Disseminated intravascular coagulation is associated with poor prognosis in patients with COVID-19.

This study aimed to investigate the incidence and significance of disseminated intravascular coagulation (DIC) in coronavirus disease 2019 (COVID-19). A multicenter cohort study was conducted using large-scale COVID-19 registry data. The patients were classified into DIC and non-DIC groups based on the diagnosis on admission (day 1) and on any of the days 1, 4, 8, and 15. In total, 23,054 patients were divided into DIC (n = 264) and non-DIC (n = 22,790) groups on admission. Thereafter, 1654 patients were divided into 181 patients with DIC and 1473 non-DIC patients based on the DIC diagnosis on any of the days from 1 to 15. DIC incidence was 1.1% on admission, increasing to 10.9% by day 15. DIC diagnosis on admission had moderate predictive performance for developing multiple organ dysfunction syndrome (MODS) on day 4 and in-hospital death and was independently associated with MODS and in-hospital death. DIC diagnosis on any of the days from 1 to 15, especially days 8 and 15, was associated with lower survival probability than those without DIC and showed significant association with in-hospital death. In conclusion, despite its low incidence, DIC, particularly late-onset DIC, plays a significant role in the pathogenesis of poor prognosis in patients with COVID-19.

Steroid initiation timing and outcome of coronavirus disease 2019 patients: A multicenter, retrospective, observational study.

Objectives: Dexamethasone's (DEXA) beneficial effect on survival when administered to critically ill patients with coronavirus disease 2019 (COVID-19) has been documented in randomized trials and meta-analyses. Here, we conducted this study to clarify the association between time from COVID-19 onset to steroid initiation and mortality and to examine the factors underlying these results.Methods: This was a multicenter, retrospective, observational study of patients enrolled in the Japanese COVID-19 Registry from January 1, 2020, to April 30, 2021. Demographic and clinical factors were extracted from patient records. Patients diagnosed with COVID-19 using polymerase chain reaction, loop-mediated isothermal amplification, or antigen tests were included. Patients aged <18 years, pregnant, with a history of chronic obstructive pulmonary disease or steroid or immunosuppressive drug use, transferred to another hospital, or with an unknown symptom onset were excluded.Results and Conclusion: The analysis included 3692 patients (men, 64.1%; median age, 68 years). Unadjusted comparisons of mortality groups showed significant differences in demographic and clinical characteristics; patients with early dexamethasone initiation had more risk factors for severe disease and significantly higher mortality than did patients with delayed initiation (13.3% vs 7.9%, p < .001). No significant differences were found in intubation rates or duration, length of hospitalization, or time from intubation to death. Multivariate analyses showed significant differences from symptom onset to steroid administration, with an adjusted odds ratio of 0.7 (p = .05) for patients who received steroids for ≥8 days. Early steroid administration to COVID-19 patients was associated with increased mortality, suggesting a subset with early severe disease and high mortality and/or adverse effects of early steroid administration.

Clinical efficacy of remdesivir for COVID-19 in children: A propensity-score-matched analysis.

Clinical efficacy of remdesivir in children with COVID-19 is unclear. This propensity-score-matched retrospective cohort study of children with COVID-19 showed that the rate of patients achieving defervescence on Day 4 was higher in the remdesivir group than in the non-remdesivir group, but was not statistically different (86.7% vs 73.3%, P = 0.333).

A systematic review regarding clinical characteristics, complications, and outcomes of surgical and non-surgical patients with fragility fracture of the pelvis.

We conducted this systematic review to clarify the clinical characteristics, complications, and outcomes of surgical and non-surgical patients with fragility fracture of the pelvis (FFP). We searched PubMed, Google Scholar, Cochrane Library, Web of Science, and MEDLINE for English language articles on FFP. We calculated pooled odds ratios (ORs) or mean differences (MDs) of surgical patients in comparison to non-surgical patients for clinical characteristics (Rommens FFP classification, age, sex, dementia, osteoporosis, diabetes mellitus, pulmonary disease, cardiovascular disease, and malignancy), complications (pneumonia, urinary tract infection, cardiac event, thrombosis, pulmonary embolism, pressure ulcer, multiple organ failure, anemia caused by surgical bleeding, and surgical site infection), and outcomes (hospital mortality and one-year mortality). Five studies involving 1,090 patients with FFP (surgical patients, n = 432; non-surgical patients, n = 658) were included. FFP type III and IV (OR = 8.44; 95% confidence interval [CI] 5.99 to 11.88; p<0.00001), a younger age (MD = -3.29; 95% CI -3.83 to -2.75; p<0.00001), the absence of dementia (OR = 0.36; 95% CI 0.23 to 0.57; p<0.0001), and the presence of osteoporosis (OR = 1.74; 95% CI 1.29 to 2.35; p = 0.0003) were significantly associated with the surgical patients. Urinary tract infection (OR = 2.06; 95% CI 1.37 to 3.10; p = 0.0005), anemia caused by surgical bleeding (OR = 4.55; 95% CI 1.95 to 10.62; p = 0.0005), and surgical site infection (OR = 16.74; 95% CI 3.05 to 91.87; p = 0.001) were significantly associated with the surgical patients. There were no significant differences in the outcomes between the surgical and non-surgical patients. Our findings may help to further understand the treatment strategy for FFP and improve clinical outcomes.

Predictors of preoperative deep vein thrombosis in hip fractures: A systematic review and meta-analysis.

BACKGROUND: The predictors of preoperative deep vein thrombosis (DVT) in patients with hip fractures remain unclear. Therefore, this study describes the results of a systematic review and meta-analysis of relevant peer-reviewed literature on this topic. METHODS: We searched PubMed, Google Scholar, Cochrane Library, Web of Science, and MEDLINE for articles published in English on the predictors of preoperative DVT in hip fractures. We calculated pooled odds ratios (OR) or mean differences (MD) for the DVT groups as compared with the non-DVT groups for each variable, including gender, age, body mass index, injury side, current smoking status, time from injury to admission, time from injury to surgery, fracture type, hypertension, arrhythmia, coronary artery disease, diabetes, stroke, kidney disease, liver disease, lung disease, malignancy, rheumatoid arthritis, D-dimer, fibrinogen, activated partial thromboplastin time, prothrombin time, thrombin time, hemoglobin, albumin, total cholesterol, and triglycerides. RESULTS: We included 9 studies involving 3,123 Asian patients with hip fractures (DVT, n = 570; non-DVT, n = 2,553). Being female (OR = 1.27; 95% confidence interval [CI] 1.04-1.56; p = 0.02), being of advanced age (MD = 1.63; 95% CI 0.80-2.47; p = 0.0001), having a longer time from injury to admission (MD = 0.80; 95% CI 0.48-1.12; p < 0.00001), having a longer time from injury to surgery (MD = 2.20; 95% CI 1.53-2.88; p < 0.00001), and the presence of kidney disease (OR = 1.76; 95% CI 1.04-2.96; p = 0.03) were correlated with a high risk of DVT. However, we found no significant differences between the two groups in the other predictors. CONCLUSIONS: Evidence indicates that being female, being of advanced age, having a longer time from injury to admission, having a longer time from injury to surgery, and having kidney disease are significantly correlated with a high risk of preoperative DVT in Asian patients with hip fracture. Further investigations with patients of other ethnicities are required.

Comparison of clinical characteristics of COVID-19 in pregnant women between the Delta and Omicron variants of concern predominant periods.

BACKGROUND: Information regarding effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains on clinical manifestations and outcomes of coronavirus disease 2019 (COVID-19) in pregnant women is limited. METHODS: A retrospective observational study was conducted using the data from the nationwide COVID-19 registry in Japan. We identified pregnant patients with symptomatic COVID-19 hospitalized during the study period. The Delta and Omicron variants of concern (VOC) predominant periods were defined as August 1 to December 31, 2021 and January 1 to May 31, 2022, respectively. Clinical characteristics were compared between the patients in the Delta and Omicron VOC periods. In addition, logistic regression analysis was performed to identify risk factors for developing moderate-to-severe COVID-19. RESULTS: During the study period, 310 symptomatic COVID-19 cases of pregnant women were identified; 111 and 199 patients were hospitalized during the Delta and Omicron VOC periods, respectively. Runny nose and sore throat were more common, and fatigue, dysgeusia, and olfactory dysfunction were less common manifestations observed in the Omicron VOC period. In the multivariable logistic regression analysis, onset during the later stage of pregnancy (OR: 2.08 [1.24-3.71]) and onset during the Delta VOC period (OR: 2.25 [1.08-4.90]) were independently associated with moderate-to-severe COVID-19, whereas two doses of SARS-CoV-2 vaccine were protective against developing moderate-to-severe COVID-19 (OR: 0.34 [0.13-0.84]). CONCLUSIONS: Clinical manifestations of COVID-19 in pregnant women differed between the Delta and Omicron VOC periods. SARS-CoV-2 vaccination was still effective in preventing severe COVID-19 throughout the Delta and Omicron VOC periods.

Temporal trends in microbial detection during the COVID-19 pandemic: Analysis of the Japan surveillance for Infection Prevention and Healthcare Epidemiology (J-SIPHE) database.

The impact of the COVID-19 pandemic on the incidence of microbial infections and other metrics related to antimicrobial resistance (AMR) has not yet been fully described. Using data from Japan Surveillance for Infection Prevention and Healthcare Epidemiology (J-SIPHE), a national surveillance database system that routinely collects clinical and epidemiological data on microbial infections, infection control practices, antimicrobial use, and AMR emergence from participating institutions in Japan, we assessed the temporal changes in AMR-related metrics before and after the start of the COVID-19 pandemic. We found that an apparent decrease in the incidence of microbial infections in 2020 compared with 2019 may have been driven primarily by a reduction in bed occupancy, although the incidence showed a constant or even slightly increasing trend after adjusting for bed occupancy. Meanwhile, we found that the incidence of Streptococcus pneumoniae dramatically decreased from April 2020 onward, probably due to stringent non-pharmaceutical interventions against COVID-19. Antimicrobial use showed a weak increasing trend, while the use of hand sanitiser at the included medical institutions increased by about 50% in 2020 compared with 2019.

Association between physical activity status and severity of COVID-19 in older adults.

The risk factors specific to the elderly population for severe coronavirus disease 2019 (COVID-19) caused by the Omicron variant of concern (VOC) are not yet clear. We performed an exploratory analysis using logistic regression to identify risk factors for severe COVID-19 illness among 4,868 older adults with a positive severe acute respiratory coronavirus 2 (SARS-CoV-2) test result who were admitted to a healthcare facility between 1 January 2022 and 16 May 2022. We then conducted one-to-one propensity score (PS) matching for three factors - dementia, admission from a long-term care facility and poor physical activity status - and used Fisher's exact test to compare the proportion of severe COVID-19 cases in the matched data. We also estimated the average treatment effect on treated (ATT) in each PS matching analysis. Of the 4,868 cases analysed, 1,380 were severe. Logistic regression analysis showed that age, male sex, cardiovascular disease, cerebrovascular disease, chronic lung disease, renal failure and/or dialysis, physician-diagnosed obesity, admission from a long-term care facility and poor physical activity status were risk factors for severe disease. Vaccination and dementia were identified as factors associated with non-severe illness. The ATT for dementia, admission from a long-term care facility and poor physical activity status was -0.04 (95% confidence interval -0.07 to -0.01), 0.09 (0.06 to 0.12) and 0.17 (0.14 to 0.19), respectively. Our results suggest that poor physical activity status and living in a long-term care facility have a substantial association with the risk of severe COVID-19 caused by the Omicron VOC, while dementia may be associated with non-severe illness.

Clinical characteristics of COVID-19 in hospitalized children during the Omicron variant predominant period.

INTRODUCTION: Information regarding the clinical manifestations and outcomes of coronavirus disease 2019 (COVID-19) in children under the Omicron variant predominant period is still limited. METHODS: A nationwide retrospective cohort study was conducted. Pediatric COVID-19 patients (<18 years of age) hospitalized between August 1, 2021 and March 31, 2022 were enrolled. Epidemiological and clinical characteristics between the Delta variant predominant period (August 1 to December 31, 2021) and the Omicron variant predominant period (January 1 to March 31, 2022) were compared. RESULTS: During the study period, 458 cases in the Delta predominant period and 389 cases in the Omicron predominant period were identified. Median age was younger (6.0 vs. 8.0 years, P = 0.004) and underlying diseases were more common (n = 65, 16.7% vs. n = 53, 11.6%) in the Omicron predominant period than those in the Delta variant predominant era. For clinical manifestations, fever ≥38.0 °C at 2 to <13 years old, sore throat at ≥ 13 years, and seizures at 2 to <13 years old were more commonly observed, and dysgeusia and olfactory dysfunction at ≥ 6 years old were less commonly observed in the Omicron variant predominant period. The number of patients requiring noninvasive oxygen support was higher in the Omicron predominant period than that in the Delta predominant period; however, intensive care unit admission rates were similar and no patients died in both periods. CONCLUSIONS: In the Omicron variant predominant period, more pediatric COVID-19 patients experienced fever and seizures, although the overall outcomes were still favorable.

Predictive model of risk factors of High Flow Nasal Cannula using machine learning in COVID-19.

With the rapid increase in the number of COVID-19 patients in Japan, the number of patients receiving oxygen at home has also increased rapidly, and some of these patients have died. An efficient approach to identify high-risk patients with slowly progressing and rapidly worsening COVID-19, and to avoid missing the timing of therapeutic intervention will improve patient prognosis and prevent medical complications. Patients admitted to medical institutions in Japan from November 14, 2020 to April 11, 2021 and registered in the COVID-19 Registry Japan were included. Risk factors for patients with High Flow Nasal Cannula invasive respiratory management or higher were comprehensively explored using machine learning. Age-specific cohorts were created, and severity prediction was performed for the patient surge period. We were able to obtain a model that was able to predict severe disease with a sensitivity of 57% when the specificity was set at 90% for those aged 40-59 years, and with a specificity of 50% and 43% when the sensitivity was set at 90% for those aged 60-79 years and 80 years and older, respectively. We were able to identify lactate dehydrogenase level (LDH) as an important factor in predicting the severity of illness in all age groups. Using machine learning, we were able to identify risk factors with high accuracy, and predict the severity of the disease. We plan to develop a tool that will be useful in determining the indications for hospitalisation for patients undergoing home care and early hospitalisation.

Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations.

In our previous study, we used genome resequencing to detect all candidate polymorphisms within a quantitative trait loci (QTL) region for beef marbling reported previously at 10-30 Mbp on bovine chromosome 7, and we selected 6044 polymorphisms as candidate quantitative trait nucleotides (QTNs). In the present study, we aimed to identify quantitative trait genes (QTGs) and QTNs in this QTL region by verifying the effect of SNPs on beef marbling in two Japanese Black cattle populations using a Dynamic Array integrated fluidic circuit. In total, 96 selected SNPs were genotyped in 441 and 529 animals in Hyogo and Miyazaki cattle populations, respectively. The most significant p-values were detected in a SNP in a splice region of ALDH7A1 (SNP93_ALDH7A1; p = 3.46 × 10-5) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (ICAM1) (SNP37_ICAM1; p = 3.33 × 10-4) in Miyazaki cattle. Interestingly, SNP93_ALDH7A1 was not significant (p = 0.459) in Miyazaki cattle, and SNP37_ICAM1 showed a weakly significant association (p = 0.043) in Hyogo cattle. Thus, each population would likely have different QTGs and QTNs for beef marbling in the QTL region. In the Hyogo population, it was not possible to determine the accurate range of the linkage disequilibrium (LD) block in LD block analysis because of a strong LD structure throughout the assessed region. In Miyazaki cattle, however, an LD block containing SNP37_ICAM1 had a range of 15.8-16.1 Mbp, suggesting that QTNs would be located within this region. The functions of 19 genes in the LD block were investigated. ICAM1 is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37_ICAM1 was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_ICAM1 on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation.

Comparison of the clinical characteristics and outcomes of COVID-19 in children before and after the emergence of Delta variant of concern in Japan.

Delta variant of concern (VOC) is the current predominant severe acute respiratory coronavirus type 2 strain causing coronavirus disease 2019 (COVID-19); however, information regarding the impact of the Delta VOC on clinical features and outcomes in pediatric patients with COVID-19 is limited. We conducted a retrospective observational study using the data of patients <18 years of age in COVIREGI-JP, the COVID-19 registry in Japan. The patients were divided into two groups according to the timing of enrollment in the registry (pre-Delta VOC era, October 2020 to May 2021; and Delta VOC era, August to October 2021), and the clinical characteristics and outcomes were compared between the two groups. During the study period, 950 and 349 pediatric patients were registered in the pre-Delta VOC and Delta VOC eras, respectively. The median patient age was younger and the proportion of patients with underlying diseases was higher in the Delta VOC era than that in the pre-Delta VOC era (10.0 vs 7.0 years, P < 0.001, and 7.4% [n = 70] vs. 12.6% [n = 44], P = 0.004, respectively). Significantly more patients were admitted to the intensive care unit in the Delta VOC era than in the pre-Delta VOC era (1.4% [ n = 5] vs. 0.1% [n = 1], P = 0.006), but no patient in either group died or required mechanical ventilation or extracorporeal membrane oxygenation throughout the study period, suggesting that the overall outcomes in children with COVID-19 remained favorable even in the Delta VOC era in Japan.

Impact of regional heterogeneity on the severity of COVID-19.

The main objective of the study is to assess the impact of regional heterogeneity on the severity of COVID-19 in Japan. We included 27,865 cases registered between January 2020 and February 2021 in the COVID-19 Registry of Japan, to examine the relationship between the National Early Warning Score (NEWS) of COVID-19 patients on the day of admission and the prefecture where the patients live. A hierarchical Bayesian model was used to examine the random effect of each prefecture in addition to the patients' backgrounds. Additionally, we compared the results of two models; one model included the number of beds secured for COVID-19 patients in each prefecture as one of the fixed effects, and the other model did not. The results indicated that the prefecture had a substantial impact on the severity of COVID-19 on admission, even when considering the effect of the number of beds separately. Our analysis revealed a possible association between regional heterogeneity and increased/decreased risk of severe COVID-19 infection on admission. This heterogeneity was derived not only from the number of beds secured in each prefecture but also from other factors.

Clinical Characteristics and Outcomes of Coronavirus Disease 2019 (COVID-19) in Pregnant Women: A Propensity Score-Matched Analysis of Data From the COVID-19 Registry Japan.

BACKGROUND: Several studies have investigated whether pregnancy is a risk factor for developing severe coronavirus disease 2019 (COVID-19); however, the results remain controversial. In addition, the information regarding risk factors for developing severe COVID-19 in pregnant women is limited. METHODS: A retrospective cohort study analyzing the data from the nationwide COVID-19 registry in Japan was conducted. Propensity score-matched analysis was performed to compare COVID-19 severity between pregnant and nonpregnant women. Multivariate analysis was also conducted to evaluate risk factors for developing moderate-to-severe COVID-19 in pregnant women. RESULTS: During the study period, 254 pregnant and 3752 nonpregnant women of reproductive age were identified. After propensity score matching, 187 pregnant women and 935 nonpregnant women were selected. A composite outcome of moderate-to-severe COVID-19 was more frequently observed in pregnant women than that of nonpregnant women (n = 18 [9.6%] vs n = 46 [4.9%]; P = .0155). In multivariate analysis, the presence of underlying diseases and being in the second-to-third trimester of pregnancy were recognized as risk factors for moderate-to-severe COVID-19 in pregnant women (odds ratio [95% confidence interval]: 5.295 [1.21-23.069] and 3.871 [1.201-12.477], respectively). CONCLUSIONS: Pregnancy could be a risk factor for moderate-to-severe COVID-19 for women in Japan. In addition to the presence of comorbidities, advanced pregnancy stages may contribute to greater risks for developing moderate-to-severe COVID-19 in pregnant women.

Clinical Characteristics of Hospitalized COVID-19 in Children: Report From the COVID-19 Registry in Japan.

A total of 1038 pediatric patients with COVID-19 were identified. Among these, 308 (30%) had asymptomatic COVID-19. The overall outcome was good, and no patients died. A significant rate of patients aged <24 months and ≥13 years were found in the symptomatic group.

Improved penicillin susceptibility of Streptococcus pneumoniae and increased penicillin consumption in Japan, 2013-18.

OBJECTIVES: To examine the association between penicillin susceptibility of Streptococcus pneumoniae and penicillin consumption in Japan. METHODS: We used Japan Nosocomial Infection Surveillance data on the susceptibility of S. pneumoniae and sales data obtained from IQVIA Services Japan K.K. for penicillin consumption. We analysed both sets of data by decomposing them into seasonality and chronological trend components. The cross-correlation function was checked using Spearman's rank correlation coefficient to examine the correlation between susceptibility and consumption. RESULTS: After adjusting for seasonality, the susceptibility of S. pneumoniae to penicillins gradually improved (55.7% in 2013 and 60.6% in 2018, respectively) and penicillin consumption increased during the same period (0.76 defined daily doses per 1,000 inhabitants per day [DID] in 2013, and 0.89 DID in 2018). The results showed positive cross-correlation (coefficient 0.801, p-value < 0.001). In contrast, cephalosporin consumption decreased (3.91 DID in 2013 and 3.19 DID in 2018) and showed negative cross-correlation with susceptibility of S. pneumoniae to penicillins (coefficient -0.981, p-value < 0.001). CONCLUSIONS: The rates of penicillin-susceptible S. pneumoniae isolates did not negatively correlate with penicillin consumption at the population level. Increased penicillin consumption might not impair the penicillin susceptibility of S. pneumoniae.

Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole-genome resequencing in Japanese Black cattle.

In our previous study, we performed genome-wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10-30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole-genome resequencing data. Based on whole-genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p-value (p = .0009) than the most significant SNP in GWAS (p = .0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR.

Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle.

Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full-length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.

A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle.

The objective of this study was to identify genomic regions associated with fat-related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool-based genome-wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS-BFGL-NGS-35463 and Hapmap23838-BTA-163815) and one SNP on BTA12 (ARS-BFGL-NGS-2915) significantly affected fat percentage (FAR). The significance of ARS-BFGL-NGS-35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR-associated genes and mutations, which can lead to the development of DNA markers for marker-assisted selection for the genetic improvement of beef quality.

Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle.

BACKGROUND: Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 animals. RESULTS: We identified a deleted-type CNV ranging from 378,127 to 412,061 bp on bovine chromosome 8, which was associated with embryonic mortality at 30-60 days after artificial insemination (AI). The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). Analysis of sequence traces from the CNV identified that 63 bp reads bridging the breakpoint were present on both sides of the CNV, indicating that the CNV was generated by non-allelic homologous recombination using the 63 bp homologous sequences. Western blot analysis showed that the CNV results in a null allele of ANXA10. This association was replicated using a sample population size of 2552 animals. To elucidate the function of ANXA10 in vivo, we generated Anxa10 null mice using the CRISPR/Cas9 system. Crossbreeding experiments showed that litter size from crosses of both Anxa10 -/- and Anxa10 +/- females had fewer pups than did Anxa10 +/+ females, and embryos of Anxa10 -/- females died between implantation stages E4.5 and E12.5. These results indicate that loss of maternal Anxa10 causes embryonic mortality. CONCLUSIONS: This study identified a deleted-type CNV encompassing ANXA10 in cows that was associated with embryonic mortality at 30-60 days after AI. Using a mouse model, we confirmed that litter sizes were smaller in crosses of both Anxa10 -/- and Anxa10 +/- females relative to those of wild females. These results indicate that ANXA10 is a maternal factor that is critical for embryo development.