In this study ,we established Cross Priming Amplification (CPA ) technology for detection of influenza A virus (H1N1) approach ,and evaluated the method through clinical specimens .A set of specific primers were designed for CPA ac‐cording to the conservative gene sequences ,designed and realized in the same temperature reverse transcription of RNA and DNA amplification . The amplification products can be totally enclosed nucleic acid detection device for testing . Fourteen healthy pharyngeal swab specimens ,seven other respiratory viruses ,and six arboviruses strains were used as the controls .We used a method that application of gradient dilution to the H 1N1 virus strain as the control to test the sensitivity of the CPA .We also used 102 clinical pharyngeal swab specimens of H1N1 patients for detection object to evaluate the feasibility of CPA clinical detection .Results showed that the CPA reaction did not appear cross reaction on health cases samples and other viruses .The sensitivity of the CPA was approximately 10 copies/uL in the established method that exactly titer H1N1 virus strain gradient dilution test .As to the positive results among the clinical pharyngeal swab samples collected from patients at different stages after onset ,the CPA had the highest positive detection rate during the first three days after onset (100% ) .While the detection rate from day 4 to day 6 after onset was 79 .31% .After 7 days ,the detection rate was 9 .09% .The established CPA assay was a highly sensitive ,specific and reproducible approach for rapid detection of H1N1 virus ,which is conducive to the early diagno‐sis of influenza A virus (H1N1) for basic medical units .

Objective:To analyze the epidemiological characteristics of novel coronavirus positive cases including confirmed cases with clinical symptoms and asymptomatic infected cases in Guangzhou.Methods:Epidemiological data were collected on the nucleic acid positive cases of COVID-19 in Guangzhou from January to September 2020. The epidemiological characteristics, the distribution of time intervals between the confirmed/isolation date and the date of the first positive detection were analyzed, at last the influencing factors for the confirmed cases and asymptomatic infected persons were discussed.Results:From January 7 to September 4 in 2020, a total of 1 097 nucleic acid positive cases were identified, including 658 confirmed cases (59.98%) and 439 asymptomatic infected cases (40.02%). Among the 658 confirmed cases, the median age was 42 years old, the cases indicated two significant peaks. one of the peaks was related to the imported and associated cases from Hubei province, and the other peak was connected with individuals from overseas. In terms of 439 asymptomatic infected cases, the median age was 32 years old. There were two stages in these cases. The first stage followed the second peak of confirmed cases, and the second stage overlapped with the confirmed cases in Guangzhou when the epidemic was in a period of normal prevention and control, mainly related to imported cases from abroad. The asymptomatic infected persons accounted for 57.32% in all the imported infected cases. In both of asymptomatic and symptomatic cases, the positive rate of pharyngeal swabs was higher than that of nasopharyngeal swabs and anal swabs. There were statistically significant differences in age, source of infection and gender composition between confirmed cases and asymptomatic infected persons ( P<0.05). Older age groups were more likely to have clinical symptoms, with ≥40 years being the risk factor for confirmed cases (OR=2.334, P=0.001), and 20-39 years less likely to have clinical symptoms (OR=0.620, P=0.047), compared with the 0-19 years old group. Compared with those infected in China, those infected abroad were less likely to develop clinical symptoms and became confirmed cases (OR=0.723, P=0.013). Women were more likely to have clinical symptoms than men (OR=1.574, P=0.001). Conclusions:At present, asymptomatic infected persons and confirmed patients with clinical symptoms co-existed, and the number of asymptomatic infected patients was higher than that of confirmed cases in Guangzhou. High age, domestic infection and female may be risk factors for confirmed cases. It was of great value to further explore these underlying mechanisms for the prevention and treatment of the COVID-19.

Objective To construct adenovirus vector vaccine against H5N1 influenza virus and study on the immunogeuicity. Methods In this study, we amplified hemagglutinin (HA) gene sequence of H5N1 influenza virus (A/Anhui/1/2005), then constructed an adenovirus vector vaccine (Adv-HA), followed by tests in BALB/c mice for the immunogenicity with the vaccine and immunization strategies. Results The recombinate Adv-HA vaccine could effectively induce both humoral and cellular immunity against human H5N1 influenza virus. Conclusion The Adv-HA vaccination against H5N1 influenza is a potential strategy and worthy of further investigation.

Objective:To investigate the pathogenic spectrum of hand, foot and mouth disease(HFMD)from 2017 to 2019 in Guangzhou, and analyze molecular epidemiological characteristics of coxsackievirus A6 (CV-A6).Methods:Enterovirus A71 (EV-A71), CV-A16, CV-A6 and enterovirus were tested by reverse transcription-quantitative polymerase chain reaction(RT-qPCR). The CV-A6 representative samples were isolated and the VP1 region of isolates were amplified and analized by Mega5.0 and SeqMen.Results:A total of 7 578 enterovirus-positive specimens were detected from 2017 to 2019, 320 specimens were positive for EV-A71, 1481 specimens were positive for CV-A16, 3171specimens were positive for CV-A6, and 2606 specimens were positive for other enterovirus. Children under the age of 5 years were the most vulnerable population, and the male/female incidence ratio was 1.56∶ 1.The incidence occurred in all seasons, one peak between May and July, the other between September and November. The virus was isolated from 80 CV-A6 positive specimens and the full length of VP1 gene region was sequenced and nucleotide sequence similarity analysis was performed. The nucleotide homology in the VP1 region was 93%-100%, and the amino acid homology was 98%-100%. The nucleotide homology with the CV-A6 prototype strain (Gdula) VP1 region was 79%-81%, and the amino acid homology was 95%-97%. The nucleotide homology with the representative strain of D3 subtype was 92%-98%, and the amino acid homology was 98%-100%. Phylogenetic tree shows that all CV-A6 belonged to the sub-genotype D3 and distributed in multiple branches.Conclusions:CV-A6 is emerging as one of the major pathogen causing HFMD in Guangzhou, and all insolates belonged to D3 subtype. Closely monitoring the molecular characteristics of CV-A6 and changes in the pathogen spectrum can provide scientific basis for HFMD prevention and control.

Objective:To establish a rapid pipeline for whole genome sequencing of Chikungunya virus (CHIKV) by combining imbricated multiplex-PCR amplification and Illumina high-throughput sequencing platform.Methods:The primary reference sequences of CHIKV were downloaded from the National Center for Biotechnology Information (NCBI) database, covering all genotypes of CHIKV. After multiple alignments using the Mafft software and phylogenetic analysis, the 20 CHIKV references were selected for primer design. The Primal Scheme tool and Geneious Prime software were used to design, evaluate and optimize the primer panel. Finally, seven CHIKV-positive samples were involved in the validation of the primer panel.Results:All the amplicons of the designed panel were generated successfully. The consensuses generated from the mapping results could cover 100.00% of the coding region of the CHIKV genome when the Ct-value of the sample was less than 33, as the percentage would decrease to 99.38% when the Ct-value reached 35. The mapping percentage could be increased by 5.70%-25.43% when using the stepwise correction mapping strategy.Conclusion:The multiplex-PCR amplification method for CHIKV whole genome sequencing is relatively simple and convenient, which only requires two tubes of PCR amplification and performs well on CHIKV-positive clinical samples with different concentration levels of virus.

Objective:To establish a rapid pipeline for whole genome sequencing of Chikungunya virus (CHIKV) by combining imbricated multiplex-PCR amplification and Illumina high-throughput sequencing platform.Methods:The primary reference sequences of CHIKV were downloaded from the National Center for Biotechnology Information (NCBI) database, covering all genotypes of CHIKV. After multiple alignments using the Mafft software and phylogenetic analysis, the 20 CHIKV references were selected for primer design. The Primal Scheme tool and Geneious Prime software were used to design, evaluate and optimize the primer panel. Finally, seven CHIKV-positive samples were involved in the validation of the primer panel.Results:All the amplicons of the designed panel were generated successfully. The consensuses generated from the mapping results could cover 100.00% of the coding region of the CHIKV genome when the Ct-value of the sample was less than 33, as the percentage would decrease to 99.38% when the Ct-value reached 35. The mapping percentage could be increased by 5.70%-25.43% when using the stepwise correction mapping strategy.Conclusion:The multiplex-PCR amplification method for CHIKV whole genome sequencing is relatively simple and convenient, which only requires two tubes of PCR amplification and performs well on CHIKV-positive clinical samples with different concentration levels of virus.

Objective:To investigate the epidemiological and clinical characteristics of a case infected with avian influenza A (H5N6) virus associated with exposure to aerosol and provide evidence for the prevention and control of human infection with avian influenza virus.Methods:Epidemiological investigation was conducted to identify the history of exposure, infection route, and disease progression. Real-time fluorescent quantitative RT-PCR was used to test the samples collected from the case, close contacts, environment and poultry market.Results:The case had no history of exposure to live poultry and poultry market. But before the onset the case had a history of exposure to the live poultry placed in a car with doors and windows closed. The samples collected from the case’s lower respiratory tract and the remaining frozen chicken meat were all influenza A (H5N6) virus positive.Conclusions:The source of infection was the live poultry, and the infection route might be the exposure to aerosol in a car with doors and windows closed, where the poultry were temporarily stored. It is necessary to promote centralized poultry slaughtering, cold chain distribution and fresh poultry sale, as well as strengthen health education and establish the concept of consuming fresh poultry.

To monitor and analyze the molecular variation of the H3N2 influenza virus in Guangzhou during the COVID-19 pandemic, respiratory samples of influenza-like cases from influenza monitoring sentinel hospitals were collected from influenza monitoring sentinel hospitals for virus isolation and whole genome sequencing. The results showed that during COVID-19, there was only one peak of H3N2 influenza in the second quarter of 2022 in Guangzhou (the positive rate was 52.23%), and the epidemic intensity and duration were both higher than those in 2019. The HA gene and NA gene of the epidemic strain in Guangzhou in 2022 belonged to the 3C.2a1b. 2a. 1a. 1 branch, which had a good antigenic site matching with the vaccine strain (A/Cambodia/e0826360/2020) from 2021 to 2022 and had no antigen drift. In 2022 strains, the variation of antigen determinant mainly occurred in the I48T of C region, while no variation occurred in the A, B, D, and E regions. The binding site of the HA protein receptor was consistent with the vaccine strain (A/Cambodia/e0826360/2020). Most of the strains in 2022 carried 13 glycosylation sites on the HA protein, but an outbreak of strains caused a loss of glycosylation sites at 24-NST. In conclusion, the strains that caused the epidemic of H3N2 influenza in Guangzhou in 2022 were not evolved or transmitted from the local strains in 2019 during the COVID-19 pandemic.

To monitor and analyze the molecular variation of the H3N2 influenza virus in Guangzhou during the COVID-19 pandemic, respiratory samples of influenza-like cases from influenza monitoring sentinel hospitals were collected from influenza monitoring sentinel hospitals for virus isolation and whole genome sequencing. The results showed that during COVID-19, there was only one peak of H3N2 influenza in the second quarter of 2022 in Guangzhou (the positive rate was 52.23%), and the epidemic intensity and duration were both higher than those in 2019. The HA gene and NA gene of the epidemic strain in Guangzhou in 2022 belonged to the 3C.2a1b. 2a. 1a. 1 branch, which had a good antigenic site matching with the vaccine strain (A/Cambodia/e0826360/2020) from 2021 to 2022 and had no antigen drift. In 2022 strains, the variation of antigen determinant mainly occurred in the I48T of C region, while no variation occurred in the A, B, D, and E regions. The binding site of the HA protein receptor was consistent with the vaccine strain (A/Cambodia/e0826360/2020). Most of the strains in 2022 carried 13 glycosylation sites on the HA protein, but an outbreak of strains caused a loss of glycosylation sites at 24-NST. In conclusion, the strains that caused the epidemic of H3N2 influenza in Guangzhou in 2022 were not evolved or transmitted from the local strains in 2019 during the COVID-19 pandemic.

Objective:To analyze the characteristics of spread and genetic evolution of H5 subtype avian influenza virus in Guangzhou from 2014 to 2019.Methods:H5 subtype virus was detected by fluorescence quantitative RT-PCR from the environmental samples in Guangzhou poultry markets. The genes of HA and NA of 48 isolates randomly selected were sequenced, including 46 isolates from environmental samples and 2 isolates from cases. The characteristics of molecular variation and genetic evolution were analyzed by using bioinformatics software.Results:A total of 1 094 strains of H5 subtype avian influenza virus were isolated from 52 284 samples (2.09%). All the strains belonged to Clade 2.3.4.4.C. NA gene belonged to H6N6 of Eurasian lineage. The cleavage sites of all the strains showed the characteristics of highly pathogenicity. Receptor binding sites were avian-derived receptors. However, mutations of S123P, S133A and T156A occurred, which implied that these strains could tend to bind to human receptors. There was an additional glycosylation site at 140 in strains isolated after 2017. The variation of antigen loci mainly occurred in B and E regions.Conclusions:H5 subtype avian influenza virus spread in Guangzhou from 2014 to 2019 with annual increased proportion of positive rate, and the sequencing results indicated that it belonged to Clade 2.3.4.4.C of H5N6 highly pathogenic virus, and genetic evolution and mutation continued, especially the common mutations which could enhance the binding capacity to human receptors. It is necessary to strengthen the surveillance.