A full genome tiling array enhanced the inspection and quarantine of SARS-CoV-2.

As the worldwide spreading epidemic of SARS-CoV-2, quick inspection and quarantine of passengers for SARS-CoV-2 infection are essential for controlling the spread of SARS-CoV-2, especially the cross-border transmission. This study reports a SARS-CoV-2 genome sequencing method based on a re-sequencing tiling array successfully used in border inspection and quarantine. The tiling array chip has four cores, with one core of 240,000 probes dedicated to the whole genome sequencing of the SAR-CoV-2 genome. The assay protocol has been improved to reduce the detection time to within one day and can detect 96 samples in parallel. The detection accuracy has been validated. This fast and simple procedure is also of low cost and high accuracy, and it is particularly suitable for the rapid tracking of viral genetic variants in custom inspection applications. Combining these properties means this method has significant application potential in the clinical investigation and quarantine of SARS-CoV-2. We used this SARS-CoV-2 genome re-sequencing tiling array to inspect and quarantine China's entry and exit ports in the Zhejiang Province. From November 2020 to January 2022, we observed the gradual shift of SARS-CoV-2 variants from the D614G type to the Delta Variant, and then to the dominance of the Omicron variant recently, consistently with the global emergency pattern of the new SARS-CoV-2 variant.

SARS-CoV-2 variant identification using a genome tiling array and genotyping probes.

With over 5.5 million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. The authors previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.

Throughout the COVID-19 pandemic the virus known as SARS-CoV-2 has continued to mutate and evolve. It is imperative to continue to track these mutations and where the virus has traveled to best inform healthcare practices and global strategies to combat the virus. The authors previously developed a method to investigate 95% of this viral genome with 99.9% accuracy that was more cost-effective and less time-consuming than previous methods. In this work, specific markers were added to the technology to allow tracking of mutations in the virus that have already been documented. In doing so, the accuracy and how much of the viral genome can be sequenced was improved.

Detecting SARS-CoV-2 and its variant strains with a full genome tiling array.

Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis.

Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples.

SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.

Differential diagnosis between the coronavirus disease 2019 and Streptococcus pneumoniae pneumonia by thin-slice CT features.

OBJECTIVE: The chest computed tomography (CT) features of coronavirus disease 2019 (COVID-19) and Streptococcus pneumoniae pneumonia (S. pneumoniae pneumonia) were compared to provide further evidence for the differential imaging diagnosis of patients with these two types of pneumonia. METHODS: Clinical information and chest CT data of 149 COVID-19 patients between January 9, 2020 and March 15, 2020 and 97 patients with S. pneumoniae pneumonia between January 23, 2011 and March 18, 2020 in Zhongnan Hospital of Wuhan University were retrospectively analyzed. In addition, CT features were comparatively analyzed. RESULTS: According to the chest CT images, the probability of lung segmental and lobar pneumonia in S. pneumoniae pneumonia was higher than that in COVID-19(P<0.001); the probabilities of ground-glass opacity (GGO), the "crazy paving" sign, and abnormally thickened interlobular septa in COVID-19 were higher than those in S. pneumoniae pneumonia(P = 0.005, P<0.001, P<0.001, respectively); and the probabilities of consolidation lesions, bronchial wall thickening, centrilobular nodules, and pleural effusion in S. pneumoniae pneumonia were higher than those in COVID-19 (P<0.001, P = 0.001, P = 0.003, P = 0.001, respectively). CONCLUSION: The findings of GGO, the crazy paving sign, and abnormally thickened interlobular septa on chest CT were significantly higher in COVID-19 than S. pneumoniae pneumonia. The most important differential points on chest CT signs between COVID-19 and S. pneumoniae pneumonia were whether disease lesions were distributed in entire lung lobes and segments and whether the crazy paving sign, interlobular septal thickening, and consolidation lesions were found.

Pulmonary fibrosis in critical ill patients recovered from COVID-19 pneumonia: Preliminary experience.

OBJECTIVE: To investigate chest computed tomography (CT) findings associated with severe COVID-19 pneumonia in the early recovery period. METHODS: We retrospectively analyzed the cases of patients diagnosed with severe COVID-19 pneumonia at a single center between January 12, 2020, and March 16, 2020. The twelve ICU patients studied had been diagnosed SARS-CoV-2 (COVID-19) nucleic acid positive. Patient clinical symptoms were relieved or disappeared, and basic clinical information and laboratory test results were collected. The study focused on the most recent CT imaging characteristics. RESULTS: The average age of the 12 patients was 58.8 ± 16.2 years. The most prevalent symptoms were fever (100%), dyspnea (100%), and cough (83.3%). All patients experienced acute respiratory distress syndrome (ARDS), of which 9 were moderate to severe. Six patients used noninvasive ventilators, and 4 patients used mechanical ventilation. One patient was treated with extracorporeal membrane oxygenation (ECMO). The lymphocyte count decreased to 0.67 ± 0.3 (× 10 9/L). The average day from illness onset to the last follow-up CT was 56.1 ± 7.7 d. The CT results showed a decrease in ground glass opacities (GGO), whereas fibrosis gradually increased. The common CT features included GGO (10/12, 83.3%), subpleural line (10/12, 83.3%), fibrous stripes (12/12, 100%), and traction bronchiectasis (10/12, 83.3%). Eight patients (66.7%) showed predominant reticulation and interlobular thickening. Four patients (33.3%) showed predominant GGO. Lung segments involved were 174/216 (80.6%). CONCLUSIONS: Fibrous stripes and GGO are common CT signs in critically ill patients with COVID-19 pneumonia in the early recovery period. Signs of pulmonary fibrosis in survivors should be carefully monitored.

Chest CT findings of COVID-19 pneumonia by duration of symptoms.

PURPOSE: To evaluate lung abnormalities on thin-section computed tomographic (CT) scans in patients with COVID-19 and correlate findings to duration of symptoms. METHODS: In total, 348 CT scans in 112 patients were classified according to the time after the onset of the initial symptoms, namely stage-1 (0-4 days); stage-2 (5-9 days); stage-3 (10-14 days); stage-4 (15-21 days); stage-5 (22-28 days); and stage-6 (＞28 days). Each lung lobe was evaluated for extent affected by ground-glass opacities (GGO), crazy-paving pattern and consolidation, in five categories of percentual severity. Summation of scores from all five lung lobes provided the total CT score (maximal CT score, 25). RESULTS: The predominant patterns of lung abnormalities were GGOs, crazy-paving pattern, consolidation and linear opacities. The frequency of crazy-paving pattern, consolidation and linear opacities peaked at stage-3 (62.7 %), stage-4 (75.0 %) and stage-5 (83.1 %), respectively, and decreased thereafter. Total CT scores increased from stage-1 to stage-2 (2.8 ± 3.1, vs. 6.5 ± 4.6, respectively, P < 0.01), and thereafter remained high. The lower lobes were more inclined to be involved with higher CT scores except for stage-1. At stage-6 98.1 % of CT scans still showed abnormalities (CT score 7.5 ± 4.1). CONCLUSION: Thin-section CT could provide semi-quantitative analysis of pulmonary damage severity. This disease changed rapidly at the early stage, then tended to be stable and lasted for a long time.