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

Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance

The genomic analysis of SARS-CoV-2 has served as a crucial tool for generating invaluable data that fulfils both epidemiological and clinical necessities. Long-read sequencing technology (e.g., ONT) has been widely used, providing a real-time and faster response when necessitated. A novel nanopore-based long-read sequencing platform named QNome nanopore has been successfully used for bacterial genome sequencing and assembly; however, its performance in the SARS-CoV-2 genomic surveillance is still lacking. Synthetic SARS-CoV-2 controls and 120 nasopharyngeal swab (NPS) samples that tested positive by real-time polymerase chain reaction were sequenced on both QNome and MGI platforms in parallel. The analytical performance of QNome was compared to the short-read sequencing on MGI. For the synthetic SARS-CoV-2 controls, despite the increased error rates observed in QNome nanopore sequencing reads, accurate consensus-level sequence determination was achieved with an average mapping quality score of approximately 60 (i.e., a mapping accuracy of 99.9999%). For the NPS samples, the average genomic coverage was 89.35% on the QNome nanopore platform compared with 90.39% for MGI. In addition, fewer consensus genomes from QNome were determined to be good by Nextclade compare with MGI (p < 0.05). A total of 9004 mutations were identified using QNome sequencing, with substitutions being the most prevalent, in contrast, 10 997 mutations were detected on MGI (p < 0.05). Furthermore, 23 large deletions (i.e., deletions≥ 10 bp) were identified by QNome while 19/23 were supported by evidence from short-read sequencing. Phylogenetic analysis revealed that the Pango lineage of consensus genomes for SARS-CoV-2 sequenced by QNome concorded 83.04% with MGI. QNome nanopore sequencing, though challenged by read quality and accuracy compared to MGI, is overcoming these issues through bioinformatics and computational advances. The advantage of structure variation (SV) detection capabilities and real-time data analysis renders it a promising alternative nanopore platform for the surveillance of the SARS-CoV-2.

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.

The Built Environment Assessment of Residential Areas in Wuhan during the Coronavirus Disease (COVID-19) Outbreak

The COVID-19 epidemic has emerged as one of the biggest challenges, and the world is focused on preventing and controlling COVID-19. Although there is still insufficient understanding of how environmental conditions may impact the COVID-19 pandemic, airborne transmission is regarded as an important environmental factor that influences the spread of COVID-19. The natural ventilation potential (NVP) is critical for airborne infection control in the micro-built environment, where infectious and susceptible people share air spaces. Taking Wuhan as the research area, we evaluated the NVP in residential areas to combat COVID-19 during the outbreak. We determined four fundamental residential area layouts (point layout, parallel layout, center-around layout, and mixed layout) based on the semantic similarity model for point of interest (POI) picking. Our analyses indicated that the center-around and point layout had a higher NVP, while the mixed and parallel layouts had a lower NVP in winter and spring. Further analysis showed that the proportion of the worst NVP has been rising, while the proportion of the poor NVP remains very high in Wuhan. This study suggested the need to efficiently improve the residential area layout in Wuhan for better urban ventilation to combat COVID-19 without losing other benefits.