A genome epidemiological study of SARS-CoV-2 introduction into Japan

BackgroundAfter the first case of 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 emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases appeared until early April, many with unclear infection routes exhibiting no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases until early April and characterise the genealogical networks to demonstrate possible routes of spread in Japan. MethodsNasopharyngeal specimens were collected from patients and a quantitative reverse transcription polymerase chain reaction testing for SARS-CoV-2 was performed. Positive RNA samples were subjected whole genome sequencing and a haplotype network analysis was performed. FindingsSome of the primary clusters identified during January and February in Japan directly descended from Wuhan-Hu-1-related isolates in China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that COVID-19 cases from late March through early April may have caused an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. National self-restraint during February was effective in mitigating the COVID-19 spread, but late action on stopping immigration and declaring national emergency in Japan might be involved in the later increase in cases. InterpretationGenome surveillance suggested that at least two distinct SARS-CoV-2 introductions from China and other countries occurred. FundingJapan Agency for Medical Research and Development.

Environmental sampling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a coronavirus disease (COVID-19) outbreak aboard a commercial cruise ship

BackgroundA COVID-19 outbreak occurred in a cruise ship with 3711 passengers and crew in 2020. This study is to test the hypothesis that environmental surfaces played important roles in transmission for SARS-CoV-2 during this outbreak. MethodsWe sampled environmental surfaces including air from common areas in the cruise ship and cabins in which confirmed COVID-19 cases and non-cases had stayed after they left the cabins. We tested the samples for SARS-CoV-2 by rt-PCR and conducted viral isolation. FindingsOf 601 samples tested, SARS-CoV-2 RNA was detected from 58 samples (10%) from case-cabins from which they left 1-17 days before sampling, but not from non-case-cabins. Except for one sample from an air hood in a corridor, SARS-CoV-2 RNA was not detected from samples in common areas. SARS-CoV-2 RNA was not detected from all 14 air samples. RNA was most often detected on the floor around toilet in the bathroom (39%, 13/33, cycle quantification (Cq): 26.21-37.62) and bed pillow (34%, 11/32, Cq: 34.61-38.99). There was no difference in the detection proportion between cabins for symptomatic (15%, 28/189, Cq: 29.79-38.86) and asymptomatic cases (21%, 28/131, Cq: 26.21-38.99). No SARS-CoV-2 virus was isolated from any of the samples. InterpretationThe environment around the COVID-19 cases was extensively contaminated from SARS-CoV-2 during COVID-19 outbreak in the cruise ship. Transmission risk of SARS-CoV-2 from symptomatic and asymptomatic patients seems to be similar and the environmental surface could involve viral transmission through direct contact.

Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak

The Diamond Princess (DP) cruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed as a COVID-19 case. We performed whole genome sequencing of SARS-CoV-2 directly from PCR-positive clinical specimens and conducted a haplotype network analysis of the outbreak. All tested isolates exhibited a transversion at G11083T, suggesting that SARS-CoV-2 dissemination on the DP originated from a single introduction event before the quarantine started. Although further spreading might have been prevented by quarantine, some progeny clusters were linked to transmission through mass-gathering events in the recreational areas and direct transmission among passengers who shared cabins during the quarantine. This study demonstrates the usefulness of haplotype network analysis in identifying potential infection routes. One Sentence SummaryGenome-based tracing of SARS-CoV-2 infections among passengers and crews in Diamond Princess cruise ship during the quarantine

Regional event-based surveillance in WHO’s Western Pacific Region

Abstract@#In the Western Pacific Region, event-based surveillance has been conducted for over a decade for rapid detection and assessment of acute public health events. This report describes the establishment and evolution of the Western Pacific regional event-based surveillance system and presents an analysis of public health events in the Region. Between July 2008 and June 2017 there was a total of 2396 events reported in the Western Pacific Region (average of 266 events per year). Events related to infectious diseases in humans account for the largest proportion of events recorded (49%). Maintaining this well-established system is critical in supporting rapid detection, assessment and response to acute public health events, to maintain regional health security.

Preparation for mass gathering events from the perspective of a non-host country: the experience of Japan during the 2018 PyeongChang Olympics and Paralympic Winter Games

@#The World Health Organization recommends that countries or organizations that host mass gatherings plan ahead and prepare for possible public health events to ensure a safe environment for local residents, participants and travellers.1 Public health events during mass gatherings can also affect non-host countries. There are numerous reports of the spread of infectious diseases by travellers returning from mass gatherings,2 which can potentially pose the risk of an outbreak of new infectious diseases to travellers’ home countries. With more frequent travel across borders, it is prudent that non-host countries prepare for mass gathering events.

Case-control study of risk factors for incident syphilis infection among men who have sex with men in Tokyo, Japan

Introduction@#In Japan, syphilis notifications have increased. Men who have sex with men (MSM) in Tokyo have contributed substantially to the increase in syphilis notifications. We thus aimed to determine the correlates of incident syphilis among them.@*Methods@#MSM who attended a Tokyo clinic that serves sexual minorities were recruited in a case-control study in 2015. A case was seropositive for primary/secondary/asymptomatic syphilis at enrolment visit and seronegative at prior visit or had oral ulcers positive for Treponema pallidum DNA at enrolment. For each case, two controls seronegative at enrolment and prior visit were selected. Using logistic regression, odds ratios (ORs) and 95% confidence intervals (CIs) were estimated to assess for correlates of case status.@*Results@#Among 35 cases, the median age was 37 (range = 21–63) years and was similar to the 71 controls. Among HIV-positive participants (26 cases and 67 controls), cases were independently associated with higher frequency of anal or oral sex (OR = 3.4; 95% CI = 1.4–8.6; increase per category from < 1/month, ≥ 1/month but < 1/week, to ≥ 1/week) and no or inconsistent condom use during anal or oral sex (OR = 3.0; 95% CI = 1.1–8.3; increase per category from using every time, occasionally, to never), adjusted for residency and time between visits. @*Discussion@#Modifiable behaviours were associated with incident syphilis, and dissemination of prevention messages are needed.

An approach to building Field Epidemiology Training Programme (FETP) trainees’ capacities as educators

@#Field Epidemiology Training Programmes (FETPs), which are modelled after the Centers for Disease Control and Prevention’s Epidemic Intelligence Service programme, began in 1980 and have produced graduates in more than 70 countries, including 12 in the Western Pacific Region.1,2 These programmes aim to “build sustainable capacity for detecting and responding to public health threats” and “develop expertise so that disease outbreaks can be detected locally and prevented from spreading”.3 FETPs thus include training in applied epidemiology and public health services. FETP trainees and graduates, however, often have additional responsibilities: mentoring newer trainees, supervising in the field, leading short training courses, facilitating meetings, etc. Programmes therefore must provide trainees with the knowledge and skills to fulfil these responsibilities.

Ongoing increase in measles cases following importations, Japan, March 2014: times of challenge and opportunity

Since late 2013 through March 2014, Japan experienced a rapid rise in measles cases. Here, we briefly report on the ongoing situation and share preliminarily findings, concerns and challenges and the public health actions needed over the coming months and years. Measles is a notifiable disease in Japan based on nationwide case-based surveillance legally requiring physicians to report all clinically diagnosed and laboratory-confirmed cases within seven days, but preferably within 24 hours. After a large outbreak in 2007–2008 (more than 11 000 cases reported in 2008 alone) and a goal of elimination by April 2015, a catch-up programme using the bivalent measles-rubella (MR) vaccine was offered for grades seven and 12 (ages 12–13 and 17–18 years) from April 2008 through March 2013. During this period, there was an estimated 97% decline in measles notifications, and the cumulative number of reported cases has been steadily declining over the last five years (732 cases in 2009, 447 cases in 2010, 439 cases in 2011, 293 cases in 2012 and 232 cases in 2013). However, since late 2013 through March 2014, the country experienced a resurgence only a year after a large rubella outbreak.