Lower respiratory tract samples are reliable for severe acute respiratory syndrome coronavirus 2 nucleic acid diagnosis and animal model study
摘要: 新型冠状病毒（SARS-CoV-2）及其造成的肺炎（COVID-19）持续严重影响世界各国。稳定可靠的诊断方法和评价系统的欠缺严重阻碍了有效预防和治疗策略的实施和发展。该研究通过横向和纵向研究，比较分析来源于COVID-19患者和SARS-CoV-2感染猴的不同类型样本中SARS-CoV-2的核酸检出率，分析COVID-19患者和SARS-CoV-2感染猴血清中抗SARS-CoV-2抗体的阳性率，以评估SARS-CoV-2感染诊断方法的可靠性。结果显示无论感染者的临床症状如何，痰液和气管刷样品中病毒核酸检出率较高，感染确诊率高，诊断结果稳定。而6.90% COVID-19患者血清中未检测到抗SARS-CoV-2免疫球蛋白M和G。此外，同时采集不同类型样本并结合其核酸检测的结果并不能提高诊断率。另外，与鼻拭子和咽拭子相比，痰和气管刷中SARS-CoV-2病毒载量持续时间较长，动态变化较明显。因此，痰和气管刷中SARS-CoV-2核酸检测受感染途径、疾病进展和个体差异的影响较小，用下呼吸道标本进行SARS-CoV-2核酸检测是SARS-CoV-2感染诊断和研究的可靠依据。Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 2019 (COVID-19) continue to impact countries worldwide. At present, inadequate diagnosis and unreliable evaluation systems hinder the implementation and development of effective prevention and treatment strategies. Here, we conducted a horizontal and longitudinal study comparing the detection rates of SARS-CoV-2 nucleic acid in different types of samples collected from COVID-19 patients and SARS-CoV-2-infected monkeys. We also detected anti-SARS-CoV-2 antibodies in the above clinical and animal model samples to identify a reliable approach for the accurate diagnosis of SARS-CoV-2 infection. Results showed that, regardless of clinical symptoms, the highest detection levels of viral nucleic acid were found in sputum and tracheal brush samples, resulting in a high and stable diagnosis rate. Anti-SARS-CoV-2 immunoglobulin M (IgM) and G (IgG) antibodies were not detected in 6.90% of COVID-19 patients. Furthermore, integration of nucleic acid detection results from the various sample types did not improve the diagnosis rate. Moreover, dynamic changes in SARS-CoV-2 viral load were more obvious in sputum and tracheal brushes than in nasal and throat swabs. Thus, SARS-CoV-2 nucleic acid detection in sputum and tracheal brushes was the least affected by infection route, disease progression, and individual differences. Therefore, SARS-CoV-2 nucleic acid detection using lower respiratory tract samples alone is reliable for COVID-19 diagnosis and study.
Figure 1. Sample distribution, distribution, and frequency of SARS-CoV-2 nucleic acid-positive samples
In total, 394 samples from COVID-19 patients (A) and 420 samples from SARS-CoV-2-infected monkeys (B) were included in this study. Nucleic acid was purified from COVID-19 patient samples (C, E) and SARS-CoV-2-infected monkey samples (D, F). SARS-CoV-2 was detected by real-time RT-PCR with a TaqMan probe. Distributions of SARS-CoV-2 nucleic acid-positive samples (C, D) and frequency of positive samples (E, F) are shown.
Figure 2. Diagnosis rates in individuals based on sample type and anti-SARS-CoV-2 antibody assays
Nucleic acid was purified from COVID-19 patient samples (A) and SARS-CoV-2-infected monkey samples (B). SARS-CoV-2 was detected by real-time RT-PCR with a TaqMan probe. Diagnosis rate in individuals based on sample type is shown. Each dot represents an individual. Serum from clinical patients was used for anti-SARS-CoV-2 IgM and IgG antibody (Ab) assays with magnetic particle chemiluminescence. Dynamic changes in IgM (up) and IgG (low) against SARS-CoV-2 in serum of asymptomatic, mild, moderate, and severe/critical COVID-19 patients are shown (C). Positive rates at 1, 3, 7, 12, and 18 days after hospitalization are shown (D).
Figure 3. Diagnosis rates based on integration of nucleic acid detection results from different sample types
Nucleic acid was purified from COVID-19 patient samples (A) and SARS-CoV-2-infected monkey samples (B). SARS-CoV-2 was detected by real-time RT-PCR with a TaqMan probe. Diagnosis rate in individuals based on detection rate of multiple sample types is shown. “/” means or.
Figure 4. Dynamic changes in SARS-CoV-2 load
Nucleic acid was purified from nasopharyngeal swabs (A), pharyngeal swabs (B), and sputum samples (C) obtained from COVID-19 patients or nasal swabs (D), pharyngeal swabs (E), and tracheal brushes (F) obtained from SARS-CoV-2-infected monkeys. SARS-CoV-2 was detected by real-time RT-PCR with a TaqMan probe. SARS-CoV-2 load is shown using cycle threshold (Ct). Each different colored dot and shape represent an individual.
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ZR-2020-329 Supplementary Tables and Figures.pdf