ABSTRACT
Fatal infectious diseases caused by RNA viruses, such as COVID-19, have emerged around the world. RT-PCR is widely employed for virus detection, and its accuracy depends on the primers and probes since RT-PCR can detect a virus only when the primers and probes bind to the target gene of the virus. Most of primer design methods are for a single host and so require a great deal of effort to design for RNA virus detection, including homology tests among the host and all the viruses for the host using BLAST-like tools. Furthermore, they do not consider variant sequences, which are very common in viruses. In this study, we describe VPrimer, a method of designing high-quality primer-probe sets for RNA viruses. VPrimer can find primer-probe sets that cover more than 95% of the variants of a target virus but do not cover any sequences of other viruses or the host. With VPrimer, we found 381,698,582 primer-probe sets for 3,104 RNA viruses. Multiplex PCR assays using the top 2 primer-probe sets suggested by VPrimer usually cover 100% of variants. To address the rapid changes in viral genomes, VPrimer finds the best and up-to-date primer-probe sets incrementally against the most recently reported variants.
ABSTRACT
Through a quantitative approach, this study aimed to clarify the changes in the number of visitors and visits to green spaces according to green space type before and after the COVID-19 pandemic. We explored the changes in the proportion of repeat visitors and the distance between green spaces and visitors' places of residence. We used KDDI Location Analyzer, which performs novel analysis using mobile phone GPS and census data. The study area included 10 target sites (urban parks and nature trails in the backcountry) located in the Sapporo metropolitan area in Japan. The survey period included snow-free seasons from 2019 to 2021, and 2019 was considered the period "before the pandemic." The results revealed that the number of visits during the pandemic increased compared with those before the pandemic, except for those of urban parks near the city center. In 2020, the proportion of repeat visitors increased for all 10 target sites. In addition, since the outbreak of the pandemic, distances between all urban parks and visitors' residences decreased. The same trend was observed for nature trails in the backcountry close to the city center. These findings indicate a generally decreasing trend in the number of visits to green spaces as many people have been refraining from visiting the site since the outbreak of the pandemic. Contrastingly, the number of visits by repeat visitors who reside close to the target sites has increased in some cases, which compensated for the general decreases.