PlantMine: A Machine-Learning Framework to Detect Core SNPs in Rice Genomics.

As a fundamental global staple crop, rice plays a pivotal role in human nutrition and agricultural production systems. However, its complex genetic architecture and extensive trait variability pose challenges for breeders and researchers in optimizing yield and quality. Particularly to expedite breeding methods like genomic selection, isolating core SNPs related to target traits from genome-wide data reduces irrelevant mutation noise, enhancing computational precision and efficiency. Thus, exploring efficient computational approaches to mine core SNPs is of great importance. This study introduces PlantMine, an innovative computational framework that integrates feature selection and machine learning techniques to effectively identify core SNPs critical for the improvement of rice traits. Utilizing the dataset from the 3000 Rice Genomes Project, we applied different algorithms for analysis. The findings underscore the effectiveness of combining feature selection with machine learning in accurately identifying core SNPs, offering a promising avenue to expedite rice breeding efforts and improve crop productivity and resilience to stress.

Inactivated SARS-CoV-2 Vaccine Booster Against Omicron Infection Among Quarantined Close Contacts.

Importance: Assessment of additional protection of a booster dose with an inactivated SARS-CoV-2 vaccine is key to developing vaccination strategies for billions of people worldwide who have received the primary 2-dose regimen. Objective: To estimate the relative effectiveness of a booster dose of an inactivated SARS-CoV-2 vaccine against Omicron infection. Design, Setting, and Participants: This cohort study was conducted among primary close contacts without previous SARS-CoV-2 infection identified in Shenzhen, China, between February and October 2022. Multiple strict nucleic acid testing and symptom surveillance for SARS-CoV-2 infection were regularly conducted during the 7-day centralized plus 7-day home-based quarantine. Exposure: A booster with an inactivated SARS-CoV-2 vaccine vs no booster after receipt of the primary 2-dose inactivated SARS-CoV-2 vaccine regimen. Main Outcomes and Measures: The primary outcomes were overall, symptomatic, and asymptomatic infections. Secondary outcomes were length of incubation and level of cycle threshold values. All the outcomes were assessed during the quarantine period. Results: Among 119 438 eligible participants (mean [SD] age, 37.6 [12.0] years; 66 201 men [55.4%]), 86 251 (72.2%) received a booster dose of an inactivated SARS-CoV-2 vaccine and 33 187 (27.8%) did not. A total of 671 cases infected with Omicron BA.2 were confirmed (464 symptomatic and 207 asymptomatic), and no severe infection or death events were observed. At a median (IQR) duration of 111 (75 to 134) days after booster vaccination, the relative effectiveness of a booster was 32.2% (95% CI, 11.3% to 48.2%) for overall infection, 23.8% (95% CI, -8.2% to 46.4%) for symptomatic infection, and 43.3% (95% CI, 12.3% to 63.3%) for asymptomatic infection. The effectiveness against overall infection changed nonlinearly over time following booster vaccination: 44.9% (95% CI, 4.9% to 68.1%) within 60 days, 50.4% (95% CI, 23.7% to 67.7%) at 61 to 120 days, 29.1% (95% CI, -4.8% to 52.1%) at 121 to 180 days, and 19.4% (95% CI, -14.4% to 43.2%) after 180 days (nonlinear P = .03). The effectiveness did not vary significantly according to the interval between booster vaccination and completion of primary vaccination. There was no association of booster vaccination with incubation or cycle threshold values. Conclusions and Relevance: In this cohort study, a booster dose of an inactivated SARS-CoV-2 vaccine provided additional moderate protection against mild infection for 120 days after receipt, but more research is needed to determine the optimal timing of a booster and its effectiveness in preventing severe infection for a longer duration.

Transmission characteristics and inactivated vaccine effectiveness against transmission of the SARS-CoV-2 Omicron BA.2 variant in Shenzhen, China.

We conducted a retrospective cohort study to evaluate the transmission risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 variant and the effectiveness of inactivated COVID-19 vaccine boosters in Shenzhen during a BA.2 outbreak period from 1 February to 21 April 2022. A total of 1,248 individuals were infected with the BA.2 variant, and 7,855 close contacts were carefully investigated. The risk factors for the high secondary attack rate of SARS-CoV-2 infection were household contacts [adjusted odds ratio (aOR): 1.748; 95% confidence interval (CI): 1.448, 2.110], younger individuals aged 0-17 years (aOR: 2.730; 95% CI: 2.118, 3.518), older persons aged ≥60 years (aOR: 1.342; 95% CI: 1.135, 1.588), women (aOR: 1.442; 95% CI: 1.210, 1.718), and the subjects exposed to the post-onset index cases (aOR: 8.546; 95% CI: 6.610, 11.050), respectively. Compared with the unvaccinated and partially vaccinated individuals, a relatively low risk of secondary attack was found for the individuals who received booster vaccination (aOR: 0.871; 95% CI: 0.761, 0.997). Moreover, a high transmission risk was found for the index cases aged ≥60 years (aOR: 1.359; 95% CI: 1.132, 1.632), whereas a relatively low transmission risk was observed for the index cases who received full vaccination (aOR: 0.642; 95% CI: 0.490, 0.841) and booster vaccination (aOR: 0.676; 95% CI: 0.594, 0.770). Compared with full vaccination, booster vaccination of inactivated COVID-19 vaccine showed an effectiveness of 24.0% (95% CI: 7.0%, 37.9%) against BA.2 transmission for the adults ≥18 years and 93.7% (95% CI: 72.4%, 98.6%) for the adults ≥60 years, whereas the effectiveness was 51.0% (95% CI: 21.9%, 69.3%) for the individuals of 14 days to 179 days after booster vaccination and 51.2% (95% CI: 37.5%, 61.9%) for the non-household contacts. The estimated mean values of the generation interval, serial interval, incubation period, latent period, and viral shedding period were 2.7 days, 3.2 days, 2.4 days, 2.1 days, and 17.9 days, respectively. In summary, our results confirmed that the main transmission route of Omicron BA.2 subvariant was household contact, and booster vaccination of the inactivated vaccines was relatively effective against BA.2 subvariant transmission in older people.

Acute effects of particulate matter with different sizes on respiratory mortality in Shenzhen, China.

There are relatively few studies that focus on the health effects of exposure to size-specific particles on respiratory mortality in China. We aimed to examine the association between different particle sizes and mortality from cause-specific respiratory diseases. We used a time series model with a quasi-Poisson link to investigate the relationship between different particle sizes and mortality from respiratory diseases, chronic obstructive pulmonary diseases (COPD), pneumonia, and asthma in Shenzhen during 2014-2017. A total of 3716 mortalities due to respiratory diseases were collected. Both PM1 and PM2.5 were associated with mortality of overall respiratory diseases, COPD, and pneumonia. An interquartile range (IQR) increase in PM1 at lag03 was associated with a 12.21% (95% CI: 2.59%, 22.75%) increase in respiratory mortality, and each IQR increase in PM2.5 at lag03 corresponded to a 12.09% (95% CI: 2.52%, 22.56%) increase in respiratory mortality. PM1-2.5 was not associated with mortality from all-cause or cause-specific respiratory diseases. This study suggests that both PM1 and PM2.5 may increase the risk of mortality due to respiratory diseases in Shenzhen, China.

Early warning of hand, foot, and mouth disease transmission: A modeling study in mainland, China.

BACKGROUND: Hand, foot, and mouth disease (HFMD) is a global infectious disease; particularly, it has a high disease burden in China. This study was aimed to explore the temporal and spatial distribution of the disease by analyzing its epidemiological characteristics, and to calculate the early warning signals of HFMD by using a logistic differential equation (LDE) model. METHODS: This study included datasets of HFMD cases reported in seven regions in Mainland China. The early warning time (week) was calculated using the LDE model with the key parameters estimated by fitting with the data. Two key time points, "epidemic acceleration week (EAW)" and "recommended warning week (RWW)", were calculated to show the early warning time. RESULTS: The mean annual incidence of HFMD cases per 100,000 per year was 218, 360, 223, 124, and 359 in Hunan Province, Shenzhen City, Xiamen City, Chuxiong Prefecture, Yunxiao County across the southern regions, respectively and 60 and 34 in Jilin Province and Longde County across the northern regions, respectively. The LDE model fitted well with the reported data (R2 > 0.65, P < 0.001). Distinct temporal patterns were found across geographical regions: two early warning signals emerged in spring and autumn every year across southern regions while one early warning signals in summer every year across northern regions. CONCLUSIONS: The disease burden of HFMD in China is still high, with more cases occurring in the southern regions. The early warning of HFMD across the seven regions is heterogeneous. In the northern regions, it has a high incidence during summer and peaks in June every year; in the southern regions, it has two waves every year with the first wave during spring spreading faster than the second wave during autumn. Our findings can help predict and prepare for active periods of HFMD.

Effects of breeds and dietary nutrient levels on expression patterns of paired box genes and myogenic regulatory factors in pigs.

Two experiments were conducted to investigate the effects of different breeds and dietary nutrient levels on expressions of paired box (Pax) genes and myogenic regulatory factors (MRFs) in pigs. Thirty Large White (LW) barrows and thirty Chenghua (CH, a native breed of China) barrows were performed in experiment 1. Results exhibited that in the CH pigs the abundances of Pax3 at 105 and 220 d of age, Mrf4 at 63 d of age, Myf5 and Mrf4 at 220 d of age were higher than those in the LW pigs (p < 0.05). Meanwhile, the expressions of MyHC-І and ІІa in the CH pigs were upregulated, and the abundance of MyHC-ІІb were downregulated compared with those in the LW pigs at 105 and 220 d of age (p < 0.05). Moreover, the meat quality of the CH pigs was better than in the LW pigs (p < 0.05). In experiment 2, sixty LW pigs were randomly assigned to two dietary treatments meeting their nutrient requirements (NRC) or a diet with moderately reduced digestible energy, crude protein and Lys level by 560 kJ/kg, 1.48% and 0.34%, respectively (LOW diet). The results showed that the reduced dietary nutrient level increased (p < 0.05) the expressions of MyoG and Mrf4 at 105 d of age, Pax3, Myf5, and Mrf4 at 220 d of age, and upregulated (p < 0.05) the abundance of MyHC-ІІa at 105 and 220 d of age in LW pigs. In addition, a decrease in dietary nutrient level improved the meat quality in LW pigs (p < 0.05). Collectively, the expressions of Pax genes and MRFs were markedly different between the CH and LW pigs. The CH pigs exhibited higher expression levels of Pax3, Myf5, Mrf4, MyHC-І and ІІa, which may improved the meat quality. A decrease in dietary nutrient level upregulated the abundances Pax3, Mrf4, Myf5, MyoG, and MyHC-ІІa, and might enhance the meat quality in the LW pigs.

Relative transmissibility of hand, foot and mouth disease from male to female individuals.

Hand, foot and mouth disease (HFMD) has spread widely and leads to high disease burden in many countries. However, relative transmissibility from male to female individuals remains unclear. HFMD surveillance database was built in Shenzhen City from 2013 to 2017. An intersex transmission susceptible-infectious-recovered model was developed to calculate the transmission relative rate among male individuals, among female individuals, from male to female and from female to male. Two indicators, ratio of transmission relative rate (Rß) and relative transmissibility index (RTI), were developed to assess the relative transmissibility of male vs. female. During the study period, 270 347 HFMD cases were reported in the city, among which 16 were death cases with a fatality of 0.0059%. Reported incidence of total cases, male cases and female cases was 0.0057 (range: 0.0036-0.0058), 0.0052 (range: 0.0032-0.0053) and 0.0044 (range: 0.0026-0.0047), respectively. The difference was statistically significant between male and female (t = 3.046, P = 0.002). Rß of male vs. female, female vs. female, from female to male vs. female and from male to female vs. female was 7.69, 1.00, 1.74 and 7.13, respectively. RTI of male vs. female, female vs. female, from female to male vs. female and from male to female vs. female was 3.08, 1.00, 1.88 and 1.43, respectively. Transmissibility of HFMD is different between male and female individuals. Male cases seem to be more transmissible than female.

Association between Airborne Fine Particulate Matter and Residents' Cardiovascular Diseases, Ischemic Heart Disease and Cerebral Vascular Disease Mortality in Areas with Lighter Air Pollution in China.

BACKGROUND: China began to carry out fine particulate matter (PM2.5) monitoring in 2013 and the amount of related research is low, especially in areas with lighter air pollution. This study aims to explore the association between PM2.5 and cardiovascular disease (CVD), ischemic heart disease (IHD) and cerebral vascular disease (EVD) mortality in areas with lighter air pollution. METHODS: Data on resident mortality, air pollution and meteorology in Shenzhen during 2013⁻2015 were collected and analyzed using semi-parametric generalized additive models (GAM) with Poisson distribution of time series analysis. RESULTS: Six pollutants were measured at seven air quality monitoring sites, including PM2.5, PM10, SO2, NO2, CO and O3. The PM2.5 daily average concentration was 35.0 ± 21.9 µg/m³; the daily average concentration range was from 7.1 µg/m³ to 137.1 µg/m³. PM2.5 concentration had significant effects on CVD, IHD and EVD mortality. While PM2.5 concentration of lag5 and lag02 rose by 10 µg/m³, the excess risk (ER) of CVD mortality were 1.50% (95% CI: 0.51⁻2.50%) and 2.09% (95% CI: 0.79⁻3.41%), respectively. While PM2.5 concentration of lag2 and lag02 rose by 10 µg/m³, the ER of IHD mortality were 2.87% (95% CI: 0.71⁻5.07%) and 3.86% (95% CI: 1.17⁻6.63%), respectively. While PM2.5 concentration of lag4 and lag04 rose by 10 µg/m³, the ER of EVD mortality were 2.09% (95% CI: 2.28⁻3.92%) and 3.08% (95% CI: 0.68⁻5.53%), respectively. CONCLUSIONS: PM2.5 increased CVD mortality. The government needs to strengthen the governance of air pollution in areas with a slight pollution.

Short-term effects of meteorological factors on hand, foot and mouth disease among children in Shenzhen, China: Non-linearity, threshold and interaction.

BACKGROUND: Various meteorological factors have been associated with hand, foot and mouth disease (HFMD) among children; however, fewer studies have examined the non-linearity and interaction among the meteorological factors. METHODS: A generalized additive model with a log link allowing Poisson auto-regression and over-dispersion was applied to investigate the short-term effects daily meteorological factors on children HFMD with adjustment of potential confounding factors. RESULTS: We found positive effects of mean temperature and wind speed, the excess relative risk (ERR) was 2.75% (95% CI: 1.98%, 3.53%) for one degree increase in daily mean temperature on lag day 6, and 3.93% (95% CI: 2.16% to 5.73%) for 1m/s increase in wind speed on lag day 3. We found a non-linear effect of relative humidity with thresholds with the low threshold at 45% and high threshold at 85%, within which there was positive effect, the ERR was 1.06% (95% CI: 0.85% to 1.27%) for 1 percent increase in relative humidity on lag day 5. No significant effect was observed for rainfall and sunshine duration. For the interactive effects, we found a weak additive interaction between mean temperature and relative humidity, and slightly antagonistic interaction between mean temperature and wind speed, and between relative humidity and wind speed in the additive models, but the interactions were not statistically significant. CONCLUSIONS: This study suggests that mean temperature, relative humidity and wind speed might be risk factors of children HFMD in Shenzhen, and the interaction analysis indicates that these meteorological factors might have played their roles individually.

Risk Factors for Vibrio parahaemolyticus Infection in a Southern Coastal Region of China.

OBJECTIVES: The objectives of the study were to identify dietary and medical risk factors for Vibrio parahaemolyticus (VP) infection in the coastal city Shenzhen in China. METHODS: In April-October 2012, we conducted a case-control study in two hospitals in Shenzhen, China. Laboratory-confirmed VP cases (N = 83) were matched on age, sex, and other social factors to healthy controls (N = 249). Subjects were interviewed using a questionnaire on medical history; contact with seawater; clinical symptoms and outcome; travel history over the past week; and dietary history 3 days prior to onset. Laboratory tests were used to culture, serotype, and genotype VP strains. We used logistic regression to calculate the odds ratios for the association of VP infection with potential risk factors. RESULTS: In multivariate analysis, VP infection was associated with having pre-existing chronic disease (adjusted odds ratio [aOR], 6.0; 95% confidence interval [CI], 1.5-23.7), eating undercooked seafood (aOR, 8.0; 95% CI, 1.3-50.4), eating undercooked meat (aOR, 29.1; 95% CI, 3.0-278.2), eating food from a street food vendor (aOR, 7.6; 95% CI, 3.3-17.6), and eating vegetable salad (aOR, 12.1; 95% CI, 5.2-28.2). CONCLUSIONS: Eating raw (undercooked) seafood and meat is an important source of VP infection among the study population. Cross-contamination of VP in other food (e.g., vegetables and undercooked meat) likely plays a more important role. Intervention should be taken to lower the risks of cross-contamination with undercooked seafood/meat, especially targeted at people with low income, transient workers, and people with medical risk factors.

Comparison of genomic and amino acid sequences of eight Japanese encephalitis virus isolates from bats.

We compared nucleotide and deduced amino acid sequences of eight Japanese encephalitis virus (JEV) isolates derived from bats in China. We also compared the bat JEV isolates with other JEV isolates available from GenBank to determine their genetic similarity. We found a high genetic homogeneity among the bat JEVs isolated in different geographical areas from various bat species at different time periods. All eight bat JEV isolates belonged to genotype III. The mean evolutionary rate of bat JEV isolates was lower than those of isolates of other origin, but this difference was not statistically significant. Based on these results, we presume that the bat JEV isolates might be evolutionarily conserved. The eight bat JEV isolates were phylogenetically similar to mosquito BN19 and human Liyujie isolates of JEV. These results indicate that bats might be involved in natural cycle of JEV.

[Genetic evolution of VP1 of enterovirus type 71 in Shenzhen].

OBJECTIVE: Genetic evolution of VP1 of enterovirus type 71 in Shenzhen were analyzed. METHODS: All samples were tested by RT-PCR using EV71 specific primer. The VP1 of EV71 were amplified and sequenced. A phylogenetic tree was constructed by comparison of the sequences with subgenotype A, B and C using DNAStar, BioEdit and Mega 3.1 software. RESULTS: Among 35 strains, the homogeneity of the VP1 nucleotide sequence was between 92.1%-100%. The homogeneity of the VP1 nucleotide sequence with subgenotype A and B was between 81.4% -91.1%. The VP1 nucleotide sequence of 35 strains of Shenzhen shared between 93% -97.4% identity with cluster C4. The prevalence strains of EV71 were cluster C4b from 1998 to 2004, and gradually moved to C4a since 2003. All of EV71 were C4b from 2006 to 2008. Also, the homogeneity of the VP1 nucleotide sequence with Anhui FY23 EV71 strain were 94.5% -94.7%, 95.7% -95.8%, 96.2%, 95.4% -97.5%, 96.3% -99.2% from 2003 to 2008. It shows that the homogeneity was increased year by year. There was a mutation (A --> C) at No. 66 nucleotide of VP1 of EV71 that two strains were isolated in 2003 and 8 strains in 2008, that caused amino acid mutation (Q --> H) at No. 22 of VP1. CONCLUSION: EV71 C4b was gradually moved to C4a from 1998 to 2008. There was a missense mutation at No. 66 nucleotide of VP1.

[Detection and genotype analysis of sapovirus associated with sporadic diarrhea in Shenzhen in 2009].

OBJECTIVE: To conduct an epidemiological and genotype analysis of sapovirus (SaV) associated with sporadic diarrhea in Shenzhen in the year 2009. METHODS: A total of 852 fecal samples were collected from sporadic cases of diarrhea in Shenzhen in 2009 and detected by reverse-transcription polymerase chain reaction (RT-PCR) using the primers of SLV5317/5749. The PCR products were analyzed with 1.5% agarose gel electrophoresis and sequenced to construct the phylogenetic tree. RESULTS: Sixteen samples were found positive for SaV, with a positivity rate of 1.88%. Sequence analysis identified 8 isolates as SaV GI genotype (including 3 SaV GI.1 and 5 SaV GI.2), 7 as SaV GIV genotype, and 1 as GII genotype. CONCLUSIONS: SaV infection is present in Shenzhen with GI as the predominant genotype. This is the first report of SaV GIV strains in China, which differs from the strains of Anhui-A141 and Beijing-CHN99/BJ360, suggesting the genotypic variety of SaV infection in China.

Isolation and phylogenetic characterization of bat astroviruses in southern China.

Astroviruses are associated with acute gastroenteritis of human and many animal species. Recently, two studies have reported that novel astroviruses were found in bats. In order to extensively understand the genetic and phylogenetic characterization of bat astroviruses, we tested fecal samples of nine bat species that were collected at four natural habitats in three areas of southern China. The geographic distributions of the bats involved differed from previous reports. Three out of nine species of bats were observed to harbor astroviruses. These included Miniopterus schreibersii, Scotophilus kuhlii, and Rousettus leschenaultia. Phylogenetic analysis based on amino acid sequences of partial ORFs of astroviruses revealed that the bat astroviruses are not only divergent from previously described human and other animal astroviruses but also show remarkable diversity among themselves. However, five bat astroviruses were phylogenetically related to mink astrovirus, ovine astrovirus, and the recently discovered human astroviruses VA1, VA2, and VA3. The results indicate that astroviruses may have adapted to the Chiroptera, and bats may transmit astroviruses to humans and other animals, or vice versa.

Molecular phylogeny of Coxsackievirus A16 in Shenzhen, China, from 2005 to 2009.

Phylogenetic analysis of a Coxsackievirus A16 (CA16) sequence from Shenzhen, China, and other Chinese and international CA16 sequences revealed a pattern of endemic cocirculation of strains of clusters B2a and B2b within subtype B2 viruses. Amino acid evolution and nucleotide variation in the VP1 region were slight for 5 years.

Comparison of reverse transcription loop-mediated isothermal amplification, conventional PCR and real-time PCR assays for Japanese encephalitis virus.

We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Japanese encephalitis virus (JEV). The sensitivity of the JEV RT-LAMP assay was in concordance with that of real-time RT-PCR and 10-fold more sensitive than that of conventional RT-PCR, which the detection limit was 24 copies/µl. The JEV RT-LAMP was highly specific, which no cross-reactivity was found with dengue-2 virus, rabies virus, norovirus, astrovirus and human enterovirus 71. The JEV RT-LAMP assay was more simple and less time-consuming compared to the conventional RT-PCR and real-time RT-PCR, which the amplification could be completed in a single tube within 1 h under isothermal conditions at temperature of 63°C. The results suggest that the RT-LAMP assay can be applied as a practical molecular diagnostic tool for JEV infection and surveillance.

[Development of a SPA-ELISA method for detecting anti-coronavirus IgG antibodies in serum samples from fulvous fruit bats].

OBJECTIVE: To develop an simple and sensitive method for detecting anti-coronavirus IgG antibodies in bat sera based on enzyme-linked immunosorbent assay (ELISA). METHODS: A commercial ELISA kit for detecting SARS-CoV antibody was modified for detecting coronavirus antibodies in bat serum samples. The second antibody in the kit was replaced with horseradish peroxidase-conjugated protein-A (HRP-SPA) based on the characteristics of binding between Staphylococcus aureus protein A (SPA) and mammal IgG Fc fragment. The sera of 55 fulvous fruit bats (Rousettus dasymallus) were tested using the SPA-ELISA. RESULTS: The test results of the positive and negative controls in the kit and the serum samples from convalescent ;patient were consistent with expectation. Coronavirus antibody was detected in 2 out of the 55 bat serum samples. Serum neutralization test confirmed the validity of the SPA-ELISA method. CONCLUSION: This SPA-ELISA method is applicable for detecting coronavirus antibody in bat sera.