Codon usage of host-specific P genotypes (VP4) in group A rotavirus.

BACKGROUND: Group A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and animals. However, their codon usage patterns that are essential to obtain insights into the viral evolution, host adaptability, and genetic characterization remained unclear, especially across animal hosts. RESULTS: We performed a comprehensive codon usage analysis of eight host-specific RVA P genotypes, including human RVA (P[4] and P[8]), porcine RVA (P[13] and P[23]), and zoonotic RVA (P[1], P[6], P[7] and P[19]), based on 233 VP4 complete coding sequences. Nucleotide composition, relative synonymous codon usage (RSCU), and effective number of codons (ENC) were calculated. Principal component analysis (PCA) based on RSCU values was used to explore the codon usage patterns of different RVA P genotypes. In addition, mutation pressure and natural selection were identified by using ENC-plot, parity rule 2 plot, and neutrality plot analyses. All VP4 sequences preferred using A/U nucleotides (A: 0.354-0.377, U: 0.267-0.314) than G/C nucleotides across genotypes. Similarly, majority of commonly used synonymous codons were likely to end with A/U nucleotides (A: 9/18-12/18, U: 6/18-9/18). In PCA, human, porcine, and zoonotic genotypes clustered separately in terms of RSCU values, indicating the host-specific codon usage patterns; however, porcine and zoonotic genotypes were partly overlapped. Human genotypes, P[4] and P[8], had stronger codon usage bias, as indicated by more over-represented codons and lower ENC, compared to porcine and zoonotic genotypes. Moreover, natural selection was determined to be a predominant driver in shaping the codon usage bias across the eight P genotypes. In addition, mutation pressure contributed to the codon usage bias of human genotypes. CONCLUSIONS: Our study identified a strong codon usage bias of human RVA P genotypes attributable to both natural selection and mutation pressure, whereas similar codon usage bias between porcine and zoonotic genotypes predominantly attributable to natural selection. It further suggests possible cross-species transmission. Therefore, it warrants further surveillance of RVA P genotypes for early identification of zoonotic infection.

Genomic characterization of Rocahepevirus ratti hepatitis E virus genotype C1 in Yunnan province of China.

The Rocahepevirus ratti hepatitis E virus genotype C1 (HEV-C1) has been documented to infect humans. However, the understanding of HEV-C1 remains constrained. This study aims to determine the prevalence and genomic characteristics of HEV-C1 in small animals in Yunnan province of southwestern China. A total of 444 liver tissues were collected from animals covering the orders Rodentia, Soricomorpha, Scandentia and Erinaceomorpha in three regions in Yunnan. Then Paslahepevirus balayani and Rocahepevirus were examined using RT-qPCR. The detection rate of Rocahepevirus was 12.95 % (36/278) in animals of order Rodentia, with 14.77 % (35/237) in Rattus tanezumi and 33.33 % (1/3) in Niviventer fulvescens. No Paslahepevirus balayani was detected. Additionally, two full-length Rocahepevirus sequences (MSE-17 and LHK-54) and thirty-three partial ORF1 sequences were amplified and determined to be HEV-C1. MSE-17 and LHK-54 shared moderate nucleotide identity (78.9 %-80.3 %) with HEV-C1 isolated in rats and humans. The HEV-C1 isolated from Niviventer fulvescens demonstrated a 100 % nucleotide identity with that from Rattus tanezumi. The rat HEV-C1 sequences isolated in our study and other Asian HEV-C1 sequences were phylogenetically distant from those isolated in North America and Europe. Furthermore, the two full-length sequences isolated in our study had less amino acid substitutions in the motifs of RNA-dependent RNA polymerase domain (F204L and L238F), compared with other Asian sequences. In summary, HEV-C1 commonly spreads in rats in Yunnan province of China. Our findings suggest a spatially associated phylogeny, and potential cross-species transmission of HEV-C1.

Risk factors for at-risk foot and peripheral artery disease among the population with diabetes: A multicommunity-based cross-sectional study.

AIMS: This study aimed to investigate the prevalence, characteristics, and influence factors of the at-risk foot with diabetes mellitus (DM). METHODS: This study included 3030 DM patients from the at-risk foot screening program of Shanghai in China between March 21 and April 30 in 2021. Data were collected from the questionnaire survey, physical examination, and fasting blood sample. RESULTS: The prevalence of at-risk foot was 27.8% among DM patients. After adjusted, the risk of higher at-risk grade increased with age and urinary albumin creatinine ratio (OR = 1.04, 95%CI = 1.02-1.06; OR = 1.001, 95%CI = 1.000-1.002, respectively), whereas decreased with estimated glomerular filtration rate (eGFR) (OR = 0.991, 95%CI = 0.984-0.998). The incidence of peripheral artery disease (PAD) was 11.1% in all people with DM, and age, pulse rate, and low-density lipoprotein were independent risk factors for PAD. In contrast, high-density lipoprotein, eGFR, and lymphocyte-to-monocyte ratio were independent protective factors for PAD. Glycated hemoglobin HbA1c was not an independent risk factor for increased risk grade or more severe PAD. CONCLUSIONS: The at-risk foot accounted for a high percentage among DM patients. Advanced age and renal dysfunction are independent risk factors for the at-risk foot. Glycemic control does not reduce the risk grade of at-risk foot and the incidence of PAD.

Using codon usage analysis to speculate potential animal hosts of hepatitis E virus: An exploratory study.

There has been an increase in the reported number of animals worldwide that carry the hepatitis E virus (HEV). This study aimed to explore potential animal hosts for HEV through codon usage analysis. Full-length HEV sequences of six genotypes as well as codon usage of potential animal hosts were collected. Moreover, nucleotide composition and codon usage bias were compared across HEV genotypes and animal hosts. Based on the analysis for human HEV-1 and humans, the results were basically consistent with epidemiology evidence. Among 17 potential animal hosts, all HEV genotypes exhibited a preference for guanine/cytosine in the third position of synonymous codons. Furthermore, non-human primates and humans have large high-frequency codons identical to HEV in addition to a high correlation of codon fraction with HEV. Some animals in close contact with humans showed high preference for HEV, including cattle, dogs, and rats with HEV-A, cats, dogs, and swine with HEV-C1. Codon usage bias has limited efficiency in determining the hosts for HEV, but it may provide indicative clues for potential animal hosts when combined with experimental and epidemiological evidence.

Distribution and phylogenetics of hepatitis E virus genotype 4 in humans and animals.

BACKGROUND: Worldwide, hepatitis E virus (HEV) infection is considered a significant public health concern. In particular, HEV genotype 4 (HEV-4) has spread to more areas and host species. In this study, we describe the global distribution of HEV-4 and characterize HEV-4 subtypes by host, country and year of isolation. METHODS: We retrospectively collected HEV-4 sequences available before December 31, 2019, in GenBank. HEV-4 and its subtypes were determined using phylogenetic comparison with HEV reference sequences. Information on the isolation of the sequences was extracted from the GenBank or original publications. Temporal, spatial and host characteristics of the sequences were summarized and nucleotide similarity was calculated based on five amplified fragments within HEV genome, stratified by host, country and year. RESULTS: A total of 2295 HEV-4 complete and partial nucleotide sequences were studied. The majority (92.7%) was isolated in China's mainland, Japan, Hong Kong and France. A total of 20 animal hosts were documented, though swine remained predominant (71.7%). Globally, prevalent HEV-4 subtypes changed remarkably over the last 18 years. Subtypes 4a, 4b, 4d and 4h were most commonly isolated (80.3%). Subtypes 4c, 4e, 4f, 4g and 4i remained limited in temporal distribution. High nucleotide similarities were observed between the sequences amplified in HEV ORF2, in the same and neighbouring countries, and in similar animal hosts. CONCLUSION: China and Japan are endemic for HEV-4, and have all the subtypes. In Europe, France has a high prevalence of HEV-4. Increases in affected areas and animal hosts imply consistent cross-border and cross-species transmission.

Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.

Hepatitis E virus (HEV) is an emerging zoonotic pathogen with multiple species and genotypes, which may be classified into human, animal, and zoonotic HEV. Codon usage bias of HEV remained unclear. This study aims to characterize the codon usage of HEV and elucidate the main drivers influencing the codon usage bias. A total of seven HEV genotypes, HEV-1 (human HEV), HEV-3 and HEV-4 (zoonotic HEV), HEV-8, HEV-B, HEV-C1, and HEV-C2 (emerging animal HEV), were included in the study. Complete coding sequences, ORF1, ORF2, and ORF3, were accordingly obtained in the GenBank. Except for HEV-8, the other six genotypes tended to use codons ending in G/C. Based on the analysis of relatively synonymous codon usage (RSCU) and principal component analysis (PCA), codon usage bias was determined for HEV genotypes. Codon usage bias differed widely across human, zoonotic, and animal HEV genotypes; furthermore, it varied within certain genotypes such as HEV-4, HEV-8, and HEV-C1. In addition, dinucleotide abundance revealed that HEV was affected by translation selection to form a unique dinucleotide usage pattern. Moreover, parity rule 2 analysis (PR2), effective codon number (ENC)-plot, and neutrality analysis were jointly performed. Natural selection played a leading role in forming HEV codon usage bias, which was predominant in HEV-1, HEV-3, HEV-B and HEV-C1, while affected HEV-4, HEV-8, and HEV-C2 in combination with mutation pressure. Our findings may provide insights into HEV evolution and codon usage bias.

Association between Adult Vaccine Hesitancy and Parental Acceptance of Childhood COVID-19 Vaccines: A Web-Based Survey in a Northwestern Region in China.

China has initiated the COVID-19 vaccination for children aged 15-17 years since late July 2020. This study aimed to determine the association between adult vaccine hesitancy and parental acceptance of childhood COVID-19 vaccines in a multi-ethnicity area of northwestern China. A web-based investigation was performed with a convenience sampling strategy to recruit the parents aged 20-49 years. In a total of 13,451 valid respondents, 66.1% had received the COVID-19 vaccination, 26.6% were intent to receive, while 7.3% were not intent, with an increasing vaccine hesitancy (p < 0.001). Moreover, vaccination uptake of four common vaccines in their children remained low (29.0% for influenza vaccine, 17.9% for pneumonia vaccine, 10.9% for rotavirus vaccine, 8.0% for Enterovirus-71 vaccine), while overall parental acceptance of childhood COVID-19 vaccines was 50.0% (32.7% for those aged 0-5, 46.6% for 6-10, 73.3% for 11-18; p < 0.001). Vaccination uptake of these four vaccines and parental acceptance of childhood COVID-19 vaccine were negatively associated with adult vaccine hesitancy. In addition, respondents mostly preferred childhood COVID-19 vaccines with weak mild common adverse events (ß = 1.993) and no severe adverse events (ß = 1.731), demonstrating a positive association with adult vaccine hesitancy. Thus, it warrants specific countermeasures to reduce adult vaccine hesitancy and improve strategies for childhood vaccination.

Rare disease awareness and perspectives of physicians in China: a questionnaire-based study.

BACKGROUND: It is estimated that there are over 16.8 million rare disease patients in China, representing a significant challenge for the healthcare system and society. Rare disease patients often experience delayed diagnosis, misdiagnosis, or improper treatment, which may be due to the lack of rare disease awareness among physicians. MATERIALS AND METHODS: A total of 224 physicians from different hospitals in China participated in the questionnaire, and 9 rare disease experts were interviewed with open-ended questions. RESULTS: Most physicians (83.5%) were from Tertiary hospitals, which have over 500 beds. Only 5.3% of physicians were moderately or well aware of rare diseases. Most physicians (80.1%) had suspected their patients to have rare diseases less than 3 times. There was a strong support for special legislations for rare diseases and orphan drugs. Further, multinomial logistic regression (MLR) was used to determine whether hospitals, gender, and career length has an impact on perspectives and awareness. It was shown that male physicians were more likely to think newborn screening is important (p < 0.05). The longer the career length is, the more likely physicians believe that their previous education has not provided sufficient information about rare diseases and that their hospital has paid enough attention to rare diseases. Physicians from Tertiary A hospitals were more likely to rate the affordability of orphan drugs high. In addition, nine experts believed that rare disease awareness is essential for early diagnosis and timely treatment. These experts also made recommendations on how to improve rare disease awareness through medical school education and continuing training. CONCLUSIONS: Our study highlighted the importance of improving rare disease awareness among physicians in China. Recommendations about how to improve rare disease awareness in medical school education and establish an online 'information hub' are made for considerations of policy-makers.

A questionnaire-based study to comprehensively assess the status quo of rare disease patients and care-givers in China.

BACKGROUND: There are over 16.8 million rare disease patients in China, representing a large community that should not be neglected. While the public lack the awareness of their existence and difficult status quo, for one reason that they exist as a rare and special group in our society, for another reason that all sectors of the community haven't introduced and propagandized them suitably. However, as a special group with more difficulties in all aspects than normal healthy persons, they need enough care and love from us. To provide a basis for policy-makers to better understand the status quo of rare disease patients and care-givers in China and to devise some new policies to improve their quality of life, a comprehensive analysis of the status quo, unmet needs, difficulty caused by the rare disease is essential. METHODS: A questionnaire-based online study of patients and care-givers (usually family members) was performed. The questionnaire was composed of 116 questions, such as the diagnosis process, treatment access, financial burden, views on patients' organizations, and a series of standardized tests to assess the quality of their life, including the SF-36, PHQ-9, PHQ-15, GAD-7, and PSQI. To examine the influence of age, disease type, and relationship to patients on the scores in these tests, statistical analysis with a general linear model was conducted. FINDINGS: A total of 1959 patients and care-givers participated in the survey, representing 104 rare diseases, such as lysosomal storage diseases, hemophilia, and muscular dystrophy diseases. The diagnosis was delayed for 1.4 ± 3.0 years, and patients experienced 1.6 ± 3.8 misdiagnoses between 3.2 ± 2.4 hospitals. The hospitals where diagnoses were made were highly concentrated in 10 large hospitals (43.8%) and 5 big cities (42.1%), indicating a significant inequality of medical resources. The disease often led to difficulty in social life, education, and employment, as well as financial burden that was seldom covered by medical insurance. A battery of standardized tests demonstrated poor health status, depression, somatization, anxiety, and sleeping issues among both patients and care-givers (p < 0.05). Statistical analysis of the questionnaire also showed that poor health, anxiety, depression, somatization, and sleeping problems were more prevalent in patients than in care-givers, and more prevalent in more severe diseases (e.g., hemophilia, Dravet) or undiagnosed than in other diseases. INTERPRETATIONS: This study identified the lack of rare disease awareness and legislative support as the major challenge to rare diseases in China, and makes key recommendations for policy-makers, including legislating orphan drug act, raising rare disease awareness, providing sufficient and fair opportunities about education and employment, expanding the medical insurance coverage of treatments, and protecting rights in education and employment.

COVID-19 vaccine coverage, concerns, and preferences among Chinese ICU clinicians: a nationwide online survey.

BACKGROUND: Clinicians in intensive care units (ICUs) have been prioritized for COVID-19 vaccination. We aim to understand the reasons behind vaccination refusal, and assess preferences for COVID-19 vaccines among Chinese ICU clinicians. RESEARCH DESIGN AND METHODS: ICU clinicians throughout China's mainland were contacted to participate in an online survey. We compared concerns with vaccination status, and through a discrete choice experiment (DCE) assessed preferences for vaccines in terms of effectiveness, risk of adverse reactions, duration of immunity, and whether coworkers have been vaccinated. RESULTS: Among 11,951 ICU respondents from 252 prefecture-level regions, vaccination coverage was 75.4%, with an additional 9.2% not vaccinated but intending to, and 16.1% not vaccinated and not intending to. ICU clinicians not intending to be vaccinated significantly expressed more concerns about the speed of vaccine development (30.1%) and adverse reactions (65.9%). In the DCE, the only significant difference in preferences of a COVID-19 vaccine was for safety, with those not intending to have a stronger preference for a vaccine with fewer adverse reactions (OR = 4.49), compared to those already vaccinated (OR = 2.90) or those intending to vaccinate (OR = 3.46). CONCLUSION: Increasing vaccination coverage among Chinese ICU clinicians will require strong norms surrounding vaccination and transparency about safety information.

The urgent need to empower rare disease organizations in China: an interview-based study.

BACKGROUND: Each rare disease only affects a small number of population. However, a total of 7000 rare diseases may affect 10% of the population. Due to the severity and lack of rare disease awareness, rare disease represents a huge challenge for the healthcare system. In Western countries, patient organizations have been playing an integral role in raising awareness, advocating legislation, and supporting drug development. This study aims to assess the unmet needs of rare disease patient organizations in China, and identify their unmet needs, providing essential information for the government and legislators. RESULTS: A total of 28 individuals representing 28 patient organizations in China were interviewed. Most organizations do not have official registration, employees, written standard operation protocol, or reliable financial resources. Misdiagnosis or delayed diagnosis is common, and treatment is often lacking. Due to the lack of financial resources, no organizations have been able to sponsor academic research, unlike their counterparts in Western countries. As to challenges, 71.4% of interviewees listed lack of rare disease awareness among the general public, while 67.9% selected lack of financial resources. Further, only 7.3% of these organizations received support from the government, and 28.6% received support from the general public. As to recommendations to the government, 82.1% of interviewees selected special insurance programs for rare diseases because rare diseases have been generally excluded from the national medical insurance programs. In addition, 78.6% of interviewees recommended to stimulate rare disease research, 75% recommended to import orphan drugs, and 71.4% recommended legislation of an orphan drug act, highlighting the urgent need of therapies. CONCLUSIONS: Due to lack of support and rare disease awareness, patient organizations in China are still in the early phase. To empower these patient organizations, the interviewees' recommendations, including legislating orphan drug act and releasing official definition of rare diseases, should be considered by the government and legislators.