Discovery and Full Genome Characterization of SARS-CoV-2 in Stool Specimen from a Recovered Patient, China.

SARS-CoV-2 was found in a recovered patient's stool specimen by combining quantitative reverse transcription PCR (qRT-PCR) and genome sequencing. The patient was virus positive in stool specimens for at least an additional 15 days after he was recovered, whereas respiratory tract specimens were negative. The discovery of the complete genome of SARS-CoV-2 in the stool sample of the recovered patient demonstrates a cautionary warning that the potential mode of the virus transmission cannot be excluded through the fecal-oral route after viral clearance in the respiratory tract.

Development of a recombinase-aided amplification assay for rapid and sensitive detection of porcine circovirus 3.

Porcine circovirus type 3 (PCV3) is a novel member of the genus Circovirus, first detected in the United States in 2016, with subsequent reports in many countries. PCV3 infections have caused serious economic losses in the pig industry. Alternative rapid and sensitive assays for PCV3 detection are needed for clinical diagnosis, especially in laboratories not equipped with more sophisticated equipment. Here, a real-time recombinase-aided amplification assay (RAA) was developed for PCV3 detection. Specific primers and probes targeting the conserved region of the capsid gene of PCV3 were designed. The assay was performed at 39 °C for 30 min using specialized equipment. Furthermore, 36 clinical samples were used to evaluate the RAA. The analytical sensitivity of the RAA for PCV3 was 38 copies per reaction at 95% probability level, using a probit regression model. There was no cross-reactivity with other DNA viruses belonging to the Circoviridae and Parvoviridae families. The detection rate agreed with that obtained by an established real-time PCR assay with a kappa value of 1.0. Our results demonstrated that this new RAA could be used for the rapid, accurate, and sensitive detection of PCV3.

Epidemiological Features and Forecast Model Analysis for the Morbidity of Influenza in Ningbo, China, 2006-2014.

This study aimed to identify circulating influenza virus strains and vulnerable population groups and investigate the distribution and seasonality of influenza viruses in Ningbo, China. Then, an autoregressive integrated moving average (ARIMA) model for prediction was established. Influenza surveillance data for 2006-2014 were obtained for cases of influenza-like illness (ILI) (n = 129,528) from the municipal Centers for Disease Control and virus surveillance systems of Ningbo, China. The ARIMA model was proposed to predict the expected morbidity cases from January 2015 to December 2015. Of the 13,294 specimens, influenza virus was detected in 1148 (8.64%) samples, including 951 (82.84%) influenza type A and 197 (17.16%) influenza type B viruses; the influenza virus isolation rate was strongly correlated with the rate of ILI during the overall study period (r = 0.20, p < 0.05). The ARIMA (1, 1, 1) (1, 1, 0)12 model could be used to predict the ILI incidence in Ningbo. The seasonal pattern of influenza activity in Ningbo tended to peak during the rainy season and winter. Given those results, the model we established could effectively predict the trend of influenza-related morbidity, providing a methodological basis for future influenza monitoring and control strategies in the study area.

Apodemus agrarius is a potential natural host of severe fever with thrombocytopenia syndrome (SFTS)-causing novel bunyavirus.

BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne, novel bunyavirus-caused emerging infectious disease. It becomes a threat to public health due to its high fatality rate. OBJECTIVE: To clarify the epidemiological characteristics of SFTS and natural host(s) of SFTS-causing virus (SFTSV) in East China. STUDY DESIGN: Serum antibody against SFTSV in 496 healthy villagers was examined by ELISA. SFTSV in acute sera of SFTS cases and lung tissues of house and field mouse/rats were identified using quantitative RT-PCR, cell culture, and sequencing. RESULTS: A total of 22 laboratory-confirmed SFTS cases were diagnosed between 2012 and 2014, of which 5 (22.7%) reported a history of tick-bites. The seroprevalance of SFTSV antibody was 10.5% in healthy villagers. SFTSV genomic RNAs were identified in 2 of 8 Apodemus agrarius but not in Rattus norvegicus (n=40) and Rattus losea (n=4). The 3 segments of SFTSV from 11 SFTS cases and 2 A. agrarius were successfully sequenced. Phylogenetic analyses indicated that at least 3 different SFTSV strains (inland-type, Ningbo-native-type, and their reassortant-type) were present in Ningbo. The 3 segments of the 2 SFTSV isolates from A. agrarius shared great sequence homologies to those isolated from the patients living in nearby villages. CONCLUSION: The present study indicated that A. agrarius might be a natural host of SFTSV in East China.

[Genetic variation of the hemagglutinin and neuraminidase of influenza B viruses isolated in Ningbo during 2010-2012].

OBJECTIVE: To investigate the epidemiological characteristics of influenza B viruses and explore the genetic evolution characteristics of the hemagglutinin(HA) and neuraminidase(NA) genes of local isolated strains in Ningbo, Southeast China, during 2010 to 2012. METHODS: Respiratory specimens from 3440 cases of patients with influenza-like illness(ILI) during 2010 to 2012 were collected in for virus isolation. And the 628 sera samples were collected in 2010 from the healthy community population to detect the HI antibody level against the local isolated virus.For phylogenetic analysis, the fragments of HA and NA genes were amplified and sequenced from strains isolated in different years. The association between evolution of HA and epidemiological characteristics were analyzed. RESULTS: A total of 109 strains of influenza B virus were isolated, including 102 (93.6%) Victoria-lineage strains and 7 (6.4%) Yamagata-lineage strains. Positive rates of HI antibody against Victoria-lineage strains and Yamagata-lineage strains were 51.1% (321) and 47.8% (300), respectively (χ(2) = 1.405, P > 0.05) among the 628 sera samples. The phylogenetic analysis showed that all HA fragments of isolated strains clustered the same branch with Malaysia/2506/2004 while the NA genes formed different branches. Compared with Brisbane/60/2008 strain, there were 1 to 5 Amino acid mutations in HA domain, and more mutations were detected in NA domain, ranged from 6 to 16 sites. The genetic evolution of NA in Victoria-lineage strains were faster compared with HA. CONCLUSION: The genetic evolution rates of NA genes were faster than that of HA genes in the local circulated Victoria-lineage viruses during 2010 to 2012;The comprehensive analysis of HA and NA fragments were more reliable and sensitive on surveillance of genetic evolution of influenza B viruses.

[Analysis on influenza antibodies detection rate and infected recently among infants].

OBJECTIVE: To understand the status of infants infected with influenza viruses after switch over of dominant strain in the summer of 2006. METHODS: Two groups of infants serum were collected and to be detected the antibodies of influenza viruses which the infants experienced two peaks of influenza A H1N1 circulation in the age of 3-4 and 10-11 months old and the infants only experience one circulation in 5-6 months old. RESULTS: The antibody of influenza A H1N1 viruses was 31.47% in the infants who experience two circulations in 3-4 months and 10-11 months old and was 26.42% which only experience circulation in the 5-6 months old. There were no significant difference between 2 groups (chi2 = 1.207, P > 0.05). CONCLUSION: The group of 13 months age of infants were rarely infected influenza virus in the first time exposure at the age of < or =4 months due to maternal antibodies protection. Whenas, the group of 8 months age who were exposed at the age of > or =5 months, were more easier infected the influenza virus than the group of 13 months age in the first time exposure at the age of < or =4 months.