Using an Eigenvector Spatial Filtering-Based Spatially Varying Coefficient Model to Analyze the Spatial Heterogeneity of COVID-19 and Its Influencing Factors in Mainland China

The COVID-19 pandemic has led to many deaths and economic disruptions across the world. Several studies have examined the effect of corresponding health risk factors in different places, but the problem of spatial heterogeneity has not been adequately addressed. The purpose of this paper was to explore how selected health risk factors are related to the pandemic infection rate within different study extents and to reveal the spatial varying characteristics of certain health risk factors. An eigenvector spatial filtering-based spatially varying coefficient model (ESF-SVC) was developed to find out how the influence of selected health risk factors varies across space and time. The ESF-SVC was able to take good control of over-fitting problems compared with ordinary least square (OLS), eigenvector spatial filtering (ESF) and geographically weighted regression (GWR) models, with a higher adjusted R2 and lower cross validation RMSE. The impact of health risk factors varied as the study extent changed: In Hubei province, only population density and wind speed showed significant spatially constant impact; while in mainland China, other factors including migration score, building density, temperature and altitude showed significant spatially varying impact. The influence of migration score was less contributive and less significant in cities around Wuhan than cities further away, while altitude showed a stronger contribution to the decrease of infection rates in high altitude cities. The temperature showed mixed correlation as time passed, with positive and negative coefficients at 2.42 °C and 8.17 °C, respectively. This study could provide a feasible path to improve the model fit by considering the problem of spatial autocorrelation and heterogeneity that exists in COVID-19 modeling. The yielding ESF-SVC coefficients could also provide an intuitive method for discovering the different impacts of influencing factors across space in large study areas. It is hoped that these findings improve public and governmental awareness of potential health risks and therefore influence epidemic control strategies.

Consensus on Quality Indicators for Pediatric Oncology Nursing Care in Mainland China: A Delphi Method and Analytic Hierarchy Process

Background: Because routine nursing quality indicators are not suitable to evaluate pediatric oncology nursing care, this study aimed to identify a set of quality indicators for pediatric oncology nursing care in mainland China. Method: This prospective investigation utilized a modified Delphi technique and an analytic hierarchy process. A survey questionnaire was developed using a literature review and semi-structured interviews. Fifteen invited experts evaluated the importance of potential indicators through three rounds of Delphi survey by email in 2018. The importance weight of each indicator was identified through analytic hierarchy process. Results: In the Delphi survey, the average authoritative coefficient was 0.93–0.96 for each round of the inquiry. After three rounds of survey, 29 quality indicators were identified as important nursing outcomes for assessing the quality of pediatric oncology nursing care in mainland China. The importance rating mean score of indicators ranged between 4.67–5.00 on a 5-point scale, and the variation coefficient ranged between 0–0.19. Expert-assigned indicator importance weight varied between 0.0040–0.0870. Conclusion: This study identified an indicator system with 29 nursing-sensitive quality indicators that may represent potential indicator candidates for quality assessment of pediatric oncology nursing practice in mainland China.

Spatiotemporal Cluster Patterns of Hand, Foot, and Mouth Disease at the Province level in Mainland China, 2009-2018

BackgroundAlthough three monovalent EV-A71 vaccines have been launched in mainland China since 2016, hand, foot, and mouth disease (HFMD) still causes a considerable disease burden in China. Vaccines’ use may change the epidemiological characters of HFMD. This study aims to analyze the spatiotemporal cluster of HFMD at the province level in mainland China from 2009 to 2018 and compare the difference before and after the vaccines were launched. MethodsAll HFMD cases’ data from January 2009 to December 2018 were obtained from the public health science data center given by the Chinese Center for Diseases Control and Prevention. Spatial autocorrelation analysis and space-time scan statistics analysis were used to explore the spatiotemporal distribution pattern of this disease at the provincial level in mainland China. ResultsThe median annual incidence of HFMD was 143.22 per 100,000 (ranging from 87.01 to 205.06) in mainland China from 2009 to 2018. Two peaks of infections were observed per year. Children 5 years and under were the main morbid population. The global autocorrelation analysis showed that the spatial distribution of HFMD was presented a significant clustering pattern in each year (P<0.001), and the local autocorrelation analysis indicated that the high incidence areas were clustered in the southern and southeastern coastal provinces. The distribution of HFMD cases was clustered in time and space. The range of cluster time was between April and October. The most likely cluster appeared in the southern coastal provinces (Guangxi, Guangdong, Hainan) from 2010 to 2017 and in the southeastern coastal provinces (Shanghai, Jiangsu, Zhejiang) in 2018. ConclusionChanges in the spatiotemporal cluster of HFMD after the launch of EV-A71 vaccines were observed at the province level in mainland China in 2018. It is necessary to advance the EV-A71 vaccination plan, analyze the spatial-temporal distribution characteristics of different enterovirus pathogens of HFMD, and promote HFMD multivalent vaccines.

Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.

A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China

Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.

Current Dependent Dispersal Characteristics of Japanese Glass Eel around Taiwan

Japanese eel larvae are passively transported to the East Asian Continental Shelf by the North Equatorial Current, Kuroshio and Kuroshio intrusion currents, and coastal currents. Previous studies have investigated the dispersal characteristics and pathways of Japanese glass eels. However, there are still limitations in these studies. According to long-term (2010–2020) catch data from the Fisheries Agency in Taiwan, the distribution and time series of glass eels recruitment to Taiwan are closely related to the surrounding ocean currents. Recruitment begins in eastern Taiwan via the mainstream Kuroshio and in southern Taiwan via the Taiwan Strait Warm Current. In central Taiwan, recruitment occurs from southern Taiwan, as well as from mainland China via the southern branch of the China Coast Current (CCC). The latest recruitment occurred in northern Taiwan and mainly comprised glass eels from mainland China via the northern branch of the CCC. A stronger monsoon during the La Niña phase could affect the recruitment time series in northern and eastern Taiwan. This study suggests that the recruitment directionality of glass eels is an indicator of the flow field of ocean/coastal currents and elucidates the dispersal characteristics of glass eels in the waters around Taiwan.

Development and Clinical Validation of a Potential Penside Colorimetric Loop-Mediated Isothermal Amplification Assay of Porcine Circovirus Type 3

Porcine circovirus type 3 (PCV3), a novel circovirus, imposes great burdens on the global pig industry. The penside tests for detecting PCV3 are critical for assessing the epidemiological status and working out disease prevention and control programs due to the unavailability of a commercial vaccine. A one-step molecular assay based on visual loop-mediated isothermal amplification (vLAMP) was developed for simple and rapid detection of PCV3. We compared its sensitivity and specificity with TaqMan quantitative real-time polymerase chain reaction (qPCR) and applied the developed assay in the epidemiological study of (n = 407) pooled swine sera collected from almost the entire mainland China during the years 2017–2018. We also explored the feasibility of the vLAMP assay for detecting raw samples without a prior DNA isolation step to expand its application capability. Results showed that the vLAMP assay could reliably detect the PCV3 cap gene with a detection limit of 10 DNA copies equal to that of the Taqman qPCR assay. In the epidemiological study, the PCV3 positive detection rate for 407 swine pooled sera detected by the vLAMP assay was 37.35% (152/407), whereas it was 39.01% (159/407) for Taqman qPCR. For the detection method without genome extraction, the results kept satisfactory specificity (100%) but displayed lower sensitivity (100% for CT &lt; 32), indicating the direct detection is not sensitive enough to discriminate the samples with low viral loads. The one-step vLAMP is a convenient, rapid, and cost-effective diagnostic for penside detection and will enable the epidemiological surveillance of PCV3, which has widely spread in mainland China.