ABSTRACT
We report the first pediatric patient infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant in Japan. The patient was a one-year-old boy who resided in Japan. He went abroad from 12 November 2021 to 28 November 2021 with his parents and had no known contact with COVID-19 patients there. His father tested positive for SARS-CoV-2 via quantitative antigen test on arrival at Narita International Airport on 28 November 2021. Because the boy and his mother both tested negative for SARS-CoV-2, they quarantined together at a hotel separately from his father. On 4 December 2021, the boy tested positive by reverse-transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 without symptoms and was hospitalized with his mother. He and his father were both found to be infected with SARS-CoV-2 Omicron variant. The boy had not been vaccinated for COVID-19. The RT-PCR results were negative starting 20 December 2021. The incubation period and required period for negative conversion of SARS-CoV-2 RNA of this Omicron variant case were similar to the periods of conventional cases. We have to carefully consider the potential of the SARS-CoV-2 Omicron variant to spread widely among unvaccinated children.
ABSTRACT
The World Health Organization designated Omicron (B.1.1.529 lineage) of SARS-CoV-2 as a new variant of concern on November 26, 2021. The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we describe the development of two single-nucleotide polymorphism genotyping assays targeting the G339D or T547K mutations of the spike protein to screen for the Omicron variant. A specificity test revealed that the two assays successfully discriminated the Omicron variant from the Delta and Alpha variants, each with a single nucleotide mismatch. In addition, a sensitivity test showed that the G339D and T547K assays detected at least 2.60 and 3.36 RNA copies of the Omicron variant, respectively, and 1.59 RNA copies of the Delta variant. These results demonstrate that both assays could be useful for detecting and discriminating the Omicron variant from other strains. In addition, because of the rapid and unpredictable evolution of SARS-CoV-2, combining our assays with previously developed assays for detecting other mutations may lead to a more accurate diagnostic system.
Subject(s)
COVID-19 , Genotyping Techniques , Humans , COVID-19/diagnosis , COVID-19/virology , Genotype , RNA , RNA, Viral/genetics , Polymorphism, Single NucleotideABSTRACT
We report the first pediatric patient infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant in Japan. The patient was a one-year-old boy who resided in Japan. He went abroad from 12 November 2021 to 28 November 2021 with his parents and had no known contact with COVID-19 patients there. His father tested positive for SARS-CoV-2 via quantitative antigen test on arrival at Narita International Airport on 28 November 2021. Because the boy and his mother both tested negative for SARS-CoV-2, they quarantined together at a hotel separately from his father. On 4 December 2021, the boy tested positive by reverse-transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 without symptoms and was hospitalized with his mother. He and his father were both found to be infected with SARS-CoV-2 Omicron variant. The boy had not been vaccinated for COVID-19. The RT-PCR results were negative starting 20 December 2021. The incubation period and required period for negative conversion of SARS-CoV-2 RNA of this Omicron variant case were similar to the periods of conventional cases. We have to carefully consider the potential of the SARS-CoV-2 Omicron variant to spread widely among unvaccinated children.
ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread rapidly worldwide. We report the clinical characteristics and threshold cycle (Ct) values of the first 11 patients infected with the SARS-CoV-2 Omicron variant in Japan. All patients were younger returnees from abroad; 10 patients had received two doses of vaccine. Estimated Ct values for the 11 patients were 6.0 (95% confidence interval [CI] 4.2-7.3) days for > 30, 10.6 (95% CI 9.5-11.9) days for > 35, 15.1 (95% CI 13.6-17.6) days for > 40, and 19.7 (95% CI 17.3- 23.7) days for > 45. Our results provide important insights for indicators of infection control.