Epidemiological Surveillance: Genetic Diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

Objective 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.Methods 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.Results 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.Conclusion 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.

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province,China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)with unknown origin spread rapidly to 222 countries,areas or territories.To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong,60 specimens of SARS-CoV-2 were used to perform whole genome sequencing,and genomics,amino acid variation and Spike protein structure modeling analyses.Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species,with no evolution to other coronaviruses.There were one to seven nucleotide variations(SNVs)in each genome and all SNVs were distributed in various fragments of the genome.The Spike protein bound with human receptor,an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling.Our study clarifed the characteristics of SARS-CoV-2 genomic evolution,variation and Spike protein structure in the early phase of local cases in Guangdong,which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.

Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province,China,October 2020–May 2021

Objective The pandemic of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCo V-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-Co V-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.Methods In total, 177 throat swab samples were obtained from COVID-19 patients(from October2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-Co V-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.Results We observed that the imported cases mainly occurred after January 2021, peaking in May2021, 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 1 a(ORF1 a) protein had the highest mutation density at the nucleotide level, and the D614 G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7 b, and ORF9 b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in Pub Med among all missense mutations.Conclusion These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-Co V-2 in Guangdong Province, China.

A comparative study on environmental surveillance of enterovirus:Using a two-phase separation method and a filtration method with a mixed cellulose ester(MCE)membrane

This study aimed to compare the sensitivity of two-phase separation and the filtration method using a mixed cellulose ester(MCE)membrane to detect enteroviruses in sewage samples.From December 2015 to July 2016,four domestic sewage samples(1 L/sample)were collected monthly from the Guangzhou Liede Sewage Treatment Plant,and each sewage sample was divided into two aliquots(500 mL).The sewage sample was concentrated using the two-phase separation and the filtration method using an MCE membrane,and the treated solutions were inoculated into cells for enterovirus isolation.Polymerase chain reaction amplification,VP1 sequencing,and enterovirus molecular typing were performed on the positive isolates.The detection rates of poliovirus(PV)and non-polio enterovirus(NPEV)obtained using the filtration method using an MCE membrane were higher than those using the two-phase separation method.McNemar's test showed that the detection rates of PV,NPEV,type 1 Sabin-like(SL1),type 2 Sabin-like(SL2),and type 3 Sabin-like(SL3)strain were not statistically significant(P>0.05).In Guangdong Province,China,the detection rates for PV and NPEV were 53.13%and 62.50%(20/32),respectively.Twenty-seven PVs were isolated,three highly variable strains of the type 1 vaccine,with seven nucleotide substitutions in the VP1 region,compared with the type 1 Sabin strains.Eighty-seven strains of NPEV were isolated and nine serotypes were identified,among which coxsackievirus B3(CVB3),echovirus 6(E6),and echovirus 11(E11)were the dominant strains.The filtration method using an MCE membrane is more sensitive than two-phase separation and can be used as a robust,sensitive,and cost-effective method to isolate enteroviruses from sewage.

Genome Characterization of the First Outbreak of COVID-19 Delta Variant B.1.617.2——Guangzhou City,Guangdong Province,China,May 2021

On May 20,2021,75-year-old female(Case A)went to a local hospital due to pharyngeal pain and low-grade fever in Liwan District,Guangzhou City,Guangdong Province.The oropharyngeal swab from Case A tested preliminarily positive for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)/coronavirus disease 2019(COVID-19)virus using a quantitative real-time reverse transcription polymerase chain reaction(RT-qPCR)method after a hospital visit.

Phylogenetic Analysis of Serogroup O5 Vibrio cholerae that Caused Successive Cholera Outbreaks——Guangdong Province,China,2020-2021

Introduction:Gastroenteritis caused by non-O1/non-O139 Vibrio cholerae exhibited an increasing trend in recent years in China.Whole genome sequence(WGS)data could play an important role both in the identification of the outbreaks and in the determination of the serogroup.Here,we present the employment of WGS data in the investigation of two outbreaks caused by non-O1/non-O139 V.cholerae in Guangdong,China,2020-2021.Methods:We obtained the whole genome sequence of 66 V.cholerae strains isolated in two outbreaks with next generation sequencing technology.We retrieved the publicly available WGS data of non-O1/non-O139 V.cholerae from public database.We used a pipeline integrated in China Pathogen Identification Net(PIN)to complete the phylogenetic analysis.Results:Two outbreaks caused by non-O1/non-O139 V.cholerae were identified using WGS data.These V.cholerae strains were determined as serogroup O5.Type 3 and 6 secretion systems were detected in these serogroup O5 strains.These serogroup O5 strains belonged to sequence type(ST)88.Conclusions:Our analysis indicated the risk of non-O1/non-O139 V.cholerae leading to outbreaks of diarrheal diseases.The application of genomic data played an important role in the identification of the serogroup of non-O1/non-O139 V.cholerae in the lack of antiserum,which gave an example of the application of genome data in disease surveillance and public health emergency response.

Seroprevalence of human enterovirus A71 in Guangzhou,China,2019-2021

Enterovirus A71 (EV-A71) is a significant hand-foot-mouth disease (HFMD) etiology. The inactivated EV-A71 vaccines were approved in China in 2016. However, the seroprevalence of EV-A71 after the vaccine application and its potential association with the EV-A71 epidemic in the population are rarely studied. In this study, we analyzed the incidence of EV-A71 infection and seroepidemiology in Guangzhou City, China. From 2019 to 2021, 167,920 clinically confirmed HFMD cases were reported in Guangzhou. In 6,868 enterovirus-positive samples, Coxsackievirus A6 and Coxsackievirus A16 were dominant genotypes, and only 3 EV-A71-positive samples were detected, highlighting the deficient epidemic activity of EV-A71. Microneutralization assay was performed on 1,000 representative serum samples. Notably, the seroprevalence and geometric mean titer (GMT) decreased significantly in 2020, and that in the < 3-year age group were increased and even higher than that in 3–5-year age group in 2019 and 2021, which was contrary to our previous surveillance result and other studies in Guangzhou. Furthermore, a moderate decline of GMT level was observed following the vaccination, but the seropositive serums were still detected for 49 months after second immunization, suggesting the long-term persistence of the immunity. Our seroepidemiology study revealed relatively higher neutralizing antibody activity in the susceptible population after the EV-A71 vaccine was adopted in 2016 in Guangzhou. It may be one of the reasons for the lower epidemic activity of EV-A71 in Guangzhou from 2019 to 2021.