The World Health Organization's public health intelligence activities during the COVID-19 pandemic response, December 2019 to December 2021.

The coronavirus disease (COVID-19) presented a unique opportunity for the World Health Organization (WHO) to utilise public health intelligence (PHI) for pandemic response. WHO systematically captured mainly unstructured information (e.g. media articles, listservs, community-based reporting) for public health intelligence purposes. WHO used the Epidemic Intelligence from Open Sources (EIOS) system as one of the information sources for PHI. The processes and scope for PHI were adapted as the pandemic evolved and tailored to regional response needs. During the early months of the pandemic, media monitoring complemented official case and death reporting through the International Health Regulations mechanism and triggered alerts. As the pandemic evolved, PHI activities prioritised identifying epidemiological trends to supplement the information available through indicator-based surveillance reported to WHO. The PHI scope evolved over time to include vaccine introduction, emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, unusual clinical manifestations and upsurges in cases, hospitalisation and death incidences at subnational levels. Triaging the unprecedented high volume of information challenged surveillance activities but was managed by collaborative information sharing. The evolution of PHI activities using multiple sources in WHO's response to the COVID-19 pandemic illustrates the future directions in which PHI methodologies could be developed and used.

Tool for tracking all-cause mortality and estimating excess mortality to support the COVID-19 pandemic response.

Problem: Quantifying mortality from coronavirus disease (COVID-19) is difficult, especially in countries with limited resources. Comparing mortality data between countries is also challenging, owing to differences in methods for reporting mortality. Context: Tracking all-cause mortality (ACM) and comparing it with expected ACM from pre-pandemic data can provide an estimate of the overall burden of mortality related to the COVID-19 pandemic and support public health decision-making. This study validated an ACM calculator to estimate excess mortality during the COVID-19 pandemic. Action: The ACM calculator was developed as a tool for computing expected ACM and excess mortality at national and subnational levels. It was developed using R statistical software, was based on a previously described model that used non-parametric negative binomial regression and was piloted in several countries. Goodness-of-fit was validated by forecasting 2019 mortality from 2015-2018 data. Outcome: Three key lessons were identified from piloting the tool: using the calculator to compare reported provisional ACM with expected ACM can avoid potential false conclusions from comparing with historical averages alone; using disaggregated data at the subnational level can detect excess mortality by avoiding dilution of total numbers at the national level; and interpretation of results should consider system-related performance indicators. Discussion: Timely tracking of ACM to estimate excess mortality is important for the response to COVID-19. The calculator can provide countries with a way to analyse and visualize ACM and excess mortality at national and subnational levels.

Nosocomial outbreak of coronavirus disease in two general wards during the initial wave of the pandemic in 2020, Tokyo, Japan.

Objective: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in China and subsequently spread worldwide. In Japan, many clusters occurred during the first wave in 2020. We describe the investigation of an early outbreak in a Tokyo hospital. Methods: A COVID-19 outbreak occurred in two wards of the hospital from April to early May 2020. Confirmed cases were individuals with laboratory-confirmed SARS-CoV-2 infection linked to Wards A and B, and contacts were patients or workers in Wards A or B 2 weeks before the index cases developed symptoms. All contacts were tested, and cases were interviewed to determine the likely route of infection and inform the development of countermeasures to curb transmission. Results: There were 518 contacts, comprising 472 health-care workers (HCWs) and 46 patients, of whom 517 were tested. SARS-CoV-2 infection was confirmed in 42 individuals (30 HCWs and 12 patients). The proportions of SARS-CoV-2 infections in HCWs were highest among surgeons, nurses, nursing assistants and medical assistants. Several HCWs in these groups reported being in close proximity to one another while not wearing medical masks. Among HCWs, infection was thought to be associated with the use of a small break room and conference room. Discussion: Nosocomial SARS-CoV-2 infections occurred in two wards of a Tokyo hospital, affecting HCWs and patients. Not wearing masks was considered a key risk factor for infection during this outbreak; masks are now a mandated countermeasure to prevent the spread of SARS-CoV-2 infection in hospital settings.

Facilitating the deployment of Japanese human resources for responding global outbreaks of emerging and Re-emerging infectious diseases: A cross-sectional study.

INTRODUCTION: In response to global outbreaks of infectious diseases, the need for support from organizations such as the World Health Organization Global Outbreak Alert and Response Network (GOARN) is increasing. Identifying the obstacles and support needs for applicants could increase GOARN deployments from Japan. METHODS: This cross-sectional study involved a web-based, self-administered questionnaire survey targeting Japanese participants in the GOARN Tier 1.5 training workshop, held in Tokyo in December 2019. RESULTS: All 47 Japanese participants in the workshop responded to the survey. Most responders were male and in their 30s and 40s. Participants specialized in case management (42.6%), infection prevention and control (25.6%), epidemiology and surveillance (19.1%). Only two participants (4.6%) had experienced a GOARN deployment. Their motivations for joining the GOARN training workshop were "Desire to be part of an international emerging infectious disease response team" (44.6%), "Interest in making an international contribution" (19.1%), and "Interest in working for the Japanese government in the field of international infectious diseases" (14.9%). Obstacles to GOARN deployments were "Making time for deployments" (45.7%) and "Lack of required professional skills and knowledge" (40.4%). The support needs for GOARN deployments constituted "Periodic simulation training" (51.1%), "Financial support during deployments" (44.7%), and "Technical support for deployments" (40.4%). CONCLUSIONS: Our study revealed the obstacles and support needs of Japanese candidates for GOARN deployment. Making time and upskilling for GOARN deployment were the main obstacles. More practical training (like GOARN Tier 2.0) with other supports are needed. The national framework is desirable to realize these supports.

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan.

After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries.IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise.

Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries.

Severe Acute Respiratory Syndrome Coronavirus 2 Infection among Returnees to Japan from Wuhan, China, 2020.

In early 2020, Japan repatriated 566 nationals from China. Universal laboratory testing and 14-day monitoring of returnees detected 12 cases of severe acute respiratory syndrome coronavirus 2 infection; initial screening results were negative for 5. Common outcomes were remaining asymptomatic (n = 4) and pneumonia (n = 6). Overall, screening performed poorly.

Initial Investigation of Transmission of COVID-19 Among Crew Members During Quarantine of a Cruise Ship - Yokohama, Japan, February 2020.

An outbreak of coronavirus disease 2019 (COVID-19) among passengers and crew on a cruise ship led to quarantine of approximately 3,700 passengers and crew that began on February 3, 2020, and lasted for nearly 4 weeks at the Port of Yokohama, Japan (1). By February 9, 20 cases had occurred among the ship's crew members. By the end of quarantine, approximately 700 cases of COVID-19 had been laboratory-confirmed among passengers and crew. This report describes findings from the initial phase of the cruise ship investigation into COVID-19 cases among crew members during February 4-12, 2020.