalent in females than in males (80.1% vs. 60.3%, χ2 = 44.276, p < 0.001). Though Hunan Province is located in central China, its HCV genotype priority was similar with the change trend in south and southwest China, while distinguished from those of other regions, in particular from the neighboring central province, Hubei Province.

CONCLUSIONS

HCV GT1 was the most predominant HCV genotype in Hunan Province, and GT6 and GT3 accounted for a significant percentage, especially in young patients. The HCV distribution pattern was more similar to those of the regions in south China.

Analysis of Transmission Routes of Hepatitis C Virus Based on Virus Genotyping in 341 Cases with Different Suspected Initial Infection Time Points in Hunan Province, China

Background

Few investigations have been reported on the changing trends in transmission routes of hepatitis C virus (HCV) and the corresponding HCV genotype (GT) distribution in Hunan province, China.

Material/Methods

HCV GTs, suspected viral transmission routes, and time of initial infections were investigated in 341 HCV-infected patients in 2016.

Results

Genotype 1 (GT1) (72.1%) was the most prevalent HCV GT, followed by GT6 (17.6%), GT3 (7.6%), and GT2 (2.6%). GT4 and GT5 were not found. The predominant HCV transmission routes were blood-related routes (57.5%) and intravenous drug use (IDU) (15.0%); 52.2% of the patients got HCV infection before 1994, 25.6% from 1994 to 1998, and 22.2% after 1998; 93.5% of the infections via blood-related transmission routes were with HCV GT1, 61.5% via IDU or feculent sexual contact were with HCV GT6, and 50.0% via non-healthcare invasive procedures were with HCV GT6. HCV infections via IDU or feculent sexual behavior were more prevalent in young males, while infections via invasive cosmetic procedures occurred more in young females, and both had a shorter time interval from suspected infection to confirmed clinical diagnosis. Multinomial logistic regression confirmed the time points of the initial HCV infections and suspected viral transmission routes were correlated with HCV GT distribution.

Conclusions

HCV GT1 infections via blood-related transmission routes in Hunan province have continually decreased since 1994. However, younger patients infected with HCV, especially with HCV GT6 via IDU, feculent sexual behavior, and non-healthcare invasive procedures, have significantly increased.

Molecular evolution of hepatitis C virus in China: A nationwide study

The evolutionary and epidemic history and the regional differences of hepatitis C virus (HCV) are complex and remain unclear in the vast territory China. Here we recruited 1540 HCV-RNA positive patients sampled in 29 provinces across whole China, which is the largest sample capacity and the most comprehensive geographic coverage of China to our knowledge. 1b, 2a, 3b, 6a and 3a were the major subtypes in China. 1b was the most predominant subtype which presented in every province. The second most predominant subtype, 2a, appeared to concentrate in the north of China. Subtypes 3a and 3b were mainly found in the Southwest region, while 6a was restricted in the South region. We further estimated the origins of the dominating subtypes and discovered for the first time that a Chinese-specific transmission pattern for some strains of subtype 2a which was restricted in north China, and Chinese subtype 3b originated from Thailand.

Needlestick and Sharps Injuries Among Nursing Students in Nanjing, China

Needlestick and sharps injuries (NSIs) are a major cause of occupational injuries for health care workers worldwide. In this study, the authors report the prevalence of and risk factors for NSIs among Chinese nursing students. A cross-sectional survey was distributed to 442 nursing students; 393 completed questionnaires were submitted. A total of 237 (60.3%) nursing students reported NSIs, which were more commonly reported by female students, younger students, students who worked frequent night shifts, students without safety training, and students who did not use personal protective equipment. Among those injured, 59.9% were injured by syringe needles, 21.9% by glass items, and 3.4% by scissors. Of those needles and sharps causing injuries, 36.3% of devices had been used on patients, 41% were unused, and 22.7% were unknown. Opening ampoules or vials was the most common injury agent. A total of 86.9% of NSIs were not reported to hospital infection control. Nursing students are at high risk of NSIs in China. Occupational safety training should be developed and implemented to prevent NSIs among this vulnerable population.

The role of routine screening in blood-borne pathogens in Chinese patients undergoing joint arthroplasty

Objectives

Surgeons face a substantial risk of infection because of the occupational exposure to blood-borne pathogens (BBPs) from patients undergoing high-risk orthopaedic procedures. This study aimed to determine the seroprevalence of four BBPs among patients undergoing joint arthroplasty in Shanghai, China. In addition, we evaluated the significance of pre-operative screening by calculating a cost-to-benefit ratio.

Methods

A retrospective observational study of pre-operative screening for BBPs, including hepatitis B and C viruses (HBV and HCV), human immunodeficiency virus (HIV) and Treponema pallidum (TP), was conducted for sequential patients in the orthopaedic department of a large urban teaching hospital between 01 January 2009 and 30 May 2016. Medical records were analysed to verify the seroprevalence of these BBPs among the patients stratified by age, gender, local origin, type of surgery, history of previous transfusion and marital status.

Results

Of the subjects who underwent arthroplasty surgery in our institution, pre-operative screening tests were available for 96.1% (11 609 patients). The seroprevalence of HBV, HCV, HIV and TP was 5.47%, 0.45%, 0.08% and 3.6%, respectively. A total of 761 seropositive cases (68.4%) were previously undiagnosed. Pre-operative screening for HIV resulted in a low cost to benefit ratio, followed by HCV and HBV.

Conclusion

Routine HCV and HIV screening prior to joint arthroplasty is not a cost-effective strategy. Considering the high rate of undiagnosed patients and the shortage of protective options, targeted pre-operative screening for HBV and syphilis should be considered for the protection of healthcare workers in China who have not been vaccinated.

Cite this article: Bone Joint Res 2017;6:566–571.

Genome-wide analysis for identification of adaptive diversification between hepatitis C virus subtypes 1a and 1b

Hepatitis C virus (HCV) is a major cause of liver disease and has been estimated to infect approximately 2%-3% of the world's population. HCV genotype 1 is the subject of intense research and clinical investigations because of its worldwide prevalence and poor access to treatment for patients in developing countries and marginalized populations. The predominant subtypes 1a and 1b of HCV genotype 1 present considerable differences in epidemiological features. However, the genetic signature underlying such phenotypic functional divergence is still an open question. Here, we performed a genome-wide evolutionary study on HCV subtypes 1a and 1b. The results show that adaptive selection has driven the diversification between these subtypes. Furthermore, the major adaptive divergence-related changes have occurred on proteins E1, NS4B, NS5A, and NS5B. Structurally, a number of adaptively selected sites cluster in functional regions potentially relevant to (i) membrane attachment and (ii) the interactions with viral and host cell factors and the genome template. These results might provide helpful hints about the molecular determinants of epidemiological divergence between HCV 1a and 1b.

The evolutionary patterns of hepatitis C virus subtype 2a and 6a isolates linked to an outbreak in China in 2012

An HCV outbreak occurred in 2012 in China, affecting hundreds of patients. We characterized HCV subtype 2a and 6a sequences from 60 and 102 patients, respectively, and co-analyzed them with 82 local controls and 103 calibrating references. The close grouping of the patients׳ sequences contrasted sharply with the diversity of local controls. Scaled by the calibrating references, the emergence of patients׳ isolates was estimated at 2-5 years before sampling. In contrast, the controls intermingled with the calibrating references that were much older. For both subtypes, the major and minor clusters could be defined, with the closeness to indicate linked transmission.

CONCLUSION

HCV sequences from the study patients grouped into three subtype 2a and two subtype 6a clusters, in addition to three 6a solitary branches, representing descendants of eight earlier strains that were distinct and otherwise sporadic. Due to iatrogenic transmission through reusing needles, five strains were highly selected and preferentially spread.

Needlestick and Sharps Injuries Among Nurses at a Teaching Hospital in China

Needlestick and sharps injuries (NSIs) are a major occupational injury to health care workers worldwide. This study aimed to report the prevalence and risk factors of NSIs among nurses working at a Chinese teaching hospital. From 463 nurses, 402 completed questionnaires were obtained. A total of 261 (64.9%) nurses reported needlestick or sharps injuries. NSIs were more common among females, young nurses, surgical nurses, and junior nurses. Logistic regression analysis suggests that age and work department were independent risk factors for NSIs. By type of devices, syringe needles accounted for the highest proportion of all NSIs (59%), followed by glass items (22%), and trocar core/catheter wires (4%). NSIs remain an important occupational hazard issue or Chinese nurses. Programs must be developed to prevent injuries caused by needlesticks and sharps.

The genetic diversity and evolutionary history of hepatitis C virus in Vietnam

Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2.

Migration patterns of hepatitis C virus in China characterized for five major subtypes based on samples from 411 volunteer blood donors from 17 provinces and municipalities

We investigated the migration patterns of hepatitis C virus (HCV) in China. Partial E1 and/or NS5B sequences from 411 volunteer blood donors sampled in 17 provinces and municipalities located in five large regions, the north-northeast, northwest, southwest, central south, and southeast, were characterized. The sequences were classified into eight subtypes (1a, n = 3; 1b, n = 183; 2a, n = 83; 3a, n = 30; 3b, n = 44; 6a, n = 55; 6n, n = 10; 6v, n = 1) and a new subtype candidate. Bayesian evolutionary analysis by sampling trees of the E1 sequences of the five major subtypes revealed distinct migration patterns. Subtype 1b showed four groups: one is prevalent nationwide with possible origins in the north-northeast; two are locally epidemic in the central south and northwest, respectively, and have spread sporadically to other regions; and the fourth one is likely linked to the long-distance dispersion among intravenous drug users from the northwest. Subtype 2a showed two groups: the larger one was mainly restricted to the northwest and seemed to show a trend toward migration via the Silk Road; the smaller one was geographically mixed and may represent descendants of those that spread widely during the contaminated plasma campaign in the 1990s. Subtype 3a exhibited three well-separated geographic groups that may be epidemically unrelated: one showed origins in the northwest, one showed origins in the southwest, and the other showed origins in the central south. In contrast, subtype 3b had a mixture of geographic origins, suggesting migrations from the southwest to the northwest and sporadically to other regions. Structurally resembling the tree for subtype 3a, the tree for subtype 6a showed four groups that may indicate migrations from the central south to southeast, southwest, and northwest. Strikingly, no subtype 6a strain was identified in the north-northeast.

IMPORTANCE

With a population of greater than 1.3 billion and a territory of >9.6 million square kilometers, China has a total of 34 provinces and municipalities. In such a vast country, the epidemic history and migration trends of HCV are thought to be unique and complex but variable among regions and are unlikely to be represented by those observed in only one or at best a few provinces and municipalities. However, due to the difficulties in recruiting patients, all previous studies for this purpose have been based only on data from limited regions, and therefore, geographical biases were unavoidable. In this study, such biases were greatly reduced because we utilized samples collected from volunteer blood donors in 17 provinces and municipalities. To our knowledge, this is the first study in which the HCV isolates represented such a large portion of the country, and thus, the results should shed light on the current understanding of HCV molecular epidemiology.

Molecular epidemiologic characterization of a clustering HCV infection caused by inappropriate medical care in Heyuan City of Guangdong, China

Background

From November 2011 to January 2012, a number of clustering cases of HCV infection were reported in Zijin County, Heyuan City, Guangdong, China. Most patients in the clustering cases suspected that they could be infected due to inappropriate medical care in the clinic located at the Xiangshui road. However, the molecular epidemiology of the clustering cases remains unknown.

Methodology

The residents, living at Xiangshui Road, with HCV antibody positive reported from 2011 and 2012 were recruited. A survey of the HCV infected individuals from the clustering cases was conducted. Each participant underwent a questionnaire defining demographic characteristics and health care history. HCV serological test and viral load test were performed to confirm the infection status. Molecular phylogenetic analysis and Bayesian coalescence analysis were conducted to further confirm the HCV subtype distribution and to reconstruct the associated demographic history and time-scaled phylogeny among the clustering cases.

Principal Findings

The molecular phylogenetic analysis revealed that only two HCV subtypes, 2a and 6a, were found among the clustering cases. There was no close HCV subtype evolutionary relation was observed among patients from the same family. The 6a cluster showed higher viral loads than the 2a cluster. In addition, the Bayesian skyline plot analysis showed that both the HCV 2a and 6a subtype infections among the Heyuan cases experienced an “expansion-diminishment-expansion” featured dissemination. The 2a clustering infection occurred in 2004, and the 6a clustering cases originated in 2006.

Conclusions

The molecular epidemiological characters imply that the inappropriate medical practices were possibly associated with the clustering HCV cases in Heyuan City during 2011, 2012. Latent HCV subtypes 2a and 6a infection may cause the prevalence and become a new public health issue in Guangdong, China.