Propagation research of SARS-CoV-2 based on evolutionary tree and spectral clustering

RNA viruses have the characteristics of a high mutation rate. New Coronavirus (SARS-CoV-2), as a RNA virus, has been mutated to some extent since the outbreak of New Coronavirus pneumonia (COVID-19). It is of great significance to study the evolution and variation of novel coronavirus genes to analyze the source of virus infection and understand the evolution of viruses. This research is based on the Novel Coronavirus 2019 database at the National Genomics Data Center. We combined macro and micro. We used the phylogenetic tree to analyze the gene fragments of the virus, constructed an evolutionary tree with a depth of 301, searched the root node of the tree to find the source of the virus in the data set and used spectral clustering to analyze the degree of novel Coronavirus variation in each country and the clustering results were visualized to make them easier to observe. The experimental results show that the strain sample at the top of the evolutionary tree originated in New Zealand based on the existing data. In the evolutionary tree, the evolutionary process of the virus can be divided into three branches. After clustering the virus source data and constructing the visual map of the variation degree of SARS-COV-2, we found that the viruses in South Africa, New Zealand and other countries had a higher degree of variation, and the viruses in Australia, the United States and other countries have a relatively lower degree of virus variation. © 2022 IEEE.

So what does a public health physician do, exactly? Two lessons from the pandemic

Thanks to the unprecedented circumstances of the past two years, the term “public health” is on the tongues of healthcare community members and laypeople alike more than ever. It is our duty as healthcare trainees and professionals to understand clearly what the practice of public health and preventive medicine entails, so that we may understand where we stand relative to it, and so that we may speak about it responsibly both in and out of this shared community we call medicine. Here, two key points about PHPM are discussed, with vignettes from COVID-19: one, that public health physicians are highly trained specialists;and two, that they are concerned with protecting and promoting the health of communities. © 2022, University of Toronto. All rights reserved.

POSC407 Monitoring of Reported COVID-19 Vaccination Rates in Community Oncology Settings

Objectives: As of 05/27/21, 50.5% of the United States population had initiated COVID-19 vaccination. Vaccination rates, safety and efficacy among those on active chemotherapy are not well published. As a first step towards improving cancer patient care, we explored vaccination rates among patients on active chemotherapy to gain insights on its utilization in this population and improve care of cancer patients. Methods: On 01/23/21, McKesson Specialty Health deployed a COVID Vaccine Administration survey within its iKnowMed electronic health record platform. Cancer patients who answered the survey with ongoing chemotherapy 30 days prior to or after 01/01/21 and ≥2 office visits between 01/01/21 and 05/27/21 were included in the study. Self-reported and onsite vaccination, brand, and COVID-19–related information were recorded. Chi-squared tests were used to determine significant differences between groups. Results: Selection criteria yielded 50,423 patients. The study population was 55% female (n=27,923) with a median age of 68 years (min, max 20, 80+). Approximately 60% (n=11,867) reported initiating vaccination, and 40% (n=7,797) reported being fully vaccinated. The majority of patients reported having received the vaccine by Pfizer (52%, n=10,275), followed by Moderna (45%, n=8,836), Janssen (3%, n=540), and AstraZeneca <1%. Vaccination rates did not differ significantly between females (39%, n=10,799) and males (39%, n=8,865). Patients aged ≤69 years had a significantly lower rate than those older (34%, n=8,928 vs 44%, n=10,736;p<0.0001). Patients with metastatic disease had a significantly higher vaccination rate than those without metastasis (40%, n=14,591 vs. 36%, n=5,073;p<0.0001). Conclusions: This study marks an initial review of the first 6 months post emergency use authorization of COVID-19 vaccinations. The survey responses could not be validated with external data sources. Continued research is needed to investigate reasons for lower rates, adverse effects, and treatment selection, and to monitor patient outcomes amongst vaccinated patients on chemotherapy.

POSB27 Results of Self-Reported EHR COVID Screenings Among Community Oncology Patients

Objectives: On 1/30/20, the World Health Organization declared the COVID-19 pandemic a global emergency. In March 2020, the iKnowMed electronic health records system implemented a screening tool to monitor and report the COVID-19 impact within these at-risk community oncology practices, summarized here. Methods: The study included patients with at least two office visits, on active chemotherapy within the period 30 days prior to 03/01/2020 through 05/19/2021, and within 20 US Oncology Network practices. Screening questions included COVID-19–related symptoms, travel, exposure, and testing Results: Results: A total of 132,457 unique patients satisfied inclusion criteria. Of these, 39% (n=51,620) had at least one screening record, and 564,491 unique screening responses were recorded during the study. A median of 6 (25th- 75th percentiles: 2, 14) screening records per patient was reported. The study population was 67% (n=34,548) female and 58% aged 60-79 years (n=30,042). Approximately 24% (n=12,309) reported having been tested for COVID-19, while 4% (n=499) reported a positive result. Among the COVID-positive patients, 23% (n=114) reported recent symptoms, 9% (n=45) contact with a COVID-positive person, and 1.6% (n=8) travel. Among screened patients (n=51,620), 87% (n=45,164) did not report any symptoms, 77% (n=39,761) did not report any travel outside of their community, and 90 % (n=46,406) did not report exposure to anyone positive for COVID-19. Conclusions: The inclusion of a COVID-19 screening tool within a community oncology EHR provides insights into the effects of the pandemic within a potentially immunocompromised patient population. Descriptive analysis reveals that responses relative to symptoms, travel, and exposure along with percent-positive rates among cancer patients may be lower than the general population. Opportunities to stratify data by stage of disease, metastatic indication and other clinical variables offer future directions for analysis.

COVID-19 Pandemic Impacts Volume of Evaluation & Management (E&M) Telehealth Visits within Community Oncology Practices

Objectives: The USA declared the COVID-19 pandemic a national emergency on 03/13/20. On 03/17/20, CMS expanded telehealth rules, allowing Medicare to cover telehealth visits like regular visits. This study aims to analyze the utilization of Evaluation & Management (E&M) telehealth options in community oncology pre and post pandemic. Methods: Deidentified patient visits data were obtained from iKnowMed electronic health records between 01/01/18 to 05/24/2021 from 20 US Oncology practices. A combination of patient MRN and date was used as an identifier to report number of visits for all measures. Patient visits with modifiers –GT, –95, and –GQ were classified as telehealth visits. Visit dates without modifiers were defined as non-telehealth (in-office) visits. E&M visits were defined based on standard CPT codes. Results: A total of 5,914,125 unique E&M patient visits were analyzed during the study period. Between Jan-2018 and Mar-2020 (pre-COVID-19), E&M visits rose from 30,000/week to 36,000/week (20%). Fewer than 0.01% of these visits were telehealth. By April 12, 2020, overall E&M visits had dropped 35%, but the telehealth visits had risen to 16%. Since then, the overall E&M visit count remained approximately 5% lower as compared to the pre-COVID-19 trend, and telehealth visits averaged approximately 6% thereafter. Corresponding to the 2nd wave, in Dec-2020 the telehealth proportion rose again to 10%. As of 05/23/2021, telehealth E&M visits represented approximately 5% of the total E&M visits within US Oncology practices. Conclusions: This study provides a timeline of how COVID-19 has impacted E&M visits and telehealth utilization among community oncology practices. The pandemic has led to an increase in E&M telehealth visits that may remain post pandemic. Continued research is necessary to monitor telehealth utilization and its impact on the quality of care, provider finances, and future of community oncology considering rising vaccination rates, CDC guidance, and public sentiment.

Performance of serum 2019-nCoV IgM/IgG detection in the rapid diagnosis of COVID-19

Objective: To evaluate the rapid diagnostic value of serum novel coronavirus (2019-nCoV) IgM/IgG detection in COVID-19, aiming to further improve the diagnostic and screening system of COVID-19. Methods: Blood samples were collected from 32 patients with COVID-19 (tested positive for 2019-nCoV nucleic acid by RT-PCR and presented with clinical symptoms) and 34 non-COVID-19 patients (tested negative for 2019-nCoV nucleic acid by RT-PCR and clinically confirmed as non-COVID-19 patients). Colloidal gold-based immunochromatography was used for rapid detection of 2019-nCoV IgM/IgG in these samples. The sensitivity and specificity of the test, and the correlation of serum 2019-nCoV IgM/IgG with disease course were analyzed. Results: Among the 32 COVID-19 patients, nine tested positive for 2019-nCoV IgM with a positive rate of 28.1% (9/32) and 25 positive for 2019-nCoV IgG with a positive rate of 78.1% (25/32). The total positive rate was 84.4% (27/32). Two of the 34 non-COVID-19 patients tested positive for 2019-nCoV IgG with a positive rate of 5.9% (2/34), while none of them was positive for 2019-nCoV IgM. The positive rates of serum IgM were 42.9% (3/7), 30.8% (4/13) and 16.7% (2/12) at 10-20 d, 21-30 d and 31-40 d after the patients developed the symptoms of COVID-19, respectively, which showed a decreasing tread with prolonged disease course. The positive rates of serum IgG in COVID-19 patients were 57.1% (4/7), 84.6% (11/13) and 83.3% (10/12) at 10-20 d, 21-30 d and 30-40 d after symptom onset. The rate showed an increasing trend with prolonged disease course and reached the peak in about 21-30 d. Conclusions: Serum 2019-nCoV IgM/IgG detection (using colloidal gold method) had high sensitivity (84.4%) and strong specificity (94.1%) in the diagnosis of 2019-nCoV infection. It had a great value in the diagnosis and screening of COVID-19 and could be used as a valuable complementary method to the COVID-19 diagnostic system due to its advantages of flexibility, rapidity and simplicity.

[Evaluation of the emergency response strategies and measures on the epidemic of COVID-19 in Shenzhen, China].

Objectives: This study aimed to evaluate the effect of the strategies on COVID-19 outbreak control in Shenzhen, and to clarify the feasibility of these strategies in metropolitans that have high population density and strong mobility. Methods: The epidemic feature of COVID-19 was described by different phases and was used to observe the effectiveness of intervention. Hierarchical spot map was drawn to clarify the distribution and transmission risk of infection sources at different time points. The Susceptible-Exposed-Infectious-Asymptomatic-Recovered model was established to estimate case numbers without intervention and compare with the actual number of cases to determine the effect of intervention. The positive rate of the nucleic acid test was used to reflect the risk of human exposure. A survey on COVID-19 related knowledge, attitude and behaviors were used to estimate the abilities of personal protection and emergency response. Results: The epidemic of COVID-19 in Shenzhen experienced the rising, plateau and decline stage. The case number increased rapidly at the beginning, with short duration of peak period. Although the epidemic curve showed human-to-human transmission, the "trailing" was not obvious. From the spot map, during the intervention period, the source of infection was widely distributed. More cases and higher transmission risk were observed in areas with higher population density. After the effective intervention measures, both infection sources and the risk of transmission decreased. After compared with the estimated case numbers without intervention, actual number proved the COVID-19 control strategies were effective. The positive rate of nucleic acid test for high risk populations decreased and no new cases reported since February 16. Shenzhen citizens had high knowledge, attitude and behavior level, and high protection ability and emergency response. Conclusions: Although the response initiated by the health administration department played a key role at the early stage of the epidemic, it was not enough to contain the outbreak of COVID-19. The first-level emergency response initiated by provincial and municipal government was effective and ensured the start of work resumption after the Spring Festival. Metropolitans like Shenzhen can also achieve the goals of strategies and measures for containment and mitigation of COVID-19.

[The network investigation on knowledge, attitude and practice about COVID-19 of the residents in Anhui Province].

Objective: To analyze the current situation of the knowledge, attitudes and practice about COVID-19 of the residents in Anhui Province. Methods: Anonymous network sampling survey was carried out with an electronic questionnaire that designed by the questionnaire star, and a total of 4 016 subjects from Anhui province were investigated. The content of the survey includes that the basic information of subjects,the residents' knowledge, attitudes and practice about COVID-19, as well as their satisfaction with the prevention and control measures adopted by the government and health authorities and the suggestions on future prevention. The questionnaire doesn't involve any privacy information, and all questions were mandatory to ensure the response rate. Results: The M (P(25), P(75)) age the 4 016 subjects was 21 (19, 24) years old, and the ranging from 7 to 80 years old. The number of males was 1 431 (35.6%). Social networking tools such as WeChat and QQ were the main sources of epidemic information for residents (97.8%, 3 929 respondents). Residents had higher awareness rate of cough (99.5%,n=3 997) and fever (96.0%, n=3 857) symptoms, the transmission by droplets (99.5%, n=3 995), aerosol transmission (81.1%, n=3 258), and contact transmission (92.3%, n=3 708), but lower awareness of symptoms os muscle pain or fatigue (62.7%, n=2 518). 92.6% of the subjects (n=3 720) think that the outbreak was scary. In terms of psychological behavior scores, the results showed that female (9.38±4.81), the urban (9.37±5.02) and the medical workers (10.79±5.19) had a poorer mental health than the male (8.45±5.00), the rural (8.71±4.75) and the non-medical workers (the students: 8.85±4.83; public institude workers: 9.02±5.08; others: 8.97±5.39) (P<0.05). 71.9% of the residents (n=2 887) were satisfied with the local epidemic control measures. The residents took various of the measures to prevent and control the epidemic. The ratio of residents that could achieve "no gathering and less going out" , "wear masks when going out " and " do not go to crowded and closed places " was up to 97.4% (n=3 913), 93.6% (n=3 758) and 91.5% (n=3 673) respectively. Conclusion: The residents in Anhui province have a good KAP about COVID-19, yet it is necessary to strengthen the community publicity, the mental health maintenance of residents and students' health education.

[The network investigation on knowledge, attitude and practice about Novel coronavirus pneumonia of the residents in Anhui Province].

Objective: To analyze the current situation of the knowledge, attitudes and practice about Novelcoronavirus pneumonia (NCP) of the residents in Anhui Province. Methods: Anonymous network sampling survey was carried out with an electronic questionnaire that designed by the questionnaire star, and a total of 4016 subjects from Anhui province were investigated. The content of the survey includes that the basic information of subjects,the residents' knowledge, attitudes and practice about NCP, as well as their satisfaction with the prevention and control measures adopted by the government and health authorities and the suggestions on future prevention. The questionnaire doesn't involve any privacy information, and all questions were mandatory to ensure the response rate. Results: The M (P(25), P(75)) age the 4016 subjects was 21 (19, 24), and the ranging from 7 to 80 years old. The number of males was1431(35.6%). Social networking tools such as WeChat and QQ were the main sources of epidemic information for residents (97.8%, 3 929 respondents). Residents have a high awareness rate of the main symptoms, transmission routes, using of masks, hand washing and treatment information of NCP, while a low awareness rate of the atypical symptoms. 92.6% of the subjects (n=3 720) think that the outbreak was scary. In terms of psychological behavior scores, the results showed that female (9.38±4.81), the urban (9.37±5.02) and the medical workers (10.79±5.19) had a poorer mental health than the male (8.45±5.00) , the rural (8.71±4.75) and the non-medical workers (the students: 8.85±4.83; public institude workers: 9.02±5.08; others: 8.97±5.39) (P < 0.05). 71.9% of the residents (n=2 887)were satisfied with the local epidemic control measures. The residents took various of the measures to prevent and control the epidemic. The ratio of residents that could achieve "no gathering and less going out" , "wear masks when going out" and "do not go to crowded and closed places" was up to 97.4% (n=3 913), 93.6% (n=3758) and 91.5% (n=3 673) respectively. Conclusion: The residents in Anhui province have a good KAP about NCP, yet it is necessary to strengthen the community publicity, the mental health maintenance of residents and students' health education.