Establishment and evaluation of a quantitative TaqMan RT-PCR for the detection of SARS-CoV-2 Omicron variants / 中华微生物学和免疫学杂志

Objective:To develop a rapid, simple and cost-effective quantitative TaqMan RT-PCR (RT-qPCR) that could be used as an alternative to sequencing for the detection of Omicron variants and to evaluate its performance.Methods:Primers and TaqMan probes targeting the conserved domains of SARS-CoV-2 ORF1ab and the high-frequency mutation sites in the S gene of Omicron variants were designed. Then a RT-qPCR for the detection of Omicron variants was established. The consistency of the method was verified using samples identified by whole-genome sequencing. The specificity and sensitivity of the method were also evaluated.Results:The established RT-qPCR could distinguish Omicron variants from early epidemic A strains and Alpha and Delta variants of SARS-CoV-2, and the results were consistent with those of whole-genome sequencing with a coincidence rate of 100% (28/28). There was no cross-reactivity with other six respiratory viruses or coxsackievirus group A16. For RNA standards, this method showed good linearity in the range of 10 9-10 3 copies/μl with a correlation coefficient ( R2) greater than 0.99 and detection sensitivity of 10 3 copies/μl. Conclusions:The RT-qPCR designed in this study for Omicron variant detection had good sensitivity and specificity and could be easily performed in laboratories, which would greatly facilitate the monitoring of Omicron variants.

Serotype detection and phylogenetic analysis of coxsackievirus A2 causing hand, foot and mouth disease in Yunnan Province in 2021 / 中华微生物学和免疫学杂志

Objective:To analyze the non-enterovirus A71 (non-EVA71) and non-coxsackievirus A16 (non-CVA16) enteroviruses causing hand, foot and mouth disease (HFMD) in Kunming and Qujing of Yunnan Province in 2021 by sequencing the VP4/VP2 and VP1 genes and to analyze the phylogenetic characteristics of the VP1 gene of CVA2, aiming to provide reference for the prevention and control of CVA2.Methods:The samples were made and extracted strictly according to the Laboratory Manual for Hand, Foot and Mouth Disease (China Center for Disease Control and Prevention, 2018 Edition). VP4/VP2 junction regions were firstly amplified and sequenced by MD91/OL68-1 primers. These sequences were firstly edited and then "blasted" on the GenBank to determine the virus serotype. To analyze the phylogenetic characteristics of CVA2, the entire VP1 gene sequences were amplified in two segments using enterovirus species A primers. Virus serotype was again confirmed online by "Enterovirus Genotyping Tool Version 0.1". The sequences of the reference virus genotypes/sub-genotypes were downloaded according to the reference. The phylogenetic trees were constructed by Mega5.2 software and the genetic characteristics were analyzed.Results:A total of 749 non-EVA71 and non-CVA16 enteroviruses were detected in the two areas in 2021. Group A enteroviruses were the main pathogens, with CVA16 as the predominant virus, and a small number of group B enteroviruses were reported. Only five strains of CVA2 were detected with a detection rate of 0.67% (5/749), indicating that CVA2 was a rare pathogen for HFMD in the two areas. The sequencing and serotyping results were consistent using the two genomic regions of VP4/VP2 junction region and VP1 region. Phylogenetic analysis showed that three Kunming strains belonged to genotype A, while two Qujing strains belonged to genotype D.Conclusions:The detection rate of CVA2 in Kunming and Qujing was 0.67% in 2021. CVA2 was a rare pathogen for HFMD in the two regions. Phylogenetic analysis showed genotypes A and D spread in Kunming and Qujing, respectively, but had not caused epidemics. To our knowledge, this was the first report of genotype A of CVA2 in China. Strengthening the laboratory surveillance especially molecular epidemiological surveillance is valuable for the monitor and analysis of transmission source for CVA2.

Evaluation of neutrophil/lymphocyte ratio and the end-stage liver disease-sodium model in predicting short-term prognosis of patients with HBV-related acute-on-chronic liver failure / 中华全科医师杂志

Objective:To evaluate neutrophil/lymphocyte ratio(NLR) and the model for end-stage liver disease-sodium(MELD-Na)score in predicting short-term prognosis of patients with HBV-related acute-on-chronic liver failure(HBV-ACLF).Methods:A total of 234 consecutive HBV-ACLF patients(194 males and 40 females, aged 23-85 years)admitted to Hangzhou Xixi Hospital from January 2019 to December 2021 were enrolled. According to the 12-week clinical outcomes, patients were divided into good prognosis group( n=141)and poor prognosis group( n=93). Univariate and multivariate Logistic regression were performed to identify independent risk factors for poor prognosis of HBV-ACLF patients. Receiver operating characteristics(ROC)curve was applied to evaluate the accuracy of risk factors in predicting short-term prognosis of HBV-ACLF patients. Results:The age [(48.7±11.9) vs. (52.5±9.9) years old, t=-2.59, P=0.011], proportion of males [78.0%(110/141) vs. 90.3%(84/93), χ2=5.99, P=0.014], total bilirubin[202.9(141.2, 287.6) vs. 320.0(224.4, 400.0) μmol/L, Z=-5.14, P<0.001], creatinine [71.0(59.0, 78.0) vs. 81.0(64.0, 111.0)μmol/L, Z=-3.98, P<0.001], international normalized ratio[1.66(1.52, 1.86) vs. 1.91(1.66, 2.27), Z=-5.46, P<0.001], leukocyte count[5.16(3.99, 6.95)×10 9/L vs. 6.57(4.83, 8.30)×10 9/L, Z=-4.14, P=0.001], NLR[2.77(2.02, 3.55) vs. 5.48(3.44, 8.53), Z=-8.48, P<0.001], MELD score[22.0(20.0, 24.0) vs. 26.0(24.0, 29.0), Z=-9.22, P<0.001], MELD-Na score[22.8(20.0, 25.6) vs. 29.0(25.0, 36.0), Z=-9.16, P<0.001], liver cirrhosis[77.3%(109/141) vs. 88.2%(82/93), χ2=4.41, P=0.036], hepatorenal syndrome[4/141(2.8%) vs. 12/93(12.9%), χ2=8.91, P=0.003] and the proportion of artificial liver treatment[21/141(14.9%) vs. 24/93(25.8%), χ2=4.30, P=0.038] were significantly elevated in poor prognosis group compared with survival group. Logistic regression analysis showed that NLR( OR=3.76, 95 %CI: 2.10-6.74, P<0.001)and MELD-Na score( OR=2.24, 95 %CI: 1.17-4.29, P=0.015) were independent risk factors for poor short-term prognosis of HBV-ACLF patients. The area under the ROC curve(AUC)of NLR, and MELD-Na for the short-term prognosis of HBV-ACLF patients was 0.792 and 0.822, respectively. The AUC of the combination of NLR with MELD-Na was 0.858, which was significantly higher than that of NLR( Z=-3.04, P=0.001) or MELD-Na score( Z=-2.16, P=0.031)alone. Based on the cut-off value of the combined model, patients were classified into high combined model score (≥0.04) group and low combined model score (<0.04) group, the survival rate of the high group was significantly higher than that of the low group( χ2=67.47, P<0.001). Conclusions:NLR and MELD-Na score are independent risk factors of the short-term prognosis of HBV-ACLF patients. The combination of NLR and MELD-Na score will be beneficial to predict the short-term prognosis of HBV-ACLF patients.

Outcomes with and without outpatient SARS-CoV-2 treatment for patients with COVID-19 and systemic autoimmune rheumatic diseases: A retrospective cohort study

ObjectiveTo investigate temporal trends, severe outcomes, and rebound among systemic autoimmune rheumatic disease (SARD) patients according to outpatient SARS-CoV-2 treatment. MethodsWe performed a retrospective cohort study investigating outpatient SARS-CoV-2 treatments among SARD patients at Mass General Brigham (23/Jan/2022-30/May/2022). We identified SARS-CoV-2 infection by positive PCR or antigen test (index date=first positive test) and SARDs using diagnosis codes and immunomodulator prescription. Outpatient treatments were confirmed by medical record review. The primary outcome was hospitalization or death within 30 days following the index date. COVID-19 rebound was defined as documentation of negative then newly-positive SARS-CoV-2 tests. The association of any vs. no outpatient treatment with hospitalization/death was assessed using multivariable logistic regression. ResultsWe analyzed 704 SARD patients with COVID-19 (mean age 58.4 years, 76% female, 49% with rheumatoid arthritis). Treatment as outpatient increased over calendar time (p<0.001). A total of 426(61%) received outpatient treatment: 307(44%) with nirmatrelvir/ritonavir, 105(15%) with monoclonal antibodies, 5(0.7%) with molnupiravir, 3(0.4%) with outpatient remdesivir, and 6(0.9%) with combinations. There were 9/426 (2.1%) hospitalizations/deaths among those treated as outpatient compared to 49/278 (17.6%) among those with no outpatient treatment (adjusted odds ratio [aOR] 0.12, 0.05 to 0.25). 25/318 (8%) of patients who received oral outpatient treatment had documented COVID-19 rebound. ConclusionOutpatient treatment was strongly associated with lower odds of severe COVID-19 compared to no outpatient treatment. At least 8% of SARD patients experienced COVID-19 rebound. These findings highlight the importance of outpatient COVID-19 treatment for SARD patients and the need for further research on rebound. KEY MESSAGES What is already known on this topic?O_LIPrevious studies suggest that monoclonal antibodies are an effective outpatient treatment option for patients at high-risk of severe COVID-19, including those with systemic autoimmune rheumatic diseases (SARDs). C_LIO_LINirmatrelvir/ritonavir and molnupiravir are recently-authorized effective oral outpatient SARS-CoV-2 treatment options, but clinical trials were performed among the general population, mostly among unvaccinated and prior to Omicron viral variants. C_LIO_LIOral outpatient SARS-CoV-2 treatments may result in COVID-19 rebound, characterized by newly-positive COVID-19 testing and recurrent symptoms, but no studies have investigated rebound prevalence among SARD patients. C_LI What this study adds?O_LIThis is one of the first studies investigating outpatient SARS-CoV-2 treatments among SARD patients that includes oral options and quantifies the prevalence of COVID-19 rebound. C_LIO_LIOutpatient treatment was associated with 88% reduced odds of severe COVID-19 compared to no treatment. C_LIO_LIAt least 8% of SARDs receiving oral outpatient treatment experienced COVID-19 rebound. C_LI How this study might affect research, practice, or policy?O_LIThese results should encourage clinicians to prescribe and SARD patients to seek prompt outpatient COVID-19 treatment. C_LIO_LIThis research provides an early estimate of the prevalence of COVID-19 rebound after oral outpatient treatment to quantify this risk to clinicians and SARD patients and encourage future research. C_LI

Impact of vaccination on post-acute sequelae of SARS CoV-2 infection in patients with rheumatic diseases

ObjectiveVaccination decreases the risk of severe COVID-19 but its impact on post-acute sequelae of COVID-19 (PASC) is unclear among patients with systemic autoimmune rheumatic diseases (SARDs) who may have blunted vaccine immunogenicity and be vulnerable to PASC. MethodsWe prospectively enrolled SARD patients from a large healthcare system who survived acute infection to complete surveys. The symptom-free duration and the odds of PASC (any symptom lasting [≥] 28 or 90 days) were evaluated using restricted mean survival time and multivariable logistic regression, respectively, among those with and without breakthrough infection ([≥] 14 days after initial vaccine series). ResultsAmong 280 patients, the mean age was 53 years, 80% were female, and 82% were white. The most common SARDs were inflammatory arthritis (59%) and connective tissue disease (24%). Those with breakthrough infection had more upper respiratory symptoms, and those with non-breakthrough infection had more anosmia, dysgeusia, and joint pain. Compared to those with non-breakthrough COVID-19 infection (n=164), those with breakthrough infection (n=116) had significantly more symptom-free days over the follow-up period (+28.9 days, 95% CI: 8.83, 48.89; p=0.005) and lower odds of PASC at 28 and 90 days (aOR 0.49, 95% CI: 0.29, 0.83 and aOR 0.10, 95% CI: 0.04, 0.22, respectively). ConclusionVaccinated patients with SARDs were less likely to experience PASC compared to those not fully vaccinated. These findings support the benefits of vaccination for patients with SARDs and suggest that the immune response to acute infection is important in the pathogenesis of PASC in SARD patients. Key MessagesO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIPost-acute sequelae of COVID-19 (PASC) affects 20-50% of COVID-19 survivors, though the impact of vaccination on the risk and severity of PASC is unclear, especially among those with systemic autoimmune rheumatic diseases (SARDs) who may have impaired responses to vaccines and be particularly vulnerable to PASC. C_LI What this study adds?O_LIIn this prospective cohort of SARD patients recovering from COVID-19, we found that those with breakthrough vs non-breakthrough infection had more symptom-free days over the follow-up period (adjusted difference +28.9 days, 95% CI: 8.38, 48.89; p=0.005) and a lower odds of PASC at 28 days (aOR 0.49, 95% CI: 0.29, 0.83) and at 90 days (aOR 0.10, 95% CI: 0.04, 0.22). C_LIO_LIPatient-reported pain and fatigue scores were lower, reflecting less severe pain and fatigue, in those with breakthrough infection compared to those with non-breakthrough infection. C_LI How this study might affect research, practice, or policy?O_LIThis study extends our understanding of the benefits of vaccination against COVID-19 in patients living with SARDs and reinforces the importance of vaccinating this vulnerable population. C_LIO_LIOur findings suggest that the initial immune response to acute SARS-CoV-2, as influenced by vaccination, affects PASC risk but this requires further study. C_LI

Factors Associated with COVID-19 Breakthrough Infection in the Pre-Omicron Era Among Vaccinated Patients with Rheumatic Diseases: A Cohort Study

ObjectiveRheumatic disease patients on certain immunomodulators are at increased risk of impaired humoral response to SARS-CoV-2 vaccines. We aimed to identify factors associated with breakthrough infection among patients with rheumatic diseases. MethodsWe identified patients with rheumatic diseases being treated with immunomodulators in a large healthcare system who received at least two doses of either the mRNA-1273 (Moderna) or BNT162b2 (Pfizer-BioNTech) vaccines or one dose of the Johnson & Johnson-Janssen (J&J) vaccine. We followed patients until SARS-CoV-2 infection, death, or December 15, 2021, when the Omicron variant became dominant in our region. We estimated the association of baseline characteristics with the risk of breakthrough infection using multivariable Cox regression. ResultsWe analyzed 11,468 patients (75% female, mean age 60 years). Compared to antimalarial monotherapy, multiple immunomodulators were associated with higher risk of infection: anti-CD20 monoclonal antibodies (aHR 5.20, 95% CI: 2.85, 9.48), CTLA-4 Ig (aHR 3.52, 95% CI: 1.90, 6.51), mycophenolate (aHR 2.31, 95% CI: 1.25, 4.27), IL-6 inhibitors (aHR 2.15, 95% CI: 1.09, 4.24), JAK inhibitors (aHR 2.02, 95% CI: 1.01, 4.06), and TNF inhibitors (aHR 1.70, 95% CI: 1.09, 2.66). mRNA-1273 recipients had a lower risk of breakthrough infection compared to BNT162b2 recipients (aHR 0.66, 95% CI: 0.50, 0.86). There was no association of sex, body mass index, smoking status, race, or ethnicity with risk of breakthrough infection. ConclusionAmong patients with rheumatic diseases, multiple immunomodulators were associated with increased risk of breakthrough infection. These results highlight the need for additional mitigation strategies in this vulnerable population.

DMARD disruption, disease flare, and prolonged symptom duration after acute COVID-19 among participants with rheumatic disease: A prospective study

ObjectiveTo describe disease-modifying antirheumatic drug (DMARD) disruption, rheumatic disease flare/activity, and prolonged COVID-19 symptom duration among COVID-19 survivors with systemic autoimmune rheumatic diseases (SARDs). MethodsWe surveyed patients with SARDs after confirmed COVID-19 at Mass General Brigham to investigate post-acute sequelae of COVID-19. We obtained data on demographics, clinical characteristics, COVID-19 symptoms/course, and patient-reported measures. We examined baseline predictors of prolonged COVID-19 symptom duration (defined as lasting [≥]28 days) using logistic regression. ResultsWe analyzed surveys from 174 COVID-19 survivors (mean age 52 years, 81% female, 80% White, 50% rheumatoid arthritis) between March 2021 and January 2022. Fifty-one percent of 127 respondents on any DMARD reported a disruption to their regimen after COVID-19 onset. For individual DMARDs, 56-77% had any change, except for hydroxychloroquine (23%) and rituximab (46%). SARD flare after COVID-19 was reported by 41%. Global patient-reported disease activity was worse at the time of survey than before COVID-19 (mean 6.6{+/-}2.9 vs. 7.6{+/-}2.3, p<0.001). Median time to COVID-19 symptom resolution was 14 days (IQR 9,29). Prolonged symptom duration of [≥]28 days occurred in 45%. Hospitalization for COVID-19 (OR 3.54, 95%CI 1.27-9.87) and initial COVID-19 symptom count (OR 1.38 per symptom, 95%CI 1.17-1.63) were associated with prolonged symptom duration. Respondents experiencing prolonged symptom duration had higher RAPID3 scores (p=0.007) and more pain (p<0.001) and fatigue (p=0.03) compared to those without prolonged symptoms. ConclusionDMARD disruption, SARD flare, and prolonged symptom duration were common in this prospective study of COVID-19 survivors, suggesting substantial impact on SARDs after acute COVID-19.

Etiological and phylogenetic analysis of hand, foot and mouth disease in Qujing city, Yunnan Province, 2020 / 中华微生物学和免疫学杂志

Objective:To analyze the etiological distribution and phylogenetic characteristics of hand, foot and mouth disease (HFMD) in Qujing city of Yunnan Province in 2020.Methods:Stool samples were collected from HFMD cases in Qujing city in 2020 and virus RNA was extracted directly from treated stool suspensions. Virus VP4 gene sequences were firstly amplified using MD91/OL68-1 primer pairs and sequenced, then the virus serotypes were determined by BLAST search on the GenBank. Virus entire VP1 gene sequences were amplified and sequenced. Virus serotypes were identified online using Enterovirus Genotyping Tool Version 0.1. Sequences of reference virus genotypes/sub-genotypes were downloaded according to references. Phylogenetic trees were constructed by MEGA5.2 software and the genetic characteristics were analyzed.Results:A total of 47 strains of enteroviruses (EVs) were detected with a detection rate of 10.22% (47/460). The detected viruses were coxsackievirus A4 (CVA4, 0.65%, 3/460), CVA6 (7.83%, 36/460), CVA10 (0.87%, 4/460) and CVA16 (0.87%, 4/460). All were enterovirus species A (EVA), while other group viruses were not detected. The predominant virus was CVA6, accounting for 7.83% (36/460). EVA71 was not detected. CVA4 strains of C2 and C4 subgenotypes were co-circulating strains in Qujing city. CVA6 subgenotype D3a and CVA16 subgenotype B1a were also circulated in Qujing city. All CVA10 strains were in a separate lineage.Conclusions:Similar to the previous situation in China, the detection rates of EVA71 and CVA16 were very low, even zero. This study showed that CVA6 was the predominant virus, indicating a HFMD outbreak caused by CVA6 in Qujing city in 2020. The phylogenetic analysis showed CVA10 isolates belonged to a separate lineage, which might be unique to Qujing city. Laboratory and molecular epidemiological surveillance of non-EVA71 and non-CVA16 viruses, especially CVA6 and CVA10 should be strengthened in the future.

COVID-19 Outcomes Among Users of CD20 Inhibitors for Immune-Mediated Diseases: A Comparative Cohort Study

ObjectivePatients with immune-mediated diseases treated with CD20 inhibitors may have worse COVID-19 outcomes due to impaired humoral immunity, but differences versus the general population are unknown. MethodsWe identified patients with immune-mediated diseases who received CD20 inhibitors within one year prior to the index date of PCR-confirmed COVID-19 between January 31, 2020, and January 31, 2021. Comparators with COVID-19 were matched up to 5:1 by age, sex, and PCR date. Hazard ratios (HRs) and 95% confidence intervals (CIs) for hospitalization, mechanical ventilation, and death in CD20 inhibitor users versus comparators were estimated using Cox regression. ResultsWe identified 114 cases with COVID-19 who had received CD20 inhibitors for immune-mediated diseases (mean age 55 years, 70% female) and 559 matched comparators with COVID-19 (mean age 54 years, 70% female). CD20 inhibitor-treated cases had higher mortality (aHR 2.16; 95% CI: 1.03 to 4.54) than matched comparators. Risks of hospitalization (aHR 0.88; 95% CI: 0.62 to 1.26) and mechanical ventilation (aHR 0.82; 95% CI: 0.36 to 1.87) were similar. Similar trends were seen in analyses according to type of indication (e.g., rheumatic or neurologic disease) and duration of CD20 inhibitor use (<1 or [≥]1 year), and after excluding patients with interstitial lung disease, cancer, and those on glucocorticoids prior to COVID-19 diagnosis. ConclusionsPatients who received CD20 inhibitors for immune-mediated diseases prior to COVID-19 had higher mortality following COVID-19 than matched comparators, highlighting the urgent need to mitigate excess risks in CD20 inhibitor users during the ongoing pandemic. Key MessagesO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIPatients with immune-mediated diseases treated with CD20 inhibitors may have worse COVID-19 outcomes than those treated with other immunomodulatory medications, but differences compared to the general population are unknown. C_LI What does this study add?O_LICD20 inhibitor-treated cases had over two-fold higher risk of mortality than matched general population comparators, although risks of hospitalization and mechanical ventilation were similar. C_LI How might this impact on clinical practice or future developments?O_LIThere is an urgent need for risk mitigation strategies, such as SARS-CoV-2 monoclonal antibodies or booster vaccinations, for patients with immune-mediated diseases treated with CD20 inhibitors during the ongoing COVID-19 pandemic. C_LI

Etiological surveillance of HFMD and the phylogenetic analysis of coxsackievirus A6 in Wenshan prefecture of Yunnan province, China, 2014 to 2018 / 中华微生物学和免疫学杂志

Objective:To analyze the etiology of hand, foot and mouth disease (HFMD) cases collected from Wenshan prefecture from 2014 to 2018 and the molecular epidemiology of coxsackievirus A6(CV-A6).Methods:Viruses were isolated by RD cells and Hep-2 cells from stool samples collected from HFMD patients in Wenshan prefecture from 2014 to 2018. Virus RNA was extracted and virus VP4/VP2 junction region sequence was firstly amplified and sequenced by MD91 and OL68-1 primer pairs, then the virus serotype was determined. Virus entire VP1 gene sequences were determined by relative primer pairs according to the references. The reference sequences of CV-A6 virus entire VP1 gene were downloaded from the GenBank and the phylogenetic tree was constructed and the genetic characteristics and molecular epidemiology were analyzed.Results:During five years of study period, a total of 581 strains of enteroviruses (EVs) was isolated with an isolation rate of 20.40% (581/2 848). Among 581 strains, 74 strains were CV-A6, accounting for 12.74% (74/581); 124 were CV-A16, accounting for 21.34% (124/581); 374 were EV-A71, accounting for 64.37% (374/581); nine were other EVs, accounting for 1.55% (9/581). The entire VP1 sequences of 74 CV-A6 strains were filtered by constructing a phylogenetic tree and the completely same strains were excluded from analysis. We finally analyzed the phylogenetic characteristics of 22 strains isolated in this study with 52 reference strains. The results showed that all 22 Wenshan strains belonged to D3a sub-genotype, of which 21 strains belonged to cluster 1, and only one strain belonged to cluster 2.Conclusions:From 2014 to 2018, the outbreaks of HFMD in Wenshan prefecture were mainly caused by EV-A71, CV-A16 and CV-A6, accounting for 64.37%, 21.34% and 12.74% respectively. Phylogenetic analysis showed, similar to the situation in China, the sub-genotype D3a of CV-A6 was the predominant virus and the cluster 1 was the main sub-genotype in this outbreak.

COVID-19 severity in asthma patients: A multi-center matched cohort study

ObjectiveThe evidence pertaining to the effects of asthma on Coronavirus disease 2019 outcomes has been unclear. To improve our understanding of the clinically important association of asthma and Coronavirus disease 2019. MethodsA matched cohort study was performed using data from the Mass General Brigham Health Care System (Boston, MA). Adult (age [≥] 18 years) patients with confirmed Coronavirus disease 2019 and without chronic obstructive pulmonary disease, cystic fibrosis, or interstitial lung disease between March 4, 2020 and July 2, 2020 were analyzed. Up to 5 non-asthma comparators were matched to each asthma patient based on age (within 5 years), sex, and date of positive test (within 7 days). The primary outcomes were hospitalization, mechanical ventilation, and death, using multivariable Cox-proportional hazards models accounting for competing risk of death, when appropriate. Patients were followed for these outcomes from diagnosis of Coronavirus disease 2019 until July 2, 2020. ResultsAmong 562 asthma patients, 199 (21%) were hospitalized, 15 (3%) received mechanical ventilation, and 7 (1%) died. Among the 2686 matched comparators, 487 (18%) were hospitalized, 107 (4%) received mechanical ventilation, and 69 (3%) died. The adjusted Hazard Ratios among asthma patients were 0.99 (95% Confidence Internal 0.80, 1.22) for hospitalization, 0.69 (95% Confidence Internal 0.36, 1.29) for mechanical ventilation, and 0.30 (95% Confidence Internal 0.11, 0.80) for death. ConclusionsIn this matched cohort study from a large Boston-based healthcare system, asthma was associated with comparable risk of hospitalization and mechanical ventilation but a lower risk of mortality.

Genetic analysis of VP1 3'region of coxsackievirus B2 isolated from Yunnan province / 中华微生物学和免疫学杂志

Objective To analyze the genetic characteristics of VP1 3'region of human coxsack-ievirus B2 (CV-B2) strains isolated from Yunnan province. Methods RT-PCR and gene sequencing were performed to analyze the VP1 3'region of 15 CV-B2 strains isolated from acute flaccid paralysis ( AFP) cases during 2005 to 2006, healthy children in 2013 and hand, foot and mouth disease (HFMD) cases in 2014 in Yunnan province. CV-B2 VP1 gene reference sequences were downloaded from the Genbank. Nucleotide (nt) and amino acid (aa) diversities were calculated by MEGA5. 2 software and a phylogenetic tree was constructed. Genetic and molecular epidemiological characteristics of CV-B2 strains circulating in Yunnan province were analyzed. Results A total of 15 CV-B2 strains were isolated, which were one from 232 AFP cases in 2005, one from 240 AFP cases in 2006, 12 from 400 healthy children in 2013 and one from 500 HFMD cases in 2014. Phylogenetic analysis of the 15 CV-B2 strains in Yunnan province and those down-loaded from the GenBank showed that CV-B2 could be genetically divided into five genotypes. The prototype strain Ohio-1 and one strain (01-1) isolated in Taiwan in 1988 belonged to genotype 1. Strains isolated in France in 2006, 2007 and 2010 belonged to genotype 2. Strains isolated in Yunnan, Shandong, Henan, Fu-jian and Taiwan belonged to genotype 3. Strains isolated in Russia, Yunnan AFP cases in 2005 and 2006 and India belonged to genotype 4. Strains isolated in Taiwan, Shandong and New South Wales, Australia be-longed to genotype 5. Different genotypes distributed in different countries/areas with some confined within specific countries/areas. Conclusions The 12 strains isolated from healthy children and one from HFMD cases in Yunnan province belonged to genotype 3, while the two strains isolated from AFP cases belonged to genotype 4. Diversities in nt and aa sequences between the strains isolated from the healthy children and HFMD case were only 0. 76％ and 0. 03％, respectively, indicating that they might come from the same transmission source. However, the nt and aa diversities between the isolates of genotype 3 ( from healthy children and HFMD case) and genotype 4 (from AFP cases in 2005 and 2006) were 15. 11％-15. 22％ and 2. 76％-2. 72％, respectively. Correlation of CV-B2 with AFP and HFMD was worthy of further study.

Etiology analysis of hand, foot and mouth disease cases and genetic characteristics of coxsackievirus A6 in six prefectures/cities of Yunnan Province in 2018 / 中华微生物学和免疫学杂志

Objective To detect the enterovirus VP4 and VP1 genes in 510 stool samples collect-ed from hand, foot and mouth disease ( HFMD) cases and analyze the phylogenetic characteristics of the en-tire VP1 genes of coxsackievirus A6 (CV-A6) strains in six prefectures/cities of Yunnan Province in 2018. Methods Viral RNA was abstracted from the stool samples. VP4 gene sequences were amplified by RT-PCR and sequenced using the MD91/OL68-1 primer pair to identify viral genotypes. Whole VP1 gene se-quences were amplified and sequenced using appropriate primer pairs. The whole VP1 gene sequences of CV-A6 reference strains were downloaded from GenBank. MEGA5. 2 software was used to analyze the simi-larity in nucleotide and amino acid sequences between different strains and phylogenetic tree was constructed for analysis of genetic characteristics and molecular epidemiology. Results VP4 and VP1 gene sequences were obtained from 57 out of 510 stool samples with a positive rate of 11. 17％ (57/510). There were 43 CV-A6 (8. 43％, 43/510), six CV-A10 (1. 17％, 6/510), two enterovirus A71 (EV-A71, 0. 39％, 2/510) and two CV-A9 (0. 39％, 2/510) strains. The other four strains were CV-A4 (0. 19％, 1/510), CV-A5 (0. 19％, 1/510), CV-B1 (0. 19％, 1/510) and E11 (0. 19％, 1/510). The phylogenetic analy-sis showed that all 43 CV-A6 strains belonged to sub-genotype D3. Conclusions In the 510 HFMD sam-ples, CV-A6 strains were mostly detected with a detection rate of 8. 43％ and accounted for 75. 44％ (43/57) of all isolates, followed by CV-A10 (1. 17％, 6/510) and EV-A71 (0. 39％, 2/510). There was a large HFMD outbreak mainly caused by CV-A6 in Yunnan Province in 2018. The outbreak was caused by CV-A6 of sub-genotype D3, as was the case with pervious outbreaks in China.

Etiology analysis of hand, foot and mouth disease cases and genetic characteristics of coxsackievirus A6 in six prefectures/cities of Yunnan Province in 2018 / 中华微生物学和免疫学杂志

Objective@#To detect the enterovirus VP4 and VP1 genes in 510 stool samples collected from hand, foot and mouth disease (HFMD) cases and analyze the phylogenetic characteristics of the entire VP1 genes of coxsackievirus A6 (CV-A6) strains in six prefectures/cities of Yunnan Province in 2018.@*Methods@#Viral RNA was abstracted from the stool samples. VP4 gene sequences were amplified by RT-PCR and sequenced using the MD91/OL68-1 primer pair to identify viral genotypes. Whole VP1 gene sequences were amplified and sequenced using appropriate primer pairs. The whole VP1 gene sequences of CV-A6 reference strains were downloaded from GenBank. MEGA5.2 software was used to analyze the similarity in nucleotide and amino acid sequences between different strains and phylogenetic tree was constructed for analysis of genetic characteristics and molecular epidemiology.@*Results@#VP4 and VP1 gene sequences were obtained from 57 out of 510 stool samples with a positive rate of 11.17% (57/510). There were 43 CV-A6 (8.43%, 43/510), six CV-A10 (1.17%, 6/510), two enterovirus A71 (EV-A71, 0.39%, 2/510) and two CV-A9 (0.39%, 2/510) strains. The other four strains were CV-A4 (0.19%, 1/510), CV-A5 (0.19%, 1/510), CV-B1 (0.19%, 1/510) and E11 (0.19%, 1/510). The phylogenetic analysis showed that all 43 CV-A6 strains belonged to sub-genotype D3.@*Conclusions@#In the 510 HFMD samples, CV-A6 strains were mostly detected with a detection rate of 8.43% and accounted for 75.44% (43/57) of all isolates, followed by CV-A10 (1.17%, 6/510) and EV-A71 (0.39%, 2/510). There was a large HFMD outbreak mainly caused by CV-A6 in Yunnan Province in 2018. The outbreak was caused by CV-A6 of sub-genotype D3, as was the case with pervious outbreaks in China.

An epidemiological survey of diarrhea outbreak caused by group A rotavirus in Yunnan / 中华实验和临床病毒学杂志

Objective@#To identify the etiology and source of infection in a diarrhea outbreak in Yunnan in May 2017 and to provide the evidence for formulating prevention and control measures.@*Methods@#Epidemiological investigation was carried out on the epidemic situation of diarrhea in the village of Lvchun County in Yunnan Province, the field sampling, laboratory testing and data analysis were also performed.@*Results@#Among the 44 patients, 11 of the 13 samples were positive for rotavirus nucleic acid in group A, and the positive rate was 84.62%. The survey showed that the water supply pipe was damaged and polluted by human and livestock manure and domestic sewage. The trend of the damaged water pipe was basically the same as the case distribution, and the rainfall was significantly related to the number of the disease.@*Conclusions@#This event was an outbreak of diarrhea caused by group A rotavirus. The direct pollution of drinking water caused by rainfall may be the risk factor of this outbreak. The health management of rural drinking water should be strengthened and the health knowledge and education of preventing intestinal infectious diseases should be promoted.

Molecular characteristics of non-O1/O139 Vibrio cholerae in Yunnan Province / 中国人兽共患病学报

Non-O1/O139 group of Vibrio cholerae can cause human acute diarrhea disease,while compared with the O1 and O139 groups;it often ignore the risk of the disease for human being.Therefore,we analyzed the molecular characteristics of 31 V.cholerae isolated from Yunnan Province.We used the agar disc diffusion method (K-B) to carry out the antibiotic sensitivity test;polymerase chain reaction (PCR) amplification for the detection of virulence gene;at the same time,all of strains were performed for pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).The drug sensitivity test showed that 67.74％ strains were resistant to rifampin,29.03％ resistant to nalidixic acid and cotrimoxazole,all of the isolates were sensitive to gentamicin and ciprofloxacin;PCR results showed that all strains had the ompW gene,87.10％ strains had hly gene,25.81％ strains had rstREl tor,16.13％ strains had rstRClassical and tcpAEl tor,while CT rfbO1 and rfbO139 gene were negative;PFGE results showed that 31 strains had a trend of discrete height,the same PFGE identity pattern was not nearly found;for the analysis of MLST,we found the one new alleles of gyrB,four new alleles of mdh gene,six new alleles of metE gene,two new alleles of pntA,three new alleles of purM and four new alleles of pyrC gene.After permutation and combination,we found 17 new ST types for V.cholerae(ST273-ST289).Non-O1/O139 group V.cholerae showed a high degree of diversity,while the non-O1/O139 group of V.cholerae in Yunnan Province has a certain geographical features,which enriched the existing molecular typing system of V.cholerae.

Clinical stages and outcomes of severe cases on hand, foot and mouth disease / 中华流行病学杂志

Objective To understand the characteristics and relation of clinical stage and outcome of severe cases on hand,foot and mouth disease (HFMD) and to establish the evaluation method for understanding severity of this disease.Methods According to factors as geographical location,economic and epidemic levels,five provinces (Henan,Shandong,Yunnan,Zhejiang and Sichuan provinces) were selected.Reported severe cases of HFMD from the National Notifiable Diseases Reporting System were selected randomly in the five provinces.Basic epidemiological information,clinical data,and pathogen testing results in the involved hospitals were collected.Clinical stages on all the patients were decided in accordance with "the clinical expert consensus on diagnosis and treatment for severe case of enterovirus type 71 (EV71) infections (2011 edition)".Data were analyzed using SPSS software 18.0 and other epidemiological methods.Results A total of 657 severe HFMD cases were investigated,with 326 cases positive of EV71,accounting for 91.3％ (326/357) among all the laboratory-confirmed cases.Of the 657 cases,542 cases (82.5％,95％CI:79.4％-85.3％) were diagnosed as in stage 2 (with nervous system involvement),99 cases (15.1％,95％CI:12.4％-18.0％) in stage 3 (early phase of function failure on heart and lung),and 16 cases (2.4％,95％CI:1.4％-3.9％) were in stage 4 (function failure of heart and lung).11 cases (1.7％,95％CI:0.9％-3.0％) were with squeal when discharged from hospital with 8 cases (1.2％,95％CI:0.6％-2.3％) died.When comparing the proportions among stage 2,stage 3 and stage 4,significant differences were found between age groups (x2=22.632,P=0.012).The younger the patient was the lower the proportions of stage 2 and the more proportion of stage 3 appeared.When comparing the proportions of clinical stages among the five provinces,significant differences (x2=41.481,P =0.000) were noticed.Proportions of different clinical stages in gender,ethnicity,occupation,place of residence types and the type of pathogen appeared no significant differences,respectively.However,the proportions of squeal and death in stage 2,stage 3 and stage 4 showed significant differences (sequela:x2=12.960,P=0.001;Death:x 2=16.850,P=0.001),respectively.Conclusions The pcrccntage of clinical stages of severe HFMD patients related to the rate of squeal and death.Clinical staging can be used for assessing the clinical severity of complications and the effectiveness of treatment,of HFMD.

Clinical stages and outcomes of severe cases on hand, foot and mouth disease / 中华流行病学杂志

Objective To understand the characteristics and relation of clinical stage and outcome of severe cases on hand,foot and mouth disease (HFMD) and to establish the evaluation method for understanding severity of this disease.Methods According to factors as geographical location,economic and epidemic levels,five provinces (Henan,Shandong,Yunnan,Zhejiang and Sichuan provinces) were selected.Reported severe cases of HFMD from the National Notifiable Diseases Reporting System were selected randomly in the five provinces.Basic epidemiological information,clinical data,and pathogen testing results in the involved hospitals were collected.Clinical stages on all the patients were decided in accordance with "the clinical expert consensus on diagnosis and treatment for severe case of enterovirus type 71 (EV71) infections (2011 edition)".Data were analyzed using SPSS software 18.0 and other epidemiological methods.Results A total of 657 severe HFMD cases were investigated,with 326 cases positive of EV71,accounting for 91.3％ (326/357) among all the laboratory-confirmed cases.Of the 657 cases,542 cases (82.5％,95％CI:79.4％-85.3％) were diagnosed as in stage 2 (with nervous system involvement),99 cases (15.1％,95％CI:12.4％-18.0％) in stage 3 (early phase of function failure on heart and lung),and 16 cases (2.4％,95％CI:1.4％-3.9％) were in stage 4 (function failure of heart and lung).11 cases (1.7％,95％CI:0.9％-3.0％) were with squeal when discharged from hospital with 8 cases (1.2％,95％CI:0.6％-2.3％) died.When comparing the proportions among stage 2,stage 3 and stage 4,significant differences were found between age groups (x2=22.632,P=0.012).The younger the patient was the lower the proportions of stage 2 and the more proportion of stage 3 appeared.When comparing the proportions of clinical stages among the five provinces,significant differences (x2=41.481,P =0.000) were noticed.Proportions of different clinical stages in gender,ethnicity,occupation,place of residence types and the type of pathogen appeared no significant differences,respectively.However,the proportions of squeal and death in stage 2,stage 3 and stage 4 showed significant differences (sequela:x2=12.960,P=0.001;Death:x 2=16.850,P=0.001),respectively.Conclusions The pcrccntage of clinical stages of severe HFMD patients related to the rate of squeal and death.Clinical staging can be used for assessing the clinical severity of complications and the effectiveness of treatment,of HFMD.

Analysis of HA and NA Genes of Influenza A H1N1 Virus in Yunnan Province during 2009-2014 / 病毒学报

To analyze influenza pathogen spectrum in Yunnan province during 2009-2014 years, and analyze HA and NA genes of influenza A H1N1. Analysis was made on the monitoring date of influenza cases in Yunnan province in recent 6 years, 23 strains of influenza virus of HA and NA gene was sequenced and analyzed by MEGA 5 software to construct phylogenetic tree. 4 times of influenza AH1N1 epidemic peak were monitored from 2009-2014 years in Yunnan Province, as the nucleic acid detection results of influenza A H1N1 accounted for 28.8% of the total. The sequencing result showed that HA and NA gene were divided into 3 groups, one was detected with H275Y mutation strains. Influenza A H1N1 is one of the important subtypes in Yunnan province and their genes have divided into three branches during the period of 2009-2014 years, the vast majority of influenza a H1N1 are still sensitive to neuraminidase inhibitors.

Study the roles of KLF2, KLF4 in prediction of acute lung injury in rats induced by endotoxin / 中华急诊医学杂志

Objective To investigate the expressions of KLF2 mRNA and KLF4 mRNA in the acute lung injury (ALl) rats induced by lipopolysaccharide (LPS),and to analyze the correlation between KLF2,KLF4 and ALI.Methods A total of 100 SD rats were randomly divided into 2 groups:normal control group and LPS treated group,then the latter group was randomly further divided into 3 subgroups as per the serum and lung tissue samples taken separately at 2,4 and 24h after modeling.The ALI model was made by injecting 5mg/kg LPS into tail vein.The pathological changes of lung tissue were observed in each group,and the expressions of KLF2,KLF4 mRNA in serum and lung tissue were detected by RT-PCR.The data of laboratory findings were analyzed with SPSS 17.0 software for statistical analysis.Results The histopathological changes showed the most obvious damage of lung tissue occurred at 4 hours after modeling.The expressions of KLF2 mRNA and KLF4 mRNA in the lung tissue and serum of control group were significantly higher compared to LPS treated subgroups (P ＜0.01).The expression of KLF2 mRNA in LPS treated subgroup at 2 hours was lower than that in LPS subgroups at 4 hours and 24 hours (P ＜ 0.01),while the expression of KLF4 mRNA in LPS treated subgroup at 4 hours was lower than that in LPS treated subgroups at 2 hours and 24 hours (P ＜ 0.01).Conclusions The expression of KLF2 mRNA was occurred earlier than the pathological changes in acute lung injury,while the expression of KLF4 was emerged synchronously,and both KLF2 and KLF4 could be used as candidates of predictive and diagnostics molecular markers of ALI.