Machao Li

Molecular Evolution Analysis and Geographic Investigation of Severe Acute Respiratory Syndrome Coronavirus-Like Virus in Palm Civets at an Animal Market and on Farms

ABSTRACT Massive numbers of palm civets were culled to remove sources for the reemergence of severe acute respiratory syndrome (SARS) in Guangdong Province, China, in January 2004, following SARS coronavirus detection in market animals. The virus was identified in all 91 palm civets and 15 raccoon dogs of animal market origin sampled prior to culling, but not in 1,107 palm civets later sampled at 25 farms, spread over 12 provinces, which were claimed to be the source of traded animals. Twenty-seven novel signature variation residues (SNVs) were identified on the spike gene and were analyzed for their phylogenetic relationships, based on 17 sequences obtained from animals in our study and from other published studies. Analysis indicated that the virus in palm civets at the live-animal market had evolved to infect humans. The evolutionary starting point was a prototype group consisting of three viral sequences of animal origin. Initially, seven SNV sites caused six amino acid changes, at positions 147, 228, 240, 479, 821, and 1080 of the spike protein, to generate low-pathogenicity viruses. One of these was linked to the first SARS patient in the 2003-2004 period. A further 14 SNVs caused 11 amino acid residue changes, at positions 360, 462, 472, 480, 487, 609, 613, 665, 743, 765, and 1163. The resulting high-pathogenicity groups were responsible for infections during the so-called early-phase epidemic of 2003. Finally, the remaining six SNVs caused four amino acid changes, at positions 227, 244, 344, and 778, which resulted in the group of viruses responsible for the global epidemic.

The Ecology, Genetic Diversity, and Phylogeny of Huaiyangshan Virus in China

ABSTRACT Surveys were carried out to better understand the tick vector ecology and genetic diversity of Huaiyangshan virus (HYSV) in both regions of endemicity and regions of nonendemicity. Haemaphysalis longicornis ticks were dominant in regions of endemicity, while Rhipicephalus microplus is more abundant in regions of nonendemicity. HYSV RNA was found in human and both tick species, with greater prevalence in H. longicornis and lesser prevalence in R. microplus. Phylogenetic analyses indicate that HYSV is a novel species of the genus Phlebovirus.

SARS-CoV infection in a restaurant from palm civet.

Contact with food animals was associated with SARS-CoV infection in the People’s Republic of China.

Identification of a new Neisseria meningitidis serogroup C clone from Anhui province, China

BACKGROUND Outbreaks of a new serogroup C meningococcal disease emerged during 2003-04 (five outbreaks with 43 cases) and in 2004-05 (five outbreaks with 29 cases), all in Anhui province, China. We describe the molecular epidemiology and features of the causative bacterial strains. METHODS We used pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) to analyse the strains. FINDINGS Of 34 strains of Neisseria meningitidis cultured during 2003-04 from Anhui province, 31 were group C meningococci, 28 of which were associated with three of five outbreaks; one from a patient and 27 from close contacts of eight patients. Of 30 strains isolated from Anhui province during 2004-05, 17 were identified as serogroup C meningococci, ten of which were associated with four of five outbreaks. In a nationwide survey, 542 strains were isolated during 2004-05; 58 were serogroup C meningococci interspersed among 11 other provinces where no serogroup C outbreak occurred. Of the 106 serogroup C strains analysed, 89 had identical PFGE patterns, designated AH1. Of 28 strains selected for MLST analyses, 25 were sequence type 4821 (ST-4821), which did not belong to any of the previously reported sequence types that can form a new hypervirulent lineage. INTERPRETATION ST-4821 seems to be unique and caused the serogroup C meningitis outbreaks during the two seasons from 2003 to 2005 in Anhui province. The emergence of this sequence type has epidemiological importance that should be monitored for future spread in China and the rest of the world.

Distribution of serogroups and sequence types in disease-associated and carrier strains of Neisseria meningitidis isolated in China between 2003 and 2008

Given the unpredictability of Neisseria meningitidis outbreaks and the increased prevalence of serogroup C strains following the introduction of serogroup A-based vaccines, we conducted an analysis of serogroups and sequence types (STs) in disease-associated and carrier N. meningitidis isolates that have emerged in China since 2003. We used multilocus sequence-typing techniques to investigate 371 N. meningitidis strains isolated from patients with meningitis and healthy carriers. Two lineages were identified in serogroup A and C isolates, genotyped as the ST5 complex and ST4821 complex, respectively. Both clonal complexes were found throughout China, although ST4821 was more concentrated in the eastern region of the country. The ST5 complex has been persistent in China since the late 1980s and has since spread across the entire country. Isolates belonging to the ST4821 complex have been a dominant lineage since 2003.

Genetic Study of Capsular Switching between Neisseria meningitidis Sequence Type 7 Serogroup A and C Strains

ABSTRACT Neisseria meningitidis is a leading cause of septicemia and meningitis worldwide. N. meningitidis capsular polysaccharides have been classified into 13 distinct serogroups which are defined by antibody reactivity and structural analysis, and the capsule plays an important role in virulence. Serogroups A, B, C, W135, and Y have been reported to be clinically important. Several newly identified serogroup C isolates belonging to the unique sequence type 7 (ST-7) were identified in China. Since most ST-7 isolates from China belonged to serogroup A, the newly identified ST-7 serogroup C strains were proposed to have arisen from those belonging to ST-7 serogroup A. In this study, six ST-7 serogroup C and three ST-7 serogroup A isolates were analyzed by pulsed-field gel electrophoresis to confirm their sequence type. In order to clarify the genetic basis of capsular switching between ST-7 serogroup A and C strains, the whole capsular gene clusters and surrounding genes of the two representative ST-7 strains belonging to serogroups A and C, respectively, were sequenced and compared. Potential recombination sites were analyzed using the RDP3 beta software, and recombination-related regions in two other ST-7 serogroup A and five ST-7 serogroup C strains were also sequenced and compared to the representative ST-7 serogroup A and C strain sequences.

Genotypic analysis of serogroups other than A, B or C of Neisseria meningitidis in China

To serologically and genetically characterize other serogroups (except A, B, and C) of Neisseria meningitidis isolates in China, we collected 56 strains of other serogroups, identified by serogroup typing and multilocus sequence typing (MLST). All of them are non-invasive isolates. The serogroups of the 56 Chinese isolates were W135 (11 isolates), Y (4), X (15), 29E (15), D (1), H (4), I (3), K (2), and non-groupable (1). By MLST, 34 different sequence types (STs) were identified, 28 of which were not found in the MLST database as of July 2006 and seemed to be unique to China. Statistical analysis of the MLST results revealed that, although the Chinese isolates seemed to be genetically divergent, they could be classified into 5 major clonal groups and other minor groups. Among these isolates, none of the well-documented ST complexes found worldwide was present.

Clonal characteristics of invasive Neisseria meningitidis following initiation of an A + C vaccination program in China, 2005–2012

OBJECTIVES To reveal the population structure of invasive Neisseria meningitidis isolates after the initiation of an A + C vaccination program in China. METHODS Multilocus sequence typing (MLST) and PorA typing were used to characterize 238 invasive N. meningitidis isolates collected in China between 2005 and 2012. RESULTS During this period, sequence type (ST)-5, ST-4821 and ST-11 complexes were dominant among serogroups A, C and W, accounting for 100%, 98.5% and 100% of each serogroup, respectively. P1.20,9, P1.7-2,14 and P1.5,2 were the dominant PorA types of serogroups A, C and W, respectively. Serogroup B showed high genetic diversity with two dominant lineages: ST-4821 complex and ST-5662 subgroup. CONCLUSIONS The population of 238 invasive N. meningitidis isolates was primarily composed of a select group of recognized hypervirulent lineages. Among these clonal complexes, ST-7 serogroup A and ST-11 serogroup W are distributed globally, and other three clones exist only in China.

Detection of Wolbachia genes in a patient with non-Hodgkin's lymphoma

Wolbachia 16S rRNA and fbpA genes were twice detected over 5 days in the blood of a patient with high fever. The patient was given fluoroquinolones and the fever resolved. Four weeks later, he was diagnosed with non-Hodgkins lymphoma and received R-CHOP (Rituximab, Cyclophosphamide, Doxorubicin, Vincristine, Prednisolone) treatment resulting in complete remission. This is the first report of detection of Wolbachia genes from the blood of human patients with non-Hodgkins lymphoma.

Genotypic characteristics of Haemophilus influenzae isolates from pediatric pneumonia patients in Chengdu city, Sichuan, China

Two hundred and seventy-three Haemophilus influenzae strains isolated from pediatric pneumonia patients in China were studied. We used Multilocus Sequence Typing (MLST) to analyze genotypic characteristics. All strains were biotyped and serotyped. Relatedness and patterns of genes among isolates were determined by the analysis of MLST and eBURST. H. influenzae primarily causes acute pneumonia in children under 1 year old. Nontypeable H. influenzae was responsible for most cases of pediatric pneumonia. All 273 strains were classified into eight biotypes. They mostly belonged to the I, II, and III biotypes (17.6%, 43.6%, and 22.7%, respectively). 62 strains (22.7%) produced b-lactamase. We found 28 novel alleles. Fifty different STs were found by MLST, of which 39 were novel. These were ST477 through ST508 and ST521 through ST527. Group 17 and predicted founders 503 were new groups in this study. No STs correlated with strains from Korea, which is adjacent to China. The H. influenzae strains from China appeared to have heterogeneous ST types patterns which may be the reason no outbreaks or epidemics of H. influenzae infections have occurred in Chengdu city, Sichuan, China.