This is the first report for molecular epidemiology of DEN-4 viruses in Vietnam. At present, DEN-4 serotype can be classified into two genetically distinct types: genotypes I and II. In this study, phylogenetic analysis of DEN-4 viruses from Vietnam as well as previously published strains indicate that DEN-4 viruses could be genetically classified into more than 2 genotypes. Most recent Vietnamese DEN-4 strains (1998-2002) were clustered within a distinct genetic type, named genotype III, a newly recognized genetic type for DEN-4 viruses. In addition, two Vietnamese strains isolated in 1990 and 1997 also grouped separately forming another independent cluster in the tree, which we designated genotype IV. In this report present for the first time the existence of two new genotypes of DEN-4 in Vietnam. Evidence for local independent evolution and temporal correlation was observed.
Dengue ; Epidemiology, Genotype

China/epidemiology* ; Genotype ; Phylogeny

The accuracy and predictability of mixture models in NONMEM® may change depending on the relative size of inter-individual differences and the size of the differences in the parameters between subpopulations. This study explored the accuracy of mixture models when dealing with missing a categorical covariate under various situations that may occur in reality. We generated simulation data under various scenarios where genotypes representing extensive metabolizers (EM) and poor metabolizers (PM) of drug-metabolizing enzymes affect the clearance of a drug by different degrees, and the inter-individual variations in clearance are different for each scenario. From each simulated datum, a specific proportion of the covariate (genotype information) was randomly removed. Based on these simulation data, the proportion of each individual subpopulation and the clearance were estimated using a mixture model. Overall, the clearance estimate was more accurate when the difference in clearance between subpopulations was large, and the inter-individual variations were small. In some scenarios that showed higher ETA or epsilon shrinkage, the clearance estimates were significantly biased. The mixture model made better predictions for individuals in the EM subpopulation than for individuals in the PM subpopulation. However, the estimated values were not significantly affected by the tested ratio, if the sample size was secured to some extent. The current simulation study suggests that when the coefficient of variation of inter-individual variations of clearance exceeds 40%, the mixture model should be used carefully, and it should be taken into account that shrinkage can bias the results.
Bias (Epidemiology) ; Genotype ; Sample Size

Humans ; Air Pollutants/adverse effects* ; Genotype ; China/epidemiology* ; Hypertension/epidemiology*

Objective: To understand the genotype distribution and transmission pattern of rubella virus (RuV) circulating in Yunnan Province. Methods: Throat swab samples were collected from rubella outbreaks and sporadic cases in nine prefectures/cities of Yunnan Province from 2011 to 2021. Virus isolation, amplification of target genes and sequence determination were performed on the RuV-positive samples. The genotypes and lineages of Yunnan strains were determined by comparing them with the reference strains, and further phylogenetic analysis was performed with Yunnan strains and strains circulating in other provinces of China during the same period. Results: RuV circulating in Yunnan province during 2011-2021 showed significant genetic diversity, and three lineages, 1E-L1, 2B-L1 and 1E-L2, were detected. Two lineage-switches were also identified, including the conversion of 1E-L1 to 2B-L1 between 2012 and 2013, and the replacement of 2B-L1 to 1E-L2 after 2018. The time of the switches was basically consistent with the outbreak in Yunnan province in 2012 and the time of the rubella reemergence and epidemic between 2018 and 2019. The amino acid sequence of RuV virus strains in Yunnan province was highly conserved, and no important functional regions were changed. Conclusions: The transmission pattern of RuV in Yunnan province is generally consistent with the epidemic trend of RuV in other provinces of China.
Humans ; Rubella virus/genetics* ; Phylogeny ; China/epidemiology* ; Rubella/epidemiology* ; Genotype

Objective: To understand the genotype distribution and transmission pattern of rubella virus (RuV) circulating in Yunnan Province. Methods: Throat swab samples were collected from rubella outbreaks and sporadic cases in nine prefectures/cities of Yunnan Province from 2011 to 2021. Virus isolation, amplification of target genes and sequence determination were performed on the RuV-positive samples. The genotypes and lineages of Yunnan strains were determined by comparing them with the reference strains, and further phylogenetic analysis was performed with Yunnan strains and strains circulating in other provinces of China during the same period. Results: RuV circulating in Yunnan province during 2011-2021 showed significant genetic diversity, and three lineages, 1E-L1, 2B-L1 and 1E-L2, were detected. Two lineage-switches were also identified, including the conversion of 1E-L1 to 2B-L1 between 2012 and 2013, and the replacement of 2B-L1 to 1E-L2 after 2018. The time of the switches was basically consistent with the outbreak in Yunnan province in 2012 and the time of the rubella reemergence and epidemic between 2018 and 2019. The amino acid sequence of RuV virus strains in Yunnan province was highly conserved, and no important functional regions were changed. Conclusions: The transmission pattern of RuV in Yunnan province is generally consistent with the epidemic trend of RuV in other provinces of China.
Humans ; Rubella virus/genetics* ; Phylogeny ; China/epidemiology* ; Rubella/epidemiology* ; Genotype

OBJECTIVETo study the epidemiology of genotyping Yersinia pestis isolated in the fulminant epidemics of human plague in Qinghai province in 2004.

METHODSPrimer pairs targeting the twenty-three different identified regions (DFRs) were designed to detect the presence or deletion of each DFR in 13 strains of Yersinia pestis isolated from the fulminant epidemic of human plague in Qinghai province in 2004.

RESULTSThere were 4 genomovars, i.e. Genomovar 8, 10, 15 and 16 in the 13 strains of Yersinia pestis identified. The genomovar of all the strains of Yersinia pestis isolated from Nangqian county was Genomovar 10. Among the two strains of Yersinia pestis isolated from Wulan county, the genomovar of one strain was Genomovar 8 and the other was Genomovar 10. The genomovars of all the strains of Yersinia pestis isolated from Qilian, Qumalai and Chengduo county belonged to Genomovar 16.

CONCLUSIONIt was demonstrated that the genotyping of Yersinia pestis appeared to be a powerful tool for investigating human plague epidemics.

China ; epidemiology ; Disease Outbreaks ; Genotype ; Humans ; Molecular Epidemiology ; Plague ; epidemiology ; Yersinia pestis ; genetics ; isolation & purification

BACKGROUNDMycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) and Beijing family typing based on detecting the deletion of RD105 sequence are two common genotyping methods used to study the molecular epidemiologic characteristics of Mycobacterium (M.) tuberculosis. We collected 218 strains of M. tuberculosis between 2004 and 2006 in the Linxia Hui Autonomous Prefecture of Gansu province in Northwest China.

METHODSMIRU-VNTR analysis and Beijing family typing based on detecting the deletion of RD105 sequence were used to type the 218 strains, and their typing power was evaluated to look for practical and efficient genotyping methods suitable for the region.

RESULTSThe MIRU typing yielded 115 distinct genotypes, including 98 unique isolates and 17 different clusters containing 120 isolates (55.05%); the cluster rate was 47.25%. By detecting the deletion of RD105 sequence, 188 of 218 (86.23%) isolates belonged to Beijing family. Combination of Beijing family typing and MIRU typing yielded 118 distinct patterns, including 101 unique isolates and 17 clusters containing 117 isolates (54.13%). The largest cluster contained 58 strains with MIRU genotype of 223325173533 which contained 50 strains belonging to Beijing family and 8 strains belonging to non-Beijing family.

CONCLUSIONSThe Beijing family strains occupied a large proportion and the Beijing family MIRU genotype 223325173533 is a dominant strain in Linxia of Gansu. Combining detecting the deletion of RD105 and MIRU typing together provides a simple, fast, and effective method which is low in cost and might be practical and suitable for M. tuberculosis genotyping in China.

Alleles ; China ; epidemiology ; Genotype ; Molecular Epidemiology ; Multiplex Polymerase Chain Reaction ; Mycobacterium tuberculosis ; genetics ; pathogenicity ; Tuberculosis ; epidemiology

OBJECTIVE: To clarify the epidemiological characteristics and spatial distribution patterns of human norovirus outbreaks in China, identify high-risk areas, and provide guidance for epidemic prevention and control. METHODS: This study analyzed 964 human norovirus outbreaks involving 50,548 cases in 26 provinces reported from 2012 to 2018. Epidemiological analysis and spatiotemporal scanning analysis were conducted to analyze the distribution of norovirus outbreaks in China. RESULTS: The outbreaks showed typical seasonality, with more outbreaks in winter and fewer in summer, and the total number of infected cases increased over time. Schools, especially middle schools and primary schools, are the most common settings of norovirus outbreaks, with the major transmission route being life contact. More outbreaks occurred in southeast coastal areas in China and showed significant spatial aggregation. The highly clustered areas of norovirus outbreaks have expanded northeast over time. CONCLUSION By identifying the epidemiological characteristics and high-risk areas of norovirus outbreaks, this study provides important scientific support for the development of preventive and control measures for norovirus outbreaks, which is conducive to the administrative management of high-risk settings and reduction of disease burden in susceptible areas.
Humans ; Gastroenteritis/epidemiology* ; Norovirus ; Caliciviridae Infections/epidemiology* ; Disease Outbreaks ; China/epidemiology* ; Genotype

Genome-Wide Association Study ; Genotype ; Humans ; Molecular Epidemiology ; methods