Project description:H3N2 canine influenza virus (CIV) emerged in dogs in China or Korea around 2005 and was first reported in 2008. In 2015, H3N2 CIV was detected in the United States and caused a huge outbreak. To date, H3N2 CIV is continuously circulating in dog populations in China, Korea, and the United States. For continuous monitoring of H3N2 CIV in China, we collected 180 dog nasal swab samples and 196 cat nasal swabs from veterinary hospitals in Guangdong Province between 2018 and 2021. Six emerging H3N2 CIV strains were isolated. Following full genome sequencing and phylogenetic analyses, we found that A/canine/Guangdong/1-3/2018 and A/canine/Guangdong/1-3/2021 diverged from the reported sequences of the Chinese H3N2 CIV strains. Moreover, we found that these H3N2 CIV strains belong to the group that contains US and northern China CIV strains in 2017 and 2019 and dominate in the dog population until 2021.
Project description:BackgroundsThe coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a global threat since 2020. The emergence of the Omicron variant in 2021, which replaced Delta as the dominant variant of concern, has had a significant adverse impact on the global economy and public health. During this period, Zhejiang Province implemented dynamic zeroing and focused on preventing imported cases. This study aimed to gain clear insight into the characteristics of imported COVID-19 cases in Zhejiang Province.MethodsWe conducted a systematic molecular epidemiological analysis of 146 imported cases between July 2021 and November 2022 in Zhejiang Province. Virus samples with cycle threshold (Ct) value less than 32 were performed next generation sequencing. Basing the whole genome sequence obtained after quality control and assembly of reads, the whole genome variation map and phylogenetic tree were constructed and further analyzed.ResultsOur study identified critical months and populations for surveillance, profiled the variation of various lineages, determined the evolutionary relationships among various lineages of SARS-CoV-2, and compared the results in Zhejiang with those obtained worldwide during this period.ConclusionThe continuous molecular epidemiological surveillance of imported cases of COVID-19 in Zhejiang Province during 2021 to 2022 is consistent with the global epidemic trend.
Project description:Guangdong province, located in South China, is an important economic hub with a large domestic migrant population and was among the earliest areas to report COVID-19 cases outside of Wuhan. We conducted a cross-sectional, age-stratified serosurvey to determine the seroprevalence of antibodies against SARS-CoV-2 after the emergence of COVID-19 in Guangdong. We tested 14,629 residual serum samples that were submitted for clinical testing from 21 prefectures between March and June 2020 for SARS-CoV-2 antibodies using a magnetic particle based chemiluminescent enzyme immunoassay and validated the results using a pseudovirus neutralization assay. We found 21 samples positive for SARS-CoV-2 IgG, resulting in an estimated age- and sex-weighted seroprevalence of 0.15% (95% CI: 0.06-0.24%). The overall age-specific seroprevalence was 0.07% (95% CI: 0.01-0.24%) in persons up to 9 years old, 0.22% (95% CI: 0.03-0.79%) in persons aged 10-19, 0.16% (95% CI: 0.07-0.33%) in persons aged 20-39, 0.13% (95% CI: 0.03-0.33%) in persons aged 40-59 and 0.18% (95% CI: 0.07-0.40%) in persons ≥60 years old. Fourteen (67%) samples had pseudovirus neutralization titers to S-protein, suggesting most of the IgG-positive samples were true-positives. Seroprevalence of antibodies to SARS-CoV-2 was low, indicating that there were no hidden epidemics during this period. Vaccination is urgently needed to increase population immunity to SARS-CoV-2.
Project description:BackgroundIn Japan, a part of confirmed patients' samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics.MethodsThe number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution. An exponential growth model was fitted to the growth data of variant alpha cases over fourteen weeks in Tokyo.ResultsThe weekly incidence with variant alpha from 18-24 January 2021 was estimated at 4.2 (95% confidence interval (CI): 0.7, 44.0) cases. The expected incidence in early May ranged from 420-1120 cases per week, and the reproduction number of variant alpha was on the order of 1.5 even under the restriction of contact from January-March, 2021, Tokyo.ConclusionsThe variant alpha was predicted to swiftly dominate COVID-19 cases in Tokyo, and this has actually occurred by May 2021. Devising the proposed method, any country or location can interpret the virological sampling data.
Project description:IntroductionThe emergence of novel SARS-CoV-2 has caused a pandemic of Coronavirus Disease 19 (COVID-19) which has spread exponentially worldwide. A robust surveillance system is essential for correct estimation of the disease burden and containment of the pandemic. We evaluated the performance of COVID-19 case-based surveillance system in FCT, Nigeria and assessed its key attributes.MethodsWe used a cross-sectional study design, comprising a survey, key informant interview, record review and secondary data analysis. A self-administered, semi-structured questionnaire was administered to key stakeholders to assess the attributes and process of operation of the surveillance system using CDC's Updated Guidelines for Evaluation of Public Health Surveillance System 2001. Data collected alongside surveillance data from March 2020 to January 2021 were analyzed and summarized using descriptive statistics.ResultsOut of 69,338 suspected cases, 12,595 tested positive with RT-PCR with a positive predictive value (PPV) of 18%. Healthcare workers were identified as high-risk group with a prevalence of 23.5%. About 82% respondents perceived the system to be simple, 85.5% posited that the system was flexible and easily accommodates changes, 71.4% reported that the system was acceptable and expressed willingness to continue participation. Representativeness of the system was 93%, stability 40%, data quality 56.2% and timeliness 45.5%, estimated result turnaround time (TAT) was suboptimal.ConclusionThe system was found to be useful, simple, flexible, sensitive, acceptable, with good representativeness but the stability, data quality and timeliness was poor. The system meets initial surveillance objectives but rapid expansion of sample collection and testing sites, improvement of TAT, sustainable funding, improvement of electronic database, continuous provision of logistics, supplies and additional trainings are needed to address identified weaknesses, optimize the system performance and meet increasing need of case detection in the wake of rapidly spreading pandemic. More risk-group persons should be tested to improve surveillance effectiveness.