The first case of a child infected with SARS-CoV-2 Omicron variant in Japan, December 2021.

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.

Development of New SNP Genotyping Assays to Discriminate the Omicron Variant of SARS-CoV-2.

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.

Genome Recombination between the Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), isolated from clinical specimens in Japan. Interestingly, the recombination variant detected in this study carries a spike protein identical to that in the domestic Delta variant, thereby suggesting that further risks would not be associated with infectivity and immune escape. The recombinant was classified as an XC lineage in the PANGOLIN database. It is necessary to intensively study such marked genetic variations and characterize emerging variants after careful verification of their lineage and clade assignment.

The first eleven cases of SARS-CoV-2 Omicron variant infection in Japan: A focus on viral dynamics.

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.

Neutralising activity and antibody titre in 10 patients with breakthrough infections of the SARS-CoV-2 Omicron variant in Japan.

The Omicron variant of severe acute respiratory syndrome coronavirus 2 has multiple amino acid mutations in its spike proteins, which may allow it to evade immunity elicited by vaccination. We examined the neutralising activity and S1-IgG titres in patients with breakthrough infections caused by the Omicron variant after two doses of vaccination. We found that neutralising activity was significantly lower for the Omicron variant than for the Wuhan strain. Two doses of vaccination might not induce sufficient neutralising activity for the Omicron variant.

The Environment Encouraging COVID-19 Response at Public Health Centers and Future Challenges in Japan.

The coronavirus disease 2019 (COVID-19) pandemic has triggered the implementation of public health measures globally. The health department of local governments has played a critical role in confronting COVID-19. In Japan, public health centers (PHCs) are focal points for COVID-19 response. Understanding the response to COVID-19 in local areas is critical to ensure adequate preparation for future emergencies. Therefore, the purpose of this study is to clarify how the COVID-19 operations by PHCs in Japan were managed and facilitated at the beginning of the infection spread, and their future challenges. We designed a case study that included two PHCs with a population of approximately 400,000 in Japan. Semi-structured focus group interviews with public health nurses from these two PHCs were conducted in September and October 2020. The data were analyzed using chronological time-series analysis. The switch to crisis response was encouraged by the business continuity plan. Their operations for the prevention of COVID-19 in the community were facilitated by the existing network. Further, strengthening the knowledge and skill regarding infectious disease control and management skills during infectious disease-related health emergencies were recommended. It is important to ensure that the environment facilitates emergency response and that people-and-community-centered health promotion activities are conducted, during an emergency situation, with more innovative action and leadership.

Duration of Infectious Virus Shedding by SARS-CoV-2 Omicron Variant-Infected Vaccinees.

To determine virus shedding duration, we examined clinical samples collected from the upper respiratory tracts of persons infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in Japan during November 29-December 18, 2021. Vaccinees with mild or asymptomatic infection shed infectious virus 6-9 days after onset or diagnosis, even after symptom resolution.

Two Cases of Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections Caused by the Omicron Variant (B.1.1.529 Lineage) in International Travelers to Japan.

In November 2021, the World Health Organization designated a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern, Omicron (PANGO lineage B.1.1.529). We report on the first 2 cases of breakthrough coronavirus disease 2019 (COVID-19) caused by Omicron in Japan among international travelers returning from the country with undetected infection. The spread of infection by Omicron were considered.

Enhanced event-based surveillance for imported diseases during the Tokyo 2020 Olympic and Paralympic Games.

In 2021, the National Institute of Infectious Diseases, Japan, undertook enhanced event-based surveillance (EBS) for infectious diseases occurring overseas that have potential for importation (excluding coronavirus disease 2019 [COVID-19]) for the Tokyo 2020 Olympic and Paralympic Summer Games (the Games). The pre-existing EBS system was enhanced using the World Health Organization Epidemic Intelligence from Open Sources system and the BlueDot Epidemic Intelligence platform. The enhanced EBS before and during the Games did not detect any major public health event that would warrant action for the Games. However, information from multiple sources helped us identify events, characterize risk and improve confidence in risk assessment. The collaboration also reduced the surveillance workload of the host country, while ensuring the quality of surveillance, even during the COVID-19 pandemic.

Nudges for COVID-19 voluntary vaccination: How to explain peer information?

Vaccination promotion is a crucial strategy to end the COVID-19 pandemic; however, individual autonomy should also be respected. This study aimed to discover other-regarding information nudges that can reinforce people's intention to receive the COVID-19 vaccine without impeding their autonomous decision-making. In March 2021, we conducted an online experiment with 1595 people living throughout Japan, and randomly assigned them either of one control group and three treatment groups that received messages differently describing peer information: control, comparison, influence-gain, and influence-loss. We compared each message's effects on vaccination intention, autonomous decision-making, and emotional response. We found that the influence-gain nudge was effective in increasing the number of older adults who newly decided to receive the vaccine. The comparison and influence-loss nudges further reinforced the intention of older adults who had already planned to receive it. However, the influence-loss nudge, which conveys similar information to the influence-gain nudge but with loss-framing, increased viewers' negative emotion. These messages had no promoting effect for young adults with lower vaccination intentions at baseline. Based on the findings, we propose governments should use different messages depending on their purposes and targets, such as comparison instead of influence-loss, to encourage voluntary vaccination behavior.

Proactive Engagement of the Expert Meeting in Managing the Early Phase of the COVID-19 Epidemic, Japan, February-June 2020.

To deal with the risk of emerging diseases with many unknowns, close and timely collaboration and communication between science experts and policymakers are crucial to developing and implementing an effective science-based intervention strategy. The Expert Meeting, an ad hoc medical advisory body, was established in February 2020 to advise Japan's COVID-19 Response Headquarters. The group played an important role in the policymaking process, promoting timely situation awareness and developing science-based proposals on interventions that were promptly reflected in government actions. However, this expert group may have been overly proactive in taking on the government's role in crisis management. For the next stage of managing the coronavirus disease pandemic and future pandemics, the respective roles of the government and its advisory bodies need to be clearly defined. Leadership and strategic risk communication by the government are key.

SARS-CoV-2 detection by fluorescence loop-mediated isothermal amplification with and without RNA extraction.

Rapid and simple point-of-care detection of SARS-CoV-2 is an urgent need to prevent pandemic. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) can detect SARS-CoV-2 more rapidly than RT-PCR. Saliva is non-invasive specimen suitable for mass-screening, but data comparing utility of nasopharyngeal swab (NPS) and saliva in RT-LAMP test are lacking and it remains unclear whether SARS-CoV-2 could be detected by direct processing of samples without the need for prior RNA extraction saliva. In this study, we compared utility of saliva and NPS samples for the detection of SARS-CoV-2 by a novel RT-fluorescence LAMP (RT-fLAMP). The sensitivity and specificity of the RT-fLAMP with RNA extraction were 97% and 100%, respectively, with equivalent utility of NPS and saliva. However, sensitivity was decreased to 71% and 47% in NPS and saliva samples without RNA extraction, respectively, suggesting that RNA extraction process may be critical for the virus detection by RT-fLAMP.