Testing and diagnosis for COVID-19

Abstract

Nucleic acid amplification tests for coronavirus diseases (COVID-19) were nearly established by the end of January 2020, mainly at regional Public Health Laboratories (PHLs) nationwide. Initially, the nucleic acid amplification test was a combination of conventional PCR and sequencing, in accordance with the pathogen detection manual of the National Institute of Infectious Diseases (NIID). However, this was soon changed to a real-time PCR method (NIID method), and test reagents were distributed by the NIID. In order to cope with the further increase in the number of tests, private laboratories began testing for novel coronaviruses in March, and PHLs cooperated with the launch of testing by private laboratories. Subsequently, a large variety of test reagents that replaced the NIID method were approved by the Ministry of Health, Labour and Welfare as in vitro diagnostic products.

In December 2020, highly infectious variants of SARS-CoV-2 emerged, and the PHL also became involved in screening tests and genome analysis to identify and analyze the alpha strain and other strains specified as Variants of Concern (VOC) by the World Health Organization (WHO). The epidemic that followed was characterized by a replacement of the initial variant with new variants, and the PHL also added SARS-CoV-2 whole-genome analysis using next-generation sequencers (NGS) and variant surveillance via real-time PCR to its work. This manuscript outlines the events of the past three years, including the establishment of Nucleic acid amplification tests at PHLs and our response to new variants.