Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing

Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS

Table_1_Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing.XLSX

Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS.</p

Image_1_Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing.pdf

Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS.</p

Investigation on Risk Factors and Main Symptoms of Long COVID and Their Influences on the Follow-up Research

Background Long COVID is a common problem in the recovery period of coronavirus disease (COVID-19). The prevention and treatment of long COVID has become the focus of the medical fields of COVID-19. It is important to clarify the situation of long COVID in China and find out the follow-up research route, thus providing evidence-based evidence for clinical practice. Objective To explore the characteristics of long COVID in China, aiming to provide references for the follow-up research. Methods From January 2023 to August 2023, a self-made survey questionnaire was used to investigate the current situation of long COVID in China. The questionnaire included general information, such as gender and age, treatment expectations, symptoms and signs in acute and recovery period, etc. Results A total of 1 001 questionnaires were collected, including 901 people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and 585 (64.9%) people with long COVID. Binary Logistic regression analysis showed that female (OR=2.000, 95%CI=1.477-2.705, P&lt;0.05), history of cancer (OR=4.424, 95%CI=1.316-14.868, P&lt;0.05), and retirement (OR=1.527, 95%CI=1.048-2.224, P&lt;0.05) were risk factors for long COVID. Among the 19 symptoms and signs of long COVID, the top three were fatigue (341 people), decrease of memory, comprehension and attention (274 people), and insomnia (217 people). Low back pain was the leading pain symptom (201 people). Hair loss was the number one sign to be difficult to self-healing (58.57%). Acupuncture (55.73%) was the top 1 willingness of treatment, followed by Chinese herbal decoction (53.68%), Chinese traditional patent medicine (47.01%), Western medicine (24.79%), intravenous drip (12.14%), and hospitalization (11.97%) . Conclusion The incidence of long COVID is relatively high in China. Acupuncture therapy enjoys a widespread favor among patients. It is recommended to carry out targeted research to enhance the clinical evidence for the prevention and treatment of acupuncture therapy. Women, cancer patients, and retired individuals (elderly people) are high-risk groups for long COVID, and low immune function is a common feature among them. It is suggested to establish a database incorporating these populations and conduct cohort studies on the prevention of long COVID through acupuncture. Fatigue, insomnia, and low back pain are more representative symptoms of long COVID, and randomized controlled studies on acupuncture treatment for these three symptoms at first are recommended

SPECFEM/specfem3d_globe: SPECFEM3D_GLOBE v8.1.0

&lt;p&gt;New in SPECFEM3D_GLOBE v8.1.0:&lt;/p&gt; &lt;ul&gt; &lt;li&gt;adds EMC model support&lt;/li&gt; &lt;li&gt;minor fixes and code improvements (including newer HIP and CUDA configuration)&lt;/li&gt; &lt;li&gt;updates ADIOS2 and LIBXSMM calls&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;em&gt;with many thanks for contributions to this version&lt;/em&gt;: Daniel Peter, Julien Thurin, Lucas Sawade&lt;/p&gt