[Objects]To isolate and identify the pathogen of the large outbreak of dengue in Guangdong province in 2014. To understand the origin and the phylogenetic characteristics of the isolates ,and provide scientific foundation for the surveillance and prevention of dengue fever.[Methods]Collected the patient serum samples over all the Guangdong province during the 2014 outbreakperiod,isolated and identified the virus from these samples. Amplified complete E gene and complete genome with certain primers and sequenced all the products. Then the Phylogenetic ,Bayesian phylogeography and mutations analysis were carried.[Results]40 DENV-1 strains were isolated and identified. 40 complete E gene sequences and 6 complete genome sequences of DENV-1 were obtained. Phylogenetic analysis with E gene sequences revealed that the 40 isolates were classified into two genotypes including 16 genotypeⅠ(Asia)and 24 genotypeⅤ(America/Africa). 14 genotypeⅠisolates were clustered closest with isolates from Guangdong province(2013)and Sigapore(2013)which share the nucletide identities of 99.6% ~ 99.9%,other two genotypeⅠisolates were clustered with strains from Malaysia (2013) and both share the nucletide identities of 99.7%;24 genotypeⅤisolates were all classified in one clade with striains from Bangladesh(2009),China(2009)and Bhutan(2013)which share nucletide identities of 99.0%-99.9%. Further analysis with six complete genome sequences showed that five isolates were clustered closest with strains isolated from Guangdong province(2013)share the nucletide identities of 99.6%-99.8% while the sixth stains closest with strains isolated from Myanmar(2002)share the nucletide identities of 98.8%. The isolates have five amino acid mutations compared with strains epidemic in Guangdong province in 2013,three mutations(S88V,E203G,T275R)are in the EⅡdomain and one mutation (S305P)is in the EⅢdomain which associated with virulence.[Conclusions]During the outbreak in Guangdong province in 2014, DENV-1 is the predominant causative serotype,and there are at least two different kinds of genotypes of DENV-1 largely epidemiced in the whole province. Evolution analysis reveals the multiple origins of the isolates which may origin from Guangdong province , Sigapore,Malaysia,Myanmar so that we should enhance the study and surveillance of autochthonous and vectors in order to understand the epidemic way of dengue in Guangdong province. The isolates have had four mutations in the domain associated with virulence which remain further study to know their biological effects.

Objective:To understand the molecular characteristics of the mutant strain of polymerase basic protein 2 (PB2) gene of influenza A (H1N1pdm) in Guangdong province, and to explore its specific molecular sites, so as to provide scientific basis for the prevention and control of influenza virus.Methods:Throat swab samples were collected from 2 cases infected with PB2 gene variant strains for virus isolation, and 23 influenza virus strains were selected from Guangdong province for sequencing analysis. The reference sequences and vaccine strain sequences provided by GISAID were used to perform evolutionary analysis on hemagglutinin (HA) and PB2 genes. Virus strain antigen analysis and neuraminidase (NA) inhibition test were carried out. PB2 protein model was constructed and polymerase activity was analyzed.Results:H399N amino acid mutation occurred in the HA gene of PB2-D701N and PB2-A271S variant strains, both of which belonged to the branch of 6B.1A.5a.2a. They belonged to the same big branch and different small branches as the vaccine strain A/Victoria/4897/2022, and they are all vaccine-like strains. In the three-dimensional structure, the mutations of PB2-D701N and PB2-A271S change charge and hydrophobicity.Conclusions:PB2-D701 and A271 were highly conserved, and PB2 mutant strains were not the dominant strains. The PB2 mutant had high antigenicity with the vaccine. The PB2 mutant strain is sensitive to NA inhibitors. The three-dimensional model predicted that PB2-D701N mutation could enhance virulence and affect transmissibility of influenza virus, while PB2-A271S mutation could affect polymerase activity and polymerase complex synthesis of influenza virus.

Objective:To understand the etiology of a confirmed case of Coronavirus Disease 2019 (COVID-19).Methods:The pharyngeal swabs, serum and nasal swabs of a case of COVID-19 were inoculated into Vero-E6 cell tubes for virus isolation. The cytopathic effect (CPE) were observed daily. Collecting cell’s isolation when CPE was over 75%, after repeated freezing and thawing for 3 times, the supernatant was centrifugally taken, and the images of the virus were obtained by transmission electron microscopic observation, and the nucleic acid of the virus was extracted, second generation sequencing and sequence evolution analysis were used to identify and type the virus strains.Results:One strain of 2019 novel coronavirus (2019-nCoV) was successfully isolated from the nasal swab of this case of COVID-19, and one strain of herpes simplex virus type 1 (HSV-1) was also successfully isolated from the throat swab of the same case.Conclusions:COVID-19 cases have the possibility of co-infection with 2019-nCoV and HSV-1.

Objective:To analyze and reveal the genetic evolution and variation of influenza viruses in cases of co-infection in Guangdong Province.Methods:Throat swab samples were collected from four cases of H1N1pdm and H3N2 co-infection for viral isolation. The isolated strains were subjected to antigen analysis and neuraminidase inhibitor susceptibility test. High-throughput sequencing was used to detect the sequences of strains in three throat swab samples and one virus strain, and then genetic variations were analyzed.Results:Four influenza viruses were isolated with one strain of H1N1pdm and three of H3N2 subtype, and all of them were genetically similar to the vaccine strain in 2022-2023. The HA genes of H1N1pdm and H3N2 strains belonged to clade 6B.1A.5a.2a and 2a.3a.1, respectively. The isolated strains belonged to the same clade as the strains prevalent in Guangdong during the same period. No drug-resistant variations were detected in N1 or N2 gene, and the isolated strains were sensitive to oseltamivir and zanamivir.Conclusions:H1pdm subtype had stronger replication ability than H3 subtype in the influenza viruses isolated from co-infected cases. H1N1pdm and H3N2 subtype influenza viruses were genetically similar to the strains circulating in Guangdong at the same time. The isolated H1N1pdm and H3N2 strains were sensitive to both oseltamivir and zanamivir, indicating that they could continue to be used in the treatment of influenza virus infections caused by one or two genotypes.

Objective:To obtain the genome sequences of SARS-CoV-2 in respiratory specimens in Guangdong Province with next-generation sequencing (NGS) and analyze the factors influencing sequencing.Methods:Eight upper and lower respiratory tract specimens were collected from patients with SARS-CoV-2 infection in Guangdong Province in January 2020. RNA library construction was used to obtain the genome sequences of SARS-CoV-2. A bio-informatics software package (CLC Genomics Workbench 12.0) was used to analyze and compare the genomic sequences.Results:Five SARS-CoV-2 genome sequences were obtained from the eight specimens and two were obtained from lower respiratory tract specimens. The nucleotide homology to SARS-CoV-2 was 97.74%-99.90%. The Ct values were lower, while the sequencing depth, coverage, relative abundance and genome integrity were higher in sequencing the SARS-CoV-2 in lower respiratory tract specimens.Conclusions:The low Ct value of SARS-CoV-2 in the samples was good for sequencing.