Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Subvariant BA.2 in a Single-Source Community Outbreak.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant BA.2 sublineage has increased rapidly in Europe and Asia since January 2022. Here, we report the epidemiological and genomic analysis of a large single-source BA.2 outbreak in a housing estate. METHODS: We analyzed the epidemiological information on a community outbreak of BA.2 (STY outbreak). We performed whole viral genome sequencing using the Oxford Nanopore MinION device. We calculated the doubling time of the outbreak within a housing estate. RESULTS: The STY outbreak involved a total of 768 individuals as of 5 February 2022, including 432 residents, visitors, or staff (56.3%) from a single housing estate (KC Estate). The outbreak at the KC Estate had a short doubling time of 1.28 days (95% confidence interval: .560-1.935). The outbreak was promptly controlled with the lockdown of 3 buildings within the housing estate. Whole-genome sequencing was performed for 133 patients in the STY outbreak, including 106 residents of the KC Estate. All 133 sequences from the STY outbreak belonged to the BA.2 sublineage, and phylogenetic analysis showed that these sequences cluster together. All individuals in the STY cluster had the unique mutation C12525T. CONCLUSIONS: Our study highlights the exceptionally high transmissibility of the Omicron variant BA.2 sublineage in Hong Kong, where stringent measures are implemented as part of the elimination strategy. Continual genomic surveillance is crucial in monitoring the emergence of epidemiologically important Omicron sublineages.

Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China.

Initial cases of coronavirus disease in Hong Kong were imported from mainland China. A dramatic increase in case numbers was seen in February 2020. Most case-patients had no recent travel history, suggesting the presence of transmission chains in the local community. We collected demographic, clinical, and epidemiologic data from 50 patients, who accounted for 53.8% of total reported case-patients as of February 28, 2020. We performed whole-genome sequencing to determine phylogenetic relationship and transmission dynamics of severe acute respiratory syndrome coronavirus 2 infections. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. The estimated time to the most recent common ancestor of local coronavirus disease outbreak was December 24, 2019, with an evolutionary rate of 3.04 × 10-3 substitutions/site/year. The reproduction number was 1.84, indicating ongoing community spread.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand.

Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.

Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air.

BACKGROUND: Nine COVID-19 (Corona Virus Disease, 2019) cases were observed in one community in Guangzhou. All the cases lived in three vertically aligned units of one building sharing the same piping system, which provided one unique opportunity to examine the transmission mode of SARS-CoV-2. METHODS: We interviewed the cases on the history of travelling and close contact with the index patients. Respiratory samples from all the cases were collected for viral phylogenetic analyses. A simulation experiment in the building and a parallel control experiment in a similar building were then conducted to investigate the possibility of transmission through air. RESULTS: Index patients living in Apartment 15-b had a travelling history in Wuhan, and four cases who lived in Apartment 25-b and 27-b were subsequently diagnosed. Phylogenetic analyses showed that virus of all the patients were from the same strain of the virus. No close contacts between the index cases and other families indicated that the transmission might not occur through droplet and close contacts. Airflow detection and simulation experiment revealed that flushing the toilets could increase the speed of airflow in the pipes and transmitted the airflow from Apartment 15-b to 25-b and 27-b. Reduced exhaust flow rates in the infected building might have contributed to the outbreak. CONCLUSIONS: The outbreak of COVID-19 in this community could be largely explained by the transmission through air, and future efforts to prevent the infection should take the possibility of transmission through air into consideration. A disconnected drain pipe and exhaust pipe for toilet should be considered in the architectural design to help prevent possible virus spreading through the air.

Association of influenza outbreak in each nursery school and community in a ward in Tokyo, Japan.

In nursery schools, influenza outbreaks have occurred every year. However, influenza characteristics of its diffusion among nursery schools, within each nursery school, and among classes of different ages in nursery schools remains unclear. This paper presents an examination of these matters using the Nursery School Absenteeism Surveillance System (NSASSy). All nursery schools in ward A in Tokyo introduced to the NSASSy in 2015. The study period was November 2015 through March 2016. The data of influenza patients were extracted from NSASSy. We examined four definitions of 'starting date of community outbreak' (SDCO) of influenza: 1) the first recorded day of influenza patients (SDCO1), 2) the last day of influenza patients recorded for two consecutive days (SDCO2), 3) three consecutive days (SDCO3), and 4) four consecutive days (SDCO4). We evaluated those four definitions by duration of the initial case at each nursery school from SDCO and evaluated the proportion of nursery schools at which the initial case occurred before SDCO. The average durations of initial cases at respective nursery schools from SDCO1-4 were 40.3, 26.3, 23.1 and 13.3 days. The respective proportions of nursery schools at which the initial case occurred before SDCO1-4 were 3.1%, 6.4%, 9.4% and 40.6%. Results demonstrate that SDCO3 is an appropriate definition of SDCO. Robustness checks for other areas, seasons, and population size constitute the next challenge for research in this area.

A community outbreak of Legionnaires' disease caused by outdoor hot tubs for private use in a hotel.

During the period October-November 2017, an outbreak of Legionnaires' disease involving 27 cases occurred in the tourist area of Palmanova (Mallorca, Spain). The majority of cases were reported by the European Centre of Disease Prevention and Control (ECDC) as travel associated cases of Legionnaires' disease (TALD). Most cases belonged to different hotel cluster alerts. No cases were reported among the local population residing in the area. All tourist establishments associated with one or more TALD cases were inspected and sampled by public health inspectors. All relevant sources of aerosol emission detected were investigated and sampled. The absence of active cooling towers in the affected area was verified, by documents and on-site. Samples from hot tubs for private use located on the terraces of the penthouse rooms of a hotel in the area were included in the study. Extremely high concentrations (> 106 CFU/l) of Legionella pneumophila, including the outbreak strain, were found in the hot tubs of vacant rooms of this hotel thus identifying the probable source of infection. Meteorological situation may have contributed to the geographical distribution pattern of this outbreak. In conclusion, hot tubs for private use located outdoors should be considered when investigating community outbreaks of Legionnaires' disease of unclear origin.

The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak.

Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.

Atmospheric dispersion and transmission of Legionella from wastewater treatment plants: A 6-year case-control study.

Legionnaires Disease incidence has risen in the Netherlands in recent years. For the majority of the cases, the source of infection is never identified. Two Dutch wastewater treatment plants (WWTPs) have previously been identified as source of outbreaks of Legionnaires Disease (LD) among local residents. The objective of this study is to examine if LD patients in the Netherlands are more exposed to aerosols originating from WWTPs than controls. METHODS: An atmospheric dispersion model was used to generate nationwide exposure maps of aerosols from 776 WWTPs in the Netherlands. Municipal sewage treatment plants and industrial WWTPs were both included. Exposure of LD cases and controls at the residential address was compared, in a matched case-control design using a conditional logistic regression. Cases were notified LD cases with onset of disease in the period 2013-2018 in the Netherlands (n = 1604). RESULTS: Aerosols dispersed over a large part of the Netherlands, but modelled concentrations are estimated to be elevated in close proximity to WWTPs. A statistically significant association was found between LD and the calculated annual average aerosol concentrations originating from WWTPs (odds-ratio: 1.32 (1.06-1.63)). This association remained significant when the two outbreak-related WWTPs were removed from the analysis (odds-ratio: 1.28 (1.03-1.58)). CONCLUSION: LD cases were more exposed to aerosols from WWTPs than controls. This indicates that exposure to aerosols dispersed from WWTPs caused Legionnaires Disease in residents living near WWTPs in the period 2013-2018. In order to investigate which characteristics of WWTPs are associated with an increased LD risk, the WWTP database should be updated and more data is needed on the presence and survival of aerosolized Legionella bacteria to improve the Legionella dispersion modelling. Furthermore, it is recommended to further investigate how aerosol dispersion of WWTPs can effectively be reduced in order to reduce the potential health risk.

An unusual outbreak of rotavirus G8P[8] gastroenteritis in adults in an urban community, Singapore, 2016.

BACKGROUND: An outbreak of gastroenteritis (GE) occurred in community-dwelling adults in the Central Region of urban Singapore, in May 2016. OBJECTIVES: To investigate the cause of the outbreak. STUDY DESIGN: We conducted a case-cohort study on GE patients linked to the outbreak who presented to the emergency department of a tertiary-care hospital near the outbreak area, from 18 May to 11 June 2016. Stools were tested for gastrointestinal pathogens including rotavirus antigen and positive rotavirus samples were subject to genotyping. RESULTS: A total of 57 adult GE patients, with a median age of 40 (range 18 to 84) years, were included. Predominant symptoms were diarrhoea (98.2%), vomiting (64.9%), and abdominal discomfort (38.6%). Age 65 years and above (Adjusted OR 21.78, 95% CI 1.49-318.84; P = 0.02) was the only predictor of admission, after adjusting for comorbidities and clinical severity. Molecular microbiological investigations confirmed that the outbreak was caused by a novel human-bovine reassortant strain of rotavirus G8P[8] with DS-1-like backbone. Exposure to the market in the outbreak area was strongly associated with rotavirus infection (OR 46.14; 95% CI 43.04-49.25, P < 0.01). No particular food item could be identified as the outbreak cause. CONCLUSIONS: This is the first report of an outbreak of rotavirus G8P[8] in adults in an urban community that is not waterborne. Transmission was likely through fomites in the market and its surrounding areas, via consumption or contact with contaminated food items purchased from the market, and from person-to-person. The potential for novel G8P[8] strains to cause outbreaks cannot be overemphasized.

[Evolution and spatial analysis of leishmaniasis cases in a rural area bordering a community outbreak in Madrid: 2001-2017]. / Evolución y análisis espacial de los casos de leishmaniasis en una zona rural colindante al brote comunitario de Madrid: 2001-2017.

OBJECTIVE: Leishmaniasis is a zoonotic disease, widely spread all over the world, and an endemic disease in some Spanish regions. Within the Autonomous Region of Madrid, some south populations were affected by an outbreak from 2009. This outbreak had special features and implications related to epidemiology, reservoir and environment intervention. An increased rate in rural areas bordering the outbreak area was detected by epidemiological surveillance. This area has the same environment characteristics. The objective of this study was to research and analyze the evolution of leishmaniasis cases declared in a rural area and their comparison with the cases of the outbreak area. METHODS: The cases declared to Epidemiology Surveillance Network have been used. Kulldorff´s tools were used for the cluster analysis. A hot spot analysis (Getis-Ord Gi*) was made. Leporidae and vector information of the area was related to the location of cases. RESULTS: The number of observed cases exceeded the number of expected cases in this area (epidemic index 7.8 in 2013), after the outbreak. This showed a relation between both incidence rates. It seemed to be spatial correlation when the number of cases was analyzed by census sections and grids (Moran´s I 0,208; z= 9,336). Using the hot-spot analysis, a higher incidence of the study area could be observed, and within Health Basic Area of Griñón after the outbreak years. A spatial relation between cases and a greater presence of vectors and leporidae was found. CONCLUSIONS: The distribution of leishmaniasis cases, in the period and study area suggests a link between the community outbreak and the increase of cases in the study area last years, overall in the rural area. It would be useful to strengthen surveillance and it should apply effective measures used in the bordering area if they were necessary. These measures can help to control the spread of the outbreak.

OBJETIVO: La leishmaniasis en una enfermedad zoonótica muy extendida a nivel mundial y es endémica en algunas regiones de España. Desde 2009 un brote de leishmaniasis ha afectado a algunos municipios del sur de Madrid con características e implicaciones especiales en cuanto a epidemiología, reservorio e intervención medioambiental. Se ha observado un aumento de casos en las zonas rurales adyacentes con características ambientales similares. El objetivo de este trabajo fue estudiar y analizar la evolución de los casos de leishmaniasis declarados en una zona rural colindante y compararlos con el brote comunitario. METODOS: Se utilizó la información de los casos declarados a la Red de Vigilancia Epidemiológica de la Comunidad de Madrid en la zona de estudio desde 2001-2017 y se compararon las tasas de incidencia con las del área del brote. Se realizó un análisis espacial de los casos y de los conglomerados para cuatro unidades espaciales. Se realizó análisis de conglomerados según la técnica de Kulldorff y análisis de puntos calientes según Gi* de Getis-Ord. Se relacionó la información disponible de lepóridos y vectores con la ubicación de los casos. RESULTADOS: Los casos observados en el área de estudio superaron a los esperados tras al inicio del brote (índice epidémico 7,8 en 2013) mostrándose una relación gráfica entre las tasas de incidencia. Existió una autocorrelación espacial cuando se analizaron el número de casos por secciones censales y por cuadrículas (índice de Moran de 0,208; z= 9,336). En el análisis de puntos calientes se pudo apreciar una mayor incidencia en el área de estudio en el periodo posterior al brote, en particular en la Zona Básica de Salud de Griñón. Se constató una relación espacial entre casos y zonas de mayor presencia de lepóridos y vectores. CONCLUSIONES: La distribución de casos de leishmaniasis en el periodo y área de estudio sugiere que puede existir una asociación entre el brote comunitario y el aumento de casos de los últimos años en el área de estudio, específicamente en la zona rural, por lo que sería necesario reforzar la vigilancia y aplicar medidas de control ambiental en caso necesario, lo cual puede contribuir a limitar la extensión del brote.