Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

Random genetic drift in the population-level dynamics of an infectious disease outbreak results from the randomness of inter-host transmission and the randomness of host recovery or death. The strength of genetic drift has been found to be high for SARS-CoV-2 due to superspreading, and this is expected to substantially impact the disease epidemiology and evolution. Noise that results from the measurement process, such as biases in data collection across time, geographical areas, etc., can potentially confound estimates of genetic drift as both processes contribute "noise" to the data. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude. Corrections taking into account epidemiological dynamics (susceptible-infected-recovered or susceptible-exposed-infected-recovered models) do not explain the discrepancy. Moreover, the levels of genetic drift that we observe are higher than the estimated levels of superspreading found by modeling studies that incorporate data on actual contact statistics in England. We discuss how even in the absence of superspreading, high levels of genetic drift can be generated via community structure in the host contact network. Our results suggest that further investigations of heterogeneous host contact structure may be important for understanding the high levels of genetic drift observed for SARS-CoV-2 in England.

Type II Respiratory Failure with Systemic Sclerosis/Polymyositis Overlap Syndrome：A Case Report of Successful Respiratory Rehabilitation Therapy / The Japanese Journal of Rehabilitation Medicine

Introduction：Respiratory failures are categorized into types I and II. To our knowledge, we report the first case of pulmonary rehabilitation in a patient with systemic sclerosis/polymyositis overlap syndrome who developed type II respiratory failure.Methods：The patient was a 77-year-old woman who had received treatment for systemic sclerosis and polymyositis at another hospital. When she visited our hospital to obtain a second opinion, she suddenly lost consciousness and underwent trachea intubation because of typeⅡrespiratory failure. She received physical therapy on the third day of hospitalization and underwent a tracheotomy on the 16th day. As her thoracic movement was markedly restricted, we started physical training. After she was weaned off from the ventilator on the 43rd day, we performed muscular strength training and aerobic exercise. No exacerbation of CO2 storage was observed even if chest motion training was performed. She was discharged on the 72nd day and advised to wear retina®．Administration of therapeutic drugs such as steroids was maintained at the same dose.Conclusion：Physical therapy, such as chest mobilization, was effective for marked restriction of chest movement in a patient who had both polymyositis and systemic sclerosis.

Type II Respiratory Failure with Systemic Sclerosis/Polymyositis Overlap Syndrome：A Case Report of Successful Respiratory Rehabilitation Therapy / The Japanese Journal of Rehabilitation Medicine

Introduction：Respiratory failures are categorized into types I and II. To our knowledge, we report the first case of pulmonary rehabilitation in a patient with systemic sclerosis/polymyositis overlap syndrome who developed type II respiratory failure.Methods：The patient was a 77-year-old woman who had received treatment for systemic sclerosis and polymyositis at another hospital. When she visited our hospital to obtain a second opinion, she suddenly lost consciousness and underwent trachea intubation because of typeⅡrespiratory failure. She received physical therapy on the third day of hospitalization and underwent a tracheotomy on the 16th day. As her thoracic movement was markedly restricted, we started physical training. After she was weaned off from the ventilator on the 43rd day, we performed muscular strength training and aerobic exercise. No exacerbation of CO2 storage was observed even if chest motion training was performed. She was discharged on the 72nd day and advised to wear retina®．Administration of therapeutic drugs such as steroids was maintained at the same dose.Conclusion：Physical therapy, such as chest mobilization, was effective for marked restriction of chest movement in a patient who had both polymyositis and systemic sclerosis.

Promoter effects of adeno-associated viral vector for transgene expression in the cochlea in vivo

The aims of this study were to evaluate the expression of enhanced green fluorescent protein (EGFP) driven by 6 different promoters, including cytomegalovirus IE enhancer and chicken beta-actin promoter (CAG), cytomegalovirus promoter (CMV), neuron-specific enolase promoter (NSE), myosin 7A promoter (Myo), elongation factor 1alpha promoter (EF-1alpha), and Rous sarcoma virus promoter (RSV), and assess the dose response of CAG promoter to transgene expression in the cochlea. Serotype 1 adeno-associated virus (AAV1) vectors with various constructs were transduced into the cochleae, and the level of EGFP expression was examined. We found the highest EGFP expression in the inner hair cells and other cochlear cells when CAG promoter was used. The CMV and NSE promoter drove the higher EGFP expression, but only a marginal activity was observed in EF-1alpha promoter driven constructs. RSV promoter failed to driven the EGFP expression. Myo promoter driven EGFP was exclusively expressed in the inner hair cells of the cochlea. When driven by CAG promoter, reporter gene expression was detected in inner hair cells at a dose as low as 3 x 10(7) genome copies, and continued to increase in a dose- dependent manner. Our data showed that individual promoter has different ability to drive reporter gene expression in the cochlear cells. Our results might provide important information with regard to the role of promoters in regulating transgene expression and for the proper design of vectors for gene expression and gene therapy.

RELATIONSHIP BETWEEN SPORT ACTIVITY DURING ADOLESCENCE AND ABNORMALITIES OF LUMBAR SPINE— A RADIOLOGIC AND MAGNETIC RESONANCE IMAGING STUDY — / 体力科学

To investigate the relationship between adolescent sport activity and abnormalities of the lumbar spine on radiography and magnetic resonance imaging (MRI), 237 collegiate athletes (mean age 19.4), representing judo, wrestling, and track, were analyzed from the point of contact or noncontact sports. Radiologic and/or MRI abnormalities of the lumbar spine were found in 68.7% of contact sports athletes (judo and wrestling, n=147), 53.3% of noncontact sports athletes (track, n=90), 69.9% of athletes who have played contact sports over 9 years (C9 athletes, n=83), and 47.1% of atheletes who have done noncontact sports over 9 years (N9 athletes, n=17). Discopathy related abnormalities on radiologic examination were found in 25.3% and 11.8% of C9 and N9 athletes. Disc degeneration on MRI was found in 45.8% and 29.4% of C9 and N9 athletes. Spondylolysis was found in 31.3% of C9, 5.9% of N9, 31.3% of elementary-C (athletes who played contact sports during elementary school, n=96), 32.8% of elementary-L/I (limited contact/impact sports, n=58), and 8.6% of elementary-N athletes (noncontact sports, n=35), respectively. From these results, we concluded that contact sports activity during adolescence induces lumbar spine abnormalities at a higher rate compared to noncontact sports and that spondylolysis is related to contact or limited contact/impact sport activity during elementary school.

[Regulation of AAV-mediated glial cell-line derived neurotrophic factor expression by using improved Tet-on trans-activator].

OBJECTIVE: To control the expression of AAV-mediated glial cell-line derived neurotrophic factor (GDNF) gene purposely by incorporating novel Tet-On trans-activator rtTA2s-S2, which prevents potential harms caused by over-expression of recombinant target genes. METHODS: Oligonucleotide with specific monocloning sites was inserted into the hHG part of pAAV-GDNFflag. Trans-activator from pUHrT61-rtTA2s-S2 and TRE from pTRE-d2EGFP were amplified by PCR and inserted into pCRII-TOPO respectively. Possible mutation was eliminated by sequencing. TRE and rtTA2s-S2 were then inserted into the oligonucleotide of pAAV-GDNFflag to form pAAV-rtTA2s-S2-TRE-GDNFflag. pAAV-rtTA2s-S2-TRE-d2EGFP was constructed by replacing the GDNFflag part with d2EGFP. The plasmids were digested by Xba I and compared with theoretic values. HEK 293 cells were cultured and co-transfected with pAAV-GDNFflag and helper plasmids pHLP19 and pAdeno5 so as to complete the package of recombinant adeno-associated virus (rAAV) Crude virus lysate was purified by two-sequential continuous CsCl gradient ultracentrifugation, dialyzed and condensed by millipore filter. The titer of rAAV was determined by real-time quantitative PCR. Another HEK293 cells were cultured, transfected with rAVV, and then cultured in 2 kinds of culture fluid: with or without doxycyclin (Dox). Fluorescence microscopy was used to calculate the percentage of fluorescent cells so as to detect AAV-rtTA2s-S2-TRE-d2EGFP, and Western blotting was used to detect the GDNF protein in the lysate of the HEK293 cells, thus testifying the regulatory function in vitro of rtTA2s-S2. Twenty male Wistar mice were randomly divided into 2 groups: experiment group, fed with Dox and sucrose (Dox-positive group), and control group, fed with only sucrose (Dox-negative group). Two days after AAV-rtTA2s-S2-TRE-GDNF was injected into the gastrocnemius muscles of the mice. Two weeks the mice were killed and their gastrocnemius muscles were taken out. ELISA was used to examine the content of GDNF in the homogenate of gastrocnemius muscle so as to examine the regulatory effect of rtTA2s-S2 in vivo. RESULTS: Tests showed that the recombinant plasmids were constructed correctly. The fluorescent cell positive rate in the Dox-positive culture fluid of HEK293 cells was 52.4%, significantly higher than that in the Dox-negate culture fluid (7.2%, P < 0.01). Western blotting of the HEK 293 cell lysate showed clear band of GDNF in the Dox-positive group and failed to show visible band in the Dox-negative group. The content of GDNF in the homogenate of gastrocnemius muscles of the Dox-positive group was 32.6pg/ml +/- 2.6 pg/ml, significantly higher than that of the Dox-negative group (10.1 pg/ml +/- 2.4 pg/ml, P < 0.01). CONCLUSION: Novel Tet-on trans-activator rtTA2s-S2 regulates downstream AAV-mediated GDNF expression in a stringent manner and does not impair AAV infecting efficiency when constructed together with TRE and GDNF within one AAV vector.