Evolutionary dynamics of codon usages for peste des petits ruminants virus.

Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007-2008 and 2013-2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.

The relationship between complement changes with vaccination and length of stay in COVID-19 patients / 中国热带医学

@#Abstract: Objective　To investigate whether the complement system of COVID-19 is affected by vaccination, and also to explore the relationship between complement and length of stay in hospital, with a view to providing input for clinical diagnosis and the management of COVID-19 patients. Methods　The patients admitted from November 1st to November 30th, 2021 in the Eighth Affiliated Hospital of Guangzhou Medical University were selected as subjects. According to the time of vaccination, the patients were divided into two groups as vaccinated within half a year and over half a year. Then C3, C4, IgG, IgM, IgA, COVID-19 IgG and IgM, neutral granulocyte and lymphocyte count were detected and all patients' hospitalized days were recorded. With their hospitalization days of 14 d as a threshold, the patients were divided into two groups, and the above indicators were compared. Results　C3 concentration was (0.86±0.157) g/L in patients with vaccination within six months, which is significantly lower than (0.96±0.172) g/L in those over six months (P<0.05), but as for C4, IgG, IgM, IgA, COVID-19 IgG and IgM, neutral granulocyte and lymphocyte counts, there were no significant difference between two groups; as for the patients within 14 days of hospitalization, C3 and C4 concentrations were lower than those for more than 14 days, but the COVID-19 antibody IgG and IgM, lymphocyte counts were higher (all P<0.05). Conclusion　Vaccination within half a year can make the body's immune function and complement system to identify viruses earlier, more beneficial to remove viruses, but this effect is weakened after half a year; when admission, C3, C4, COVID-19 IgG level and lymphocyte counts can be used to predict hospitalization time in COVID-19 patients.

Prevalence and clinical features of hepatitis E virus infection in pregnant women: A large cohort study in Inner Mongolia, China.

BACKGROUND AND AIM: Hepatitis E virus (HEV) infection causes severe maternal and fetal outcomes in pregnant women. These patients are exclusively from resource-limited regions with genotype 1 HEV infection, but not from western countries with genotype 3 prevalence. Since the circulating strains in China have evolved from the waterborne genotype 1 to the zoonotic genotype 4 HEV in the past decades, this study aims to evaluate the prevalence and clinical features of HEV infection in a large cohort of pregnant women in Inner Mongolia, China. METHODS: A total of 3278 pregnant women who visited the Inner Mongolia Maternal and Child Care hospital during 2018 were enrolled. Serum samples were examined for anti-HEV IgG and anti-HEV IgM antibodies using ELISA. Demographic information, results of clinical biochemical tests, maternal and neonatal outcomes were collected. RESULTS: Among the recruited 3278 pregnant women, 6.0% were anti-HEV IgG antibody positive, 0.3% were anti-HEV IgM antibody positive and 0.3% were positive for both anti-HEV IgG and anti-HEV IgM antibodies. HEV viral RNA was not detected. Pregnant women with recent/ongoing HEV infection indicated by anti-HEV IgM positivity have slightly higher ALT level, and potential risk of developing hyperlipidemia, preterm delivery and neonatal jaundice. CONCLUSIONS: These findings indicated that HEV infection is associated with a possible increase in adverse maternal, fetal and neonatal outcomes in our cohort. Thus, the burden of HEV infection in pregnant women in China appears distinct from resource-limited regions and western countries. Nevertheless, future studies are required to confirm and extend our findings.

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas.

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus.

In this study, the systemic analyses of nucleotide, codon and amino acid usages for E2 gene of bovine viral diarrhea virus (BVDV) were carried out for estimating its genetic features. The nucleotide usage pattern at the first codon position was strongly influenced by the overall nucleotide composition, while the nucleotide usage patterns at the second and third codon positions seemed to have little link to the overall nucleotide composition. The result indicated that the mutation pressure from nucleotide composition constraint was not the single evolutionary force for genetic features of BVDV E2 gene. Just 18 out of 59 synonymous codons were similar with synonymous codon usage patterns for E2 gene between BVDV1 and BVDV2, while all synonymous codons which contain CpG dinucleotides were selected at the low level by E2 gene, suggesting that this gene suppressed the usages of codons containing CpG dinucleotides to regulate E2 gene replicate and transcript efficiently and avoid immune response from infected hosts. Amino acid usage patterns of E2 protein were generally different between BVDV1 and BVDV2. The patterns of synonymous codon and amino acid usages for E2 gene might be caused by the equilibrium of evolutionary forces from virus and host. Our work gave new investigations into the role of host origin in the formations of synonymous codon/amino acid usages and the evolutionary trend of BVDV E2 gene. The genetic characteristics that codon/amino acid usages of E2 gene adapted to the internal environment of individual animals might assist in understanding the changes of genetics and antigenicity for newly emerging BVDV.

Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus.

Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.

[The effects of 10-week core strength training on the body balance in the middle-aged men].

OBJECTIVE: To observe the effects of core strength training on the body balance of middle-aged men, which could provide evidence for improving the body balance and reducing the risk of falls in the middle-aged men. METHODS: Sixteen 50~60 years old men were randomly divided into experimental group (core strength training, n=8) and control group(n=8). Intermittent core strength trainings were used for dynamic and static training, push-pull training and unarmed lower limb strength training by suspension ropes and yoga mat. The time for training was 50~60 min/day, 4~5 times/week for a total of 10 weeks. The men in control group remained their original living habits. We measured the ability of body static balance and dynamic balance before and after the core strength training. RESULTS: ① Compared with before exercise training, both closed single foot standing time and the body dynamic balance were increased significantly in the experimental group after exercise training(P<0.01)(10.63±1.69 s vs 9.00±2.27 s; 77.38±10.94 vs 89.50±5.53). ② Compared with before exercise training, star excursion balance test(SEBT) values were significantly increased in the left leg(the right leg support) in eight directions and the right leg(the left leg support)in six directions (P<0.01). CONCLUSIONS: Ten-week core strength training can significantly increase the body static and dynamic balance in the middle-aged men.

Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. Agalactiae.

Because of the low GC content of the gene population, amino acids of the two mycoplasmas tend to be encoded by synonymous codons with an A or T end. Compared with the codon usage of ovine, Mycoplasma capricolum and M. agalactiae tend to select optimal codons, which are rare codons in ovine. Due to codon usage pattern caused by genes with key biological functions, the overall codon usage trends represent a certain evolutionary direction in the life cycle of the two mycoplasmas. The overall codon usage trends of a gene population of M. capricolum subsp. capricolum can be obviously separated from other mycoplasmas, and the overall codon usage trends of M. agalactiae are highly similar to those of M. bovis. These results partly indicate the independent evolution of the two mycoplasmas without the limits of the host cell's environment. The GC and AT skews estimate nucleotide composition bias at different positions of nucleotide triplets and the protein consideration caused by the nucleotide composition bias at codon positions 1 and 2 largely take part in synonymous codon usage patterns of the two mycoplasmas. The correlation between the codon adaptation index and codon usage variation indicates that the effect of codon usage on gene expression in M. capricolum subsp. capricolum is opposite to that of M. agalactiae, further suggesting independence of the evolutionary process influencing the overall codon usage trends of gene populations of mycoplasmas.

[Epidemiologie investigation on murine typhus in Hongta areas of Yuxi city, Yunnan province of China].

OBJECTIVE: To identify epidemic status of murine typhus in Hongta areas of Yuxi city and to provide evidence for control and prevention of the disease. METHODS: Serologic survey was conducted among residents and rodents. Isolation of Rickettsia moseri was performed. RESULTS: The overall infection rate among general population was 28.92% (96/332) with geometric meantiter (GMT) as 10.83 and there was no difference between males and females (26.71%, 43/161 vs. 30.99%, 53/171, P > 0.05). Significant differences were found between age groups (P < 0.05) with positive rates of 29.63% (8/27), 18.06% (13/72), 39.62% (42/106), 27.50% (22/80) and 23.40% (11/47) among age groups 0-6, 7-18, 19-39, 40-59 and over 60, respectively. The overall rate of infection in mouse was 44.95% (89/198) with GMT as 30.30. Five isolates of R. moseri from mouse specimen, three from fleas plus one case of murine typhus were diagnosed. Rattus norvegicus and Rattus flavipectus were the predominant species of rodent animals (99.49%, 197/198) and Xenopsylla cheopis was the major species of vector (74.26%, 303/408). Flea index and mouse density were 2.06 and 11.13% respectively. CONCLUSION: High infection rates on R. moseri were demonstrated in rodents and residents as well as high risk of murine typhus outbreak might occur in these areas.

Molecular epidemic survey on co-prevalence of scrub typhus and marine typhus in Yuxi city, Yunnan province of China.

BACKGROUND: Human rickettsioses are worldwide zoonoses and it is not easy to differentiate them from other infectious diseases because of their atypical manifestation. In recent years the number of patients with fever of unknown causes from Hongta District CDC, Yuxi city of Yunnan Province has been increasing significantly in the summer. Diagnosis of scrub typhus was made by local clinicians. In order to ascertain the disease, we undertook a laboratory investigation for such patients from August 18 to 26, 2005. METHODS: Active surveillance was conducted by Hongta District CDC Yuxi city of Yunnan Province from 2002 to 2004 and basic data were obtained from cases confirmed according to clinical definitions. Average incidences and town-level incidences were calculated during the study periods. Blood samples were analyzed by PCR and serological test. Based on the groEL gene sequences a paired general outer primers (Gro-1 and Gro-2) targeting typhus, spotted fever as well as scrub typhus and two paired inner primers (SF1, SR2 and TF1, TR2) for typhus together with spotted fever and scrub typhus, respectively, were designed to perform a multiplex-nested PCR. Serological assay was carried out by indirect immunofluorescence assay with 7 different rickettsial antigens, i.e., R.mossori, R.sibirica, R.conorii, O.tsutsugamushi, B.quintana, B.henselae and Coxilella burnetii phase II Ag. RESULTS: Epidemiological surveillance showed that from 2002 to 2004, the average incidences of the scrub typhus or scrub typhus with murine typhus were 222.1/10(5), 204.3/10(5) and 109.6/10(5), respectively. Of 13 blood samples taken during acute stage of illness, 6 showed the amplified products for scrub typhus and the sequenced products showed 100%, 99%, 99%, 99%, 99%, 99% similarity to O.tsutsugamushi Karp but they shared the same deduced amino acid sequences, which indicated 100% identity with the heat shock protein of the O.tsutsugamushi Karp strain. Five yielded PCR products for murine typhus and their corresponding nucleotide sequences exhibited 100%, 100%, 99%, 99% and 99% similarity to R. mossori Wilmington and the analyses of predicted amino acid sequences indicated 100%, 100%, 98%, 98% and 98% identity with the heat shock protein of R. mossori Wilmington strain. Of the 8 PCR positive patients, 3 showed a co-infection of scrub typhus with murine typhus. All the 13 serum samples from febrile patients were positive against O. tsutsugamushi and 8 of them were positive against R. mossori. All of the 8 paired specimens had four-fold elevation of antibody against O. tsutsugamushi, and seroconversion for typhus was demonstrated in 3 paired serum samples. Another finding in the study was that a high seropositive prevalence (76.9%) of Q fever was detected. CONCLUSION: It's confirmed that co-prevalence of scrub typhus with murine typhus are occurring in Yuxi city of Yunnan province, China. Other rickettsial diseases also need to be investigated in these areas.