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This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A (RVA) in the Pearl River Delta region of Guangdong Province, China. This study included individuals aged 28 days–85 years. A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens, including RVA, using a Gastrointestinal Pathogen Panel, followed by genotyping, virus isolation, and complete sequencing to assess the genetic diversity of RVA. The overall RVA infection rate was 14.59% (103/706), with an irregular epidemiological pattern. The proportion of co-infection with RVA and other pathogens was 39.81% (41/103). Acute gastroenteritis is highly prevalent in young children aged 0–1 year, and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea. G9P[8] (58.25%, 60/103) was found to be the predominant genotype in the RVA strains, and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis. Recombination analysis showed that gene reassortment events, selection pressure, codon usage bias, gene polymorphism, and post-translational modifications (PTMs) occurred in the G9P[8] and G3P[8] strains. This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China, further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity. Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development. [ABSTRACT FROM AUTHOR]

Human disease from low-pathogenic influenza A(H7N9) infection was first reported in 2013, and a total of 1,567 human cases have been reported (1). During the fifth wave, which started in [...]

To the Editor: Avian influenza A(H5N6) influenza viruses have circulated among poultry in southern (Jiangxi, Guangdong) and western (Sichuan) provinces of China since 2013 (1,2). In 2014, outbreaks of H5N6 [...]

There has been a rapid increase in the number of scrub typhus cases in Guangdong Province, China. For this reason, an epidemiologic study was conducted to understand the characteristics of scrub typhus epidemics in Guangdong. From 2006 to 2013, the incidence of human cases increased from 0.4321 to 3.5917 per 100,000 with a bimodal peak in human cases typically occurring between May and November. To detect the prevalence of Orientia tsutsugamushi among suspected human cases and rodents, we performed ELISA tests of IgM/IgG and nested PCR tests on 59 whole blood samples from the suspected cases and 112 spleen samples from the rodents. Suspected cases tested positive for anti-O. tsutsugamushi IgM and IgG 66.1% (39/59) and 50.8% (30/59) of the time, respectively. Additionally, 20.3% (12/59) of blood samples and 13.4% (15/112) of spleen samples were positive for PCR. Phylogenetic analysis revealed that there were four definable clusters among the 27 nucleotide sequences of the 56-kDa antigen genes: 44.4% Karp (12/27), 25.9% Kato (7/27), 22.2% Gilliam (6/27) and 7.4% TA763 (2/27). We concluded many suspected cases may result in diagnostic errors; therefore, it is necessary to perform laboratory tests on suspected cases in hospitals. The high infection rate of O. tsutsugamushi among the limited rodents tested suggested that further rodent sampling throughout the province is necessary to further define high-risk areas. Furthermore, the multiple co-circulating genotypes of O. tsutsugamushi play a key role in the pervasiveness of scrub typhus in the Guangdong area.

To the Editor: A traveler returning from the Middle East initiated an outbreak of Middle East respiratory syndrome (MERS) in South Korea in 2015, which resulted in 186 cases and [...]

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated. In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants. We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations. These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic continues to present a major challenge to public health. Vaccine development requires an understanding of the kinetics of neutralizing antibody (NAb) responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In total, 605 serum samples from 125 COVID-19 patients (from January 1 to March 14, 2020) varying in age, sex, severity of symptoms, and presence of underlying diseases were collected, and antibody titers were measured using a micro-neutralization assay with wild-type SARS-CoV-2. NAbs were detectable approximately 10 days post-onset (dpo) of symptoms and peaked at approximately 20 dpo. The NAb levels were slightly higher in young males and severe cases, while no significant difference was observed for the other classifications. In follow-up cases, the NAb titer had increased or stabilized in 18 cases, whereas it had decreased in 26 cases, and in one case NAbs were undetectable at the end of our observation. Although a decreasing trend in NAb titer was observed in many cases, the NAb level was generally still protective. We demonstrated that NAb levels vary among all categories of COVID-19 patients. Long-term studies are needed to determine the longevity and protective efficiency of NAbs induced by SARS-CoV-2. [ABSTRACT FROM AUTHOR]

To the Editor: Brucellosis is one of the most prevalent zoonotic diseases in the world. It is principally an animal disease, but globally, >500,000 human cases are reported each year [...]

A letter to the editor is presented regarding the genetic basis of continuing human infections with avian influenza A (H5N6) influenza viruses by sequencing the complete genomes of two of the four human H5N6 isolates obtained in December 2015 in Guangdong Province, China in the 2016 issue.

Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium, has emerged as a global cause of multidrug-resistant salmonellosis and has become endemic in many developing and developed countries, especially in China. Here, we have sequenced 352 clinical isolates in Guangdong, China, during 2009-2019 and performed a large-scale collection of Salmonella 4,[5],12:i:- with whole genome sequencing (WGS) data across the globe, to better understand the population structure, antimicrobial resistance (AMR) genomic characterization, and transmission routes of Salmonella 4,[5],12:i:- across Guangdong. Salmonella 4,[5],12:i:- strains showed broad genetic diversity; Guangdong isolates were found to be widely distributed among the global lineages. Of note, we identified the formation of a novel Guangdong clade (Bayesian analysis of population structure lineage 1 [BAPS1]) genetically diversified from the global isolates and likely emerged around 1990s. BAPS1 exhibits unique genomic features, including large pan-genome, decreased ciprofloxacin susceptibility due to mutation in gyrA and carriage of plasmid-mediated quinolone resistance (PMQR) genes, and the multidrug-resistant IncHI2 plasmid. Furthermore, high genetic similarity was found between strains collected from Guangdong, Europe, and North America, indicating the association with multiple introductions from overseas. These results suggested that global dissemination and local clonal expansion simultaneously occurred in Guangdong, China, and horizontally acquired resistance to first-line and last-line antimicrobials at local level, underlying emergences of extensive drug and pan-drug resistance. Our findings have increased the knowledge of global and local epidemics of Salmonella 4,[5],12:i:- in Guangdong, China, and provided a comprehensive baseline data set essential for future molecular surveillance.IMPORTANCE Salmonella 4,[5],12:i:- has been regarded as the predominant pandemic serotype causing diarrheal diseases globally, while multidrug resistance (MDR) constitutes great public health concerns. This study provided a detailed and comprehensive genome-scale analysis of this important Salmonella serovar in the past decade in Guangdong, China. Our results revealed the complexity of two distinct transmission modes, namely global transmission and local expansion, circulating in Guangdong over a decade. Using phylogeography models, the origin of Salmonella 4,[5],12:i:- was predicted from two aspects, year and country, that is, Salmonella 4,[5],12:i:- emerged in 1983, and was introduced from the UK, and subsequently differentiated into the local endemic lineage circa 1991. Additionally, based on the pan-genome analysis, it was found that the gene accumulation rate in local endemic BAPS 1 lineage was higher than in other lineages, and the horizontal transmission of MDR IncHI2 plasmid associated with high resistance played a major role, which showed the potential threat to public health., Competing Interests: The authors declare no conflict of interest.

The coronavirus disease 2019 (COVID-19) pandemic continues to pose a global threat to the human population. Identifying animal species susceptible to infection with the SARS-CoV-2/ HCoV-19 pathogen is essential for controlling the outbreak and for testing valid prophylactics or therapeutics based on animal model studies. Here, different aged Chinese tree shrews (adult group, 1 year old; old group, 5-6 years old), which are close relatives to primates, were infected with SARS-CoV-2. X-ray, viral shedding, laboratory, and histological analyses were performed on different days post-inoculation (dpi). Results showed that Chinese tree shrews could be infected by SARS-CoV-2. Lung infiltrates were visible in X-ray radiographs in most infected animals. Viral RNA was consistently detected in lung tissues from infected animals at 3, 5, and 7 dpi, along with alterations in related parameters from routine blood tests and serum biochemistry, including increased levels of aspartate aminotransferase (AST) and blood urea nitrogen (BUN). Histological analysis of lung tissues from animals at 3 dpi (adult group) and 7 dpi (old group) showed thickened alveolar septa and interstitial hemorrhage. Several differences were found between the two different aged groups in regard to viral shedding peak. Our results indicate that Chinese tree shrews have the potential to be used as animal models for SARS-CoV-2 infection.

To study the relationship between environmental and clinical populations of Vibrio parahaemolyticus, we collected in total 86 isolates from Southern China during one and a half years. Sixty-eight isolates were recovered from aquaculture ponds, a seafood market, and restaurants, and 18 isolates were recovered from clinical samples. Virulence gene analysis revealed that 25 isolates (14 clinical and 11 environmental) tested positive for tdh, but only 4 carried trh. Interestingly, none of the tdh(+) environmental isolates was recovered from ponds. Both environmental and clinical tdh(+) isolates, except for one clinical isolate, harbor type III secretion system 2α (T3SS2α) and T3SS2β-related genes, including vopB2α, which was previously suggested to be absent from environmental strains. More than 70% of clinical isolates carried the pandemic marker of new toxRS (GS-PCR(+)), which was not present in the environmental isolates. Pulsed-field gel electrophoresis and multilocus sequence typing analysis showed a high degree of genetic diversity within the environmental isolates. In contrast, the clinical population formed a tight cluster that differed from the environmental isolates. These findings suggest that the pandemic strains of V. parahaemolyticus may not directly originate from marine animals. Rather the environments where they are maintained could serve as reservoirs for toxigenic, but not pandemic strains. These environments provide an ideal place for generation of new toxigenic strains through DNA exchange, which was revealed by extensive recombination events in recA sequences of the environmental isolates.

Background: The first H7N9 human case in south of China was confirmed in Guangdong Province on August 2013, outside of the typical influenza season. For investigating the H7N9 virus source and transmission in the local community, we analyze the epidemiology and genome features of the virus isolated from the first human infection detected in Guangdong Province., Methods: The data including medical records, exposure history and time line of events for the H7N9 patient and close contacts was collected. Variation and genetic signatures of H7N9 virus in Guangdong was analyzed using ClustalW algorithm and comparison with mutations associated with changes in biological characteristics of the virus., Results: The female patient had a history of poultry exposure, and she was transferred from a local primary hospital to an intensive care unit (ICU) upon deterioration. No additional cases were reported. Similar to previous infections with avian influenza A (H7N9) virus, the patient presented with both upper and lower respiratory tract symptoms. Respiratory failure progressed quickly, and the patient recovered 4 weeks after the onset of symptoms. Genome analysis of the virus indicated that the predicted antigen city and internal genes of the virus are similar to previously reported H7N9 viruses. The isolated virus is susceptible to neuraminidase (NA) inhibitors but resistant to adamantine. Although this virus contains some unique mutations that were only detected in avian or environment-origin avian influenza A (H7N9) viruses, it is still quite similar to other human H7N9 isolates., Conclusions: The epidemiological features and genome of the first H7N9 virus in Guangdong Province are similar to other human H7N9 infections. This virus may have existed in the environment and live poultry locally; therefore, it is important to be alert of the risk of H7N9 re-emergence in China, including emergence outside the typical influenza season.

Objective: To analyze the epidemiological and etiological characteristics of diarrheal disease among children under 5 years of age in Guangdong province, in 2012., Methods: 64 hospitals in 21 cities were chosen as the diarrheal syndromic surveillance sites, of which 14 hospitals were selected to carry out etiological surveillance among children under 5 years of age, including isolation and culture of both Vibrio cholera and Shigella as well as nucleic acid detection of rotavirus and norovirus by PCR. Descriptive method was used to analyze data from syndromic and etiological surveillance programs on diarrheal, from 1932 parents of the children., Results: In 2012, the outpatient attendance rate on diarrheal among children under 5 years was 0.8%. The proportion of diarrheal in children under 5-year-olds was 63.5%, among the total number of diarrheal outpatients at the outpatient clinics under surveillance program. The morbidity of infectious diarrhea was 1454.5/10 million in children under 5 years of age. A total number of 1932 specimens were collected from children under 5 years of age, in the outpatient department. Among these specimens,Vibrio cholera appeared all negative but one was Shigella positive and proved to be Sh. sonnei. The positive rates of rotavirus and norovirus were 14.1% (273/1932)and 16.9% (326/1932). Both rotavirus and norovirus were found in 24 specimens, with a positive rate as 1.2% . 112 specimens were successfully gene sequenced for rotavirus, of which 33.9% as G1[P8] genotype, 25.9% as G9[P8], 12.5% as G2[P4] and 9.8% as G3[P8] respectively. 90 specimens were successfully gene-sequenced for norovirus, of which 76.7% as G II.4 genotype. Genetic subtypes of G II. 4/2006b, accounted for 50.0% and could be detected around the year except for June and December. New G II. 4/Sydney Strain_2012 was first detected in August and became the predominant in December. In addition, 5 specimens belonged to G I genotype with other 16 subtypes of G II., Conclusion: Results from our study proved that children under 5 years of age belonged to high-risk group for diarrheal disease in Guangdong province. Rotavirus and norovirus were both diverse in terms of genome.

Objective: In order to better understand the nature of Salmonella infection in diarrheal patients in Guangdong province, the study analyzed the serum types, antibiotic resistance and molecular determinants of the isolated Salmonella strains., Methods: In year 2010, 8405 diarrhea patients from 16 surveillant hospital in Guangzhou, Zhongshan, Dongguan, Zhuhai, Maoming, Yangjiang and Jiangmen cities in Guangdong province, were recruited in the study. A total of 8405 fecal specimen were collected and subjected to Salmonella isolation and culture. The isolated Salmonella strains were further analyzed via serotyping, antimicrobial susceptibility testing, and PFGE. The χ(2) test was applied to compare the differences between the isolated Salmonella strains in different seasons and districts. BioNumerics software was used to analyze the PFGE results in order to determine the correlation between different Salmonella strains., Results: The positive rate of the surveillant Salmonella in Guangdong province was 3.58% (301/8405) in 2010; with the gender ratio at 1.34:1 (166/124). Salmonella infection was found in all age groups, and most in infants, accounting for 57.48% (173/301). The isolated rates of Salmonella were separately 3.48% (61/1751), 4.97% (134/2695), 3.08% (73/2370) and 2.08% (33/1589) in the four seasons; and the difference was statistically significant (χ(2) = 27.29, P < 0.01). The isolated rates of Salmonella in different regions were as follows: Zhuhai 15.43% (25/162), Maoming 7.53% (18/239), Dongguan 6.51% (39/599), Yangjiang 3.64% (14/385), Zhongshan 3.03% (70/2309), Guangzhou 2.90% (126/4349) and Jiangmen 2.49% (9/362). The difference between regions was statistically significant (χ(2) = 100.75, P < 0.01). Except one strain of the isolated Salmonella cannot be serotyped, the other 300 strains were divided into 42 serotypes, of which Salmonella typhimurium and Salmonella enteritidis were dominant, account for 45.18% (136/301) and 10.96% (33/301) respectively. Although over 85% of Salmonella were sensitive to cephalosporin, ACSSuT resistance patterns (defined as resistance to at least ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline) reached 34.88% (105/301), the highest resistant rate was found in serotype Salmonella typhimurium, as high as 65.44% (89/136). 136 strains of Salmonella typhimurium were divided into 51 PFGE types, showed great genetic diversity. 33 strains of Salmonella enteritidis were divided into 18 PFGE types. The strains with same PFGE pattern may have different drug-resistant patterns, and vice versa., Conclusion: Salmonella typhimurium and Salmonella enteritidis were the dominant serotypes causing infectious diarrhea in Guangdong province. Cephalosporin was the primary choice in clinical medicine. However, Salmonella typhimurium was resistant to drug most seriously in Guangdong province. There was no significant correlation between Salmonella resistance patterns and PFGE type.