Field Evaluation of a Duplex RT-RAA Assay for Rapid Detection of SARS-CoV-2 - Hebei Province, China, January 2021

INTRODUCTION

Recently, a local cluster epidemic has occurred in Shijiazhuang City, Hebei Province. Failure to promptly identify patients with fever in rural areas was the major reason for this epidemic.

METHODS

We presented the field evaluation of a new real-time reverse transcription recombinase-aided amplification (RT-RAA) kit incorporating an endogenous internal control in a single-tube format, completed at the Hebei CDC from January 17, 2021 to January 27, 2021.

RESULTS

We evaluated the diagnostic performance of RT-RAA assay using automatic extracted RNA of 808 clinical samples. Compared with reverse transcriptase real-time quantitative PCR (qRT-PCR), RT-RAA kit achieved 92.41% sensitivity, 98.78% specificity and a 96.29% coincidence rate, demonstrating an excellent agreement between the RT-RAA assay and qRT-PCR assay. Furthermore, 58 samples were extracted using a manual extraction method within 5 minutes, but only samples with high nucleic acid concentration (cycle threshold value not higher than 32) could be stably detected.

DISCUSSION

The RT-RAA is more suitable to meet the needs of rapid, sensitive, and accurate detection in community-level medical institutions.

[Epidemiological characteristics of influenza and characteristics of hemagglutinin gene of B-Victoria strains in Hebei Province from 2018 to 2019]

Objective: To understand the epidemiological characteristics of influenza in Hebei Province from 2018 to 2019, and to analyze the characteristics and variation of hemagglutinin(HA) gene of influenza B-Victoria(BV) strains. Methods: Throat swab specimens of influenza-like cases within 3 days of fever were collected from 28 sentinel hospitals in Hebei province, meanwhile, The surveillance data was collected by the Chinese National Influenza Surveillance Network from April 2018 to March 2019, Throat swab specimens were collected from patients with influenza-like symptoms in sentinel hospitals, and tested by RT-PCR and virus isolation. 14 influenza B-Victoria strains from different regions were selected to sequence HA gene, Phylogenetic tree and the molecular characteristics were analyzed by DNASTAR 7.0 and Mega-X software. Results: From 2018 to 2019, A total of 99 266 cases of influenza-like illness (ILI) were detected from 4 689 103 cases by 28 influenza sentinel hospitals in Hebei Province, the visit percentage of ILI was 2.12%. During the period, 18 730 samples were detected, and 2 752(14.69%) samples were positive tested by RT-PCR, the peak was in the third week of 2019(44.92%), In the early stage of epidemic season, Influenza A(H1N1)pdm09 virus was the main type, while BV virus was the main type in the late stage. HA gene sequence analysis showed that the 14 BV viruses belonged to 162-164 amino acid deletion strains, the amino acid homology between HA sequences was 97.16%-100.00%, and 97.16%-98.95% compared with the vaccine strain B/Colorado/06/2017 recommended by WHO. Compared with the vaccine strains, 14 strains involved 11 amino acid site mutations. Conclusion: Influenza was prevalent in winter and spring in Hebei province from 2018 to 2019, Multiple mutations in antigenic sites of BV viruses might be related to the outbreaks.

[Analysis on influence and lag effects of meteorological factors on incidence of hand, foot and mouth disease in Shijiazhuang, 2017-2019]

Objective: To understand the influence and lag effect of meteorological factors on the incidence of hand, foot and mouth disease (HFMD) in Shijiazhuang. Methods: The daily incidence data of HFMD in Shijiazhuang during 2017-2019 were collected from Chinese Information System for Disease Control and Prevention. The hourly meteorological data were collected form meteorological stations of Shijiazhuang of Chinese meteorological data network. The distributed lag nonlinear model was built for statistical analysis by software R 3.6.2. Results: When the daily average temperature was 15-26 ℃, the risk of incidence of HFMD increased at lag 3-6 days. However, the risk was highest when the temperature was 25 ℃ at lag 3 days (RR=1.03,95%CI:1.00-1.06). When the daily average relative humidity was more than 80%, the risk of incidence of HFMD increased at lag 5-18 days. However, the risk was highest at lag 9 days (RR=1.04, 95%CI: 1.02-1.06).When the daily average air pressure ranged from 999 hPa to 1 007 hPa, the risk of incidence of HFMD increased at lag 5-8 days. However, the risk was highest at lag 6 days (RR=1.01, 95%CI: 1.00-1.02).When the daily average precipitation ranged from 15 to 32 mm, the risk of incidence of HFMD increased at lag 3-18 days. However, the risk was highest at lag 6 days (RR=1.11, 95%CI: 1.02-1.19). Conclusions: Meteorological factors increased the risk of incidence of HFMD such as higher daily average temperature (15-26 ℃), higher daily average humidity (>80%), lower daily average air pressure (999-1 007 hPa) and higher daily average precipitation (15-32 mm) in Shijiazhuang during 2017-2019. They were all correlated with the incidence of HFMD with certain lag days. It is suggested to use these meteorological indicators for the early warning of HFMD.

[Epidemiological and pathogenic characteristics of cases with severe and fatal hand, foot, and mouth disease caused by other enterovirus in Hebei province, 2013-2017]

Objective: To understand the epidemiological characteristics of cases with severe and fatal hand, foot, and mouth disease (HFMD) caused by other enterovirus in Hebei province, 2013-2017. Genetic characteristics of the main pathogen cosackie virus A6 (CoxA6) were also analyzed to further clarifying the characteristics and rules of genetic evolution on this virus. Methods: Descriptive epidemiological methods were used to analyze the distribution of severe and fatal cases with HFMD caused by other enterovirus in Hebei, 2013-2017. The VP1 sequences of CoxA6 were phylogenetically analyzed, using the Mega 5.2 software package. Results: A total of 86 severe and fatal cases with HFMD caused by other enterovirus were reported, accounting for 1.12%, comparing to all the HFMD caused by other enterovirus. Cases began to rise in April, and peaked in May-July. 65.12% of the cases occurred in children between 1 and 5 years old. The sex ratio between male and female was 1.39∶1. A total of 93.02% of the cases were children outside the child care settings. A total of 39 positive strains were identified, with positive isolation rate as 45.35%. Phylogenetic analysis on the VP1 sequences of CoxA6 strains in this study revealed that CoxA6 strains belonged to sub-genotypes D3a and D3b. Conclusions: Severe and fatal HFMD cases that caused by other enterovirus in Hebei province was with seasonal feature, consistent with the overall trend of this disease, 2013-2017. No new evolutionary branch appeared in the CoxA6 strain.

[Spatial-temporal cluster of hemorrhagic fever with renal syndrome in Hebei province, 2005-2016]

Objective: To explore the spatial-temporal distribution and epidemic characteristics of hemorrhagic fever with renal syndrome (HFRS) in Hebei province from 2005 to 2016. Methods: Records of HFRS cases reported from each county in Hebei during January 2005 to December 2016 were collected from National Notifiable Disease Surveillance System (NNDSS). Global and local spatial association statistics were used to measure the spatial autocorrelation and software GeoDa 1.2.0. Software SaTScan 9.4.1 was used to analyze spatiotemporal clusters. Software ArcGIS 10.2 was used to visualize the yearly scan results. Results: In Hebei province, a total of 8 437 human HFRS cases reported from 170 counties with an annual incidence rate of 0.99/100 000 population during 2005-2016. The peak incidence season was spring. Global spatial autocorrelation analysis on the incidence of HFRS at county-level showed that the value of Moran's I were all above 0 (P<0.05), indicating that the significant spatial cluster. The result of local indicators on spatial association (LISA) analysis revealed that identified hot spots were mainly in northeastern area, while cold spots were found in some counties of central and southern areas. Spatial-temporal scan detected that the primary cluster of HFRS incidence was mainly distributed in Qinhuangdao city and Tangshan city, including 11 counties (city/district): Beidaihe district, Haigang district, Funing district, Shanhaiguan district, Changli county, Lulong county and Qinglong Manchu autonomous county in Qinhuangdao city, and Qian'an city, Laoting county, Luanzhou city and Luannan county in Tangshan city (RR=39.64, P<0.001), during January-July in 2005. Conclusions: There were significant spatial-temporal cluster of HFRS in Hebei from 2005 to 2016. The cluster areas of HFRS were mainly in northeastern Hebei, it is necessary to strengthen the prevention and control programs of HFRS in these areas.

Long-term retrospective observation reveals stabilities and variations of hantavirus infection in Hebei, China

BACKGROUND

Hemorrhagic fever with renal syndrome (HFRS) is an emerging zoonotic infectious disease caused by hantaviruses which circulate worldwide. So far, it was still considered as one of serious public health problems in China. The present study aimed to reveal the stabilities and variations of hantavirus infection in Hebei province located in North China through a long-term retrospective observation.

METHODS

The epidemiological data of HFRS cases from all 11 cities of Hebei province since 1981 through 2016 were collected and descriptively analyzed. The rodent densities, species compositions and virus-carrying rates of different regions were collected from six separated rodent surveillance points which set up since 2007. The molecular diversity and phylogenetic relationship of hantaviruses circulating among rodents were analyzed based on partial viral glycoprotein gene.

RESULTS

HFRS cases have been reported every year in Hebei province, since the first local case was identified in 1981. The epidemic history can be artificially divided into three phases and a total of 55,507 HFRS cases with 374 deaths were reported during 1981-2016. The gender and occupational factors of susceptible population were invarible throughout, however age of that was gradually aging. The annual outbreak peak always present in spring, while the main epidemic region had gradully altered from south to northeast. Surveillance of rodents revealed that residential rodents significantly possessed higher density and virus-carring rate than field rodents. The house rat, Rattus norvegicus, was the dominant rodent species and Seoul virus S3 sub-genotype which is continued but slightly evolving perhaps to be the sole pathogen for local HFRS cases of Hebei province.

CONCLUSIONS

This long-term province-wide surveillance and epidemiological analysis has revealed the stabilities and variations of hantavirus infection in North China. In order to improve current prevention and control strategies of HFRS in China, all surveillance should be continuously enhanced and variations should be paid more attentions.

Spatiotemporal patterns of hemorrhagic fever with renal syndrome in Hebei Province, China, 2001-2016

Hemorrhagic fever with renal syndrome (HFRS) is highly endemic in China, where approximately 90% of the total human cases in the world are reported. The Hebei province, one of areas with the highest prevalence, has reported HFRS cases every year in the last two decades. This study describes the spatiotemporal patterns of HFRS in the Hebei province from 2001 to 2016, detects the high-risk spatiotemporal clusters of HFRS, and provides valuable information for planning and implementation of local preventive measures. For the purpose of the analysis, HFRS cases recorded during the sixteen years in the Hebei province were aggregated into three temporal periods (2001-2006, 2007-2012, and 2013-2016). Spatiotemporal analyses, including Global spatial autocorrelation analysis and Kulldorff's scan statistical analysis, were applied to analyze te spatiotemporal clusters of HFRS at the county level. The results revealed that the spatial extent of the HFRS epidemic in the Hebei province changed dynamically from 2001 to 2016, which indicated that a comprehensive preventative strategy should be implemented in the northeastern regions of the Hebei province in spring.

Association between TNF-α-238G/A gene polymorphism and OCD susceptibility: A meta-analysis

BACKGROUND

Tumor necrosis factor-alpha (TNF-α) is an important cytokine and has been reported to be associated with the pathogenesis of many autoimmune and inflammatory diseases. TNF-α gene is located on a region that has been found to be associated with obsessive-compulsive disorder (OCD). We performed this meta-analysis to assess the relationship between susceptibility to OCD and the TNF-α-238G/A gene polymorphism.

METHODS

An extensive search of the available literature on the association between the susceptibility to OCD and the TNF gene polymorphism was conducted by searching PubMed, Web of Knowledge, Embase, Chinese Web of Knowledge, Wanfang, and Chongqing VIP database. The database was searched up to December 2016 and includes language of English and/or Chinese with the keywords of "obsessive-compulsive disorder" or "OCD," polymorphism or variant or mutation, "tumor necrosis factor" or "TNF" or "cytokine." The association between TNF-α-238G/A gene polymorphism and the susceptibility of OCD was anticipated by odds ratio (OR) with the corresponding 95% confidence interval (95% CI).

RESULTS

Four studies including 435 cases and 1073 controls were incorporated in our meta-analysis. In general, TNF-α-238G/A gene polymorphism might lead to a decreased risk of OCD susceptibility (G vs A genotype model: OR = 1.01, 95% CI = 0.37-2.77, P = .981; GG vs AA+AG model: OR = 0.93, 95% CI = 0.37-2.36, P = .879; GG+AG vs AA model: OR = 0.22, 95% CI = 0.06-0.73, P = .014; GG vs AA model: OR = 0.21, 95% CI = 0.06-0.71, P = .012; AG vs AA model: OR = 0.29, 95% CI = 0.07-1.16, P = .081; GG+AA vs AG model: OR = 1.17, 95% CI = 0.55-2.51, P = .683).

CONCLUSION

TNF-α-238G/A gene polymorphism might lead to a decreased risk of OCD susceptibility.

Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease

Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID₅₀/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.

Genovariation Study of Hantavirus in Main Endemic Areas of Hemorrhagic Fever with Renal Syndrome in Hebei Province, China

BACKGROUND

Hemorrhagic fever with renal syndrome (HFRS) is an important infectious disease in Hebei Province. At present, cases from the northeast regions of the province account for >80% of the total incidences. However, studies that examine the region-specific genetic variations of the Hantavirus (HV), the causative pathogen for HFRS, have been lacking.

METHODS

Rodents were collected in northeast Hebei Province from 2004 to 2013, and the HV strains used in this study were isolated in 1993. Lung tissues were isolated from the rodents and HV antigen was detected by indirect immunofluorescence. The M1 and M2 fragments of HV M region were amplified by reverse transcription polymerase chain reaction (RT-PCR), cloned into pMDl9-T vector, sequenced and compared with representative standard stains for homology and phylogenetic analysis.

RESULT

A total of 21 samples of HV antigen-positive were collected. Real-time PCR analysis revealed that the 19 rodent lungs and two HV strains were positive for the SEO virus. 11 samples were chosen to sequence, and they shared 95.8%-99.8% in nucleotide homology, and 83.6%-99.2% when compared to the standard strains of SEO virus. Phylogenetic analysis demonstrated that all strains were grouped into the same S3 subtype.

CONCLUSION

SEO was the major epidemic genotype of HV in the main HFRS endemic areas in Hebei Province, and S3 was the major subtype. There was minor genetic variation in HV over short term periods, while long term variations were higher.

Pulmonary and central nervous system pathology in fatal cases of hand foot and mouth disease caused by enterovirus A71 infection

In the past 17 years, neurological disease associated with enterovirus A71 (EV-A71) has increased dramatically in the Asia-Pacific region with a high fatality rate in young infants, often due to pulmonary oedema, however the mechanism of this oedema remains obscure. We analysed the brainstem, heart and lungs of 15 fatal cases of confirmed EV-A71 infection in order to understand the pathophysiological mechanism of death and pulmonary oedema. In keeping with other case studies, the main cause of death was neurogenic pulmonary oedema. In the brainstem, 11 cases showed inflammation and all cases showed parenchymal inflammation with seven cases showing moderate or severe clasmatodendrosis. No viral antigen was detected in sections of the brainstem in any of the cases. All fatal cases showed evidence of pulmonary oedema; however, there was absence of direct pulmonary viral damage or myocarditis-induced damage and EV-A71 viral antigen staining was negative. Though there was no increase in staining for Na/K-ATPase, 11 of the 15 cases showed a marked reduction in aquaporin-4 staining in the lung, and this reduction may contribute to the development of fatal pulmonary oedema.

Epidemiology of hepatitis C virus infection and risk factor analysis in the Hebei Province, China

Background

In 1985, a hepatitis C virus (HCV) outbreak caused by plasmapheresis donation was reported in the Hebei Province, China. However, studies assessing the epidemic features and risk factors of HCV in the general population of Hebei have been limited until now.

Methods

The multicenter cluster sampling method was used to collect samples. The participants were interviewed. Relevant information was obtained from the general population using a standardized questionnaire, and association and logistic regression analyses were conducted. Serum samples were taken to test anti-HCV by enzyme immunoassays.

Results

A total of 4562 participants from 11 cities of the Hebei Province were enrolled. The average anti-HCV positive rate was 0.62% (29/4562), which was 1.07% in the rural population, compared with 0.22% in the urban population. The anti-HCV positive rate in the 40–59-year age group was higher than in those aged <40 years. History of blood transfusion and transmission in families were the main risk factors for HCV infection in this area.

Conclusion

The anti-HCV positive rate in Hebei has decreased significantly from that two decades ago. Safety of blood products and health education about HCV still need to be improved.

A case-control study of risk factors for HIV-negative children with cryptococcal meningitis in Shi Jiazhuang, China

BACKGROUND

Although cryptococcal meningitis (CM) is an emerging disease worldwide, there have been few studies of the characteristics and risk factors of CM in children.

METHODS

We used data collected from May 2007 through April 2012 in the Acute Meningitis-Encephalitis Syndrome Surveillance project in Shi Jiazhuang, China to describe the epidemiologic, clinical, and laboratory findings in children with CM. Furthermore, a matched case-control study was used to determine risk factors of CM.

RESULTS

Overall 23 HIV-negative children with CM (median age: 10.91 years; range: 5 months-17 years) were enrolled in our study. The average annual incidence of CM was 0.43/100,000 with a fatality rate of 1.7%. Most patients were males (60.87%) and rural children (73.91%). Common clinical symptoms included increased intracranial pressure, such as headaches (78.3%), nausea (60.9%), altered mental status (56.5%), vomiting (52.2%), and seizures (43.5%), and frequent laboratory findings consisted of blood leukocytosis (87.0%), decreased CSF glucose (87.0%), pleocytosis (82.6%), increased intracranial pressure (73.9%) and elevated CSF proteins (65.2%). Epidemiologic, clinical, and laboratory findings were similar between patients with and without underlying diseases. Multivariate logistic regression analysis showed that children who had contact with birds/bird droppings or saprophytes were more likely to be infected than those without such contact (odds ratio(OR) =11.82; 95% confidence interval (CI), 2.21-62.24; P = 0.004). Patients with an interval of ≥20 days from onset to admission were at high risk for CM (OR= 5.31; 95%CI, 1.58-17.89; P = 0.007).

CONCLUSIONS

Our findings show that CM is an uncommon disease with a high mortality rate in children. Although additional studies are needed to find effective prevention and treatments for CM, clinicians should consider CM as a potential cause for pediatric meningitis in children, particularly boys from rural areas, who had contact with birds/bird droppings or saprophytes and in children who did not receive prompt medical attention.

[Investigation on the source of the first human of avian influenza A (H5N1) case in Beijing]

OBJECTIVE

To investigate the source of the first human case of avian influenza A (H5N1) infection in Beijing.

METHODS

Interviewing the relatives of the case and other key persons, collecting and detecting samples of related biological, epidemiological and environmental data of the case were conducted. Later, the infection source was thoroughly investigated.

RESULTS

The case ever contacted a slaughtered duck 5 days prior to the onset of illness, and the duck was bought from a stall of a wet market in Yanjiao area of Hebei province. Ten environmental samples were collected in this stall and the neighboring stall of the market. Another 6 samples were tested positive for H5N1 virus by PCR method, with 5 virus strains isolated. The whole-genome sequencing indicated that the amino acid homology between the H5N1 virus strains from the environment and the virus isolated from the case reached 99.8% - 100%.

CONCLUSION

From both epidemiological and virological evidence, it was proved that the first human case of avian influenza A (H5N1) infection in Beijing was infected by a duck that carrying H5N1 virus the case contacted 5 days proceeding the onset of illness.

[Genotype and sequence analysis on G2 segments of hantavirus from HFRS patients in Hebei Province]

OBJECTIVE

To know the genotype and subtype of hantavirus (HV) which infected persons in Hebei province.

METHODS

According to G2 coding region of 76-118 and R22 strains, specific type primers were designed to detect and identity the types of HV in HFRS patients' sera with RT-nested PCR. Nucleotides were assayed from partial products after purification and reclaim. Then, gene analysis was done with DNAStar package.

RESULTS

17 out of 69 positive serum specimens were successfully detected by RT-PCR and the detection rate was 24.64%, among which, <or= 7 days was 34.29%, 8-14 days was 19.23%, >or= 14 days were 0. 17 positive specimens were all belonged to SEO. The nucleotide homology of 9 typical specimens was 92.0%-100%. Between HeB7 and other 8 specimens was 92%-95%, and they belonged to different subtypes. When HeB7 compared with R22 strain, it was 97.7%. HeB7 and R22 belonged to S1 subtype. The 8 specimens except HeB7 was 95.7%-100% and they all belonged to S3 subtype. When compared with 76-118 strain, 9 specimens' nucleotide homology was only 70.3%-72.7%, belonged to different type.

CONCLUSION

SEO was the major type of HV from HFRS patients in Hebei province, S3 was the major subtype and S1 was also existed. In a certain area, the HV which belonged to the same type was correspondingly conservative, and had the characteristic of regional stability.