Coronavirus Disease 2019 Clusters Research Articles

Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

In late December 2019, an outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. Data on the routes of transmission to Los Angeles, California, the US West Coast epicenter for coronavirus disease 2019 (COVID-19), and subsequent community spread are limited. To determine the transmission routes of SARS-CoV-2 to Southern California and elucidate local community spread within the Los Angeles metropolitan area. This case series included 192 consecutive patients with reverse transcription-polymerase chain reaction (RT-PCR) test results positive for SARS-CoV-2 who were evaluated at Cedars-Sinai Medical Center in Los Angeles, California, from March 22 to April 15, 2020. Data analysis was performed from April to May 2020. SARS-CoV-2 viral genomes were sequenced. Los Angeles isolates were compared with genomes from global subsampling and from New York, New York; Washington state; and China to determine potential sources of viral dissemination. Demographic data and outcomes were collected. The cohort included 192 patients (median [interquartile range] age, 59.5 [43-75] years; 110 [57.3%] men). The genetic characterization of SARS-CoV-2 isolates in the Los Angeles population pinpointed community transmission of 13 patients within a 3.81 km2 radius. Variation landscapes of this case series also revealed a cluster of 10 patients that contained 5 residents at a skilled nursing facility, 1 resident of a nearby skilled nursing facility, 3 health care workers, and a family member of a resident of one of the skilled nursing facilities. Person-to-person transmission was detected in a cluster of 5 patients who shared the same single-nucleotide variation in their SARS-CoV-2 genomes. High viral genomic diversity was identified: 20 Los Angeles isolates (15.0%) resembled SARS-CoV-2 genomes from Asia, while 109 Los Angeles isolates (82.0%) were similar to isolates originating from Europe. Analysis of other common respiratory viral pathogens did not reveal coinfection in the cohort. These findings highlight the precision of detecting person-to-person transmission and accurate contact tracing directly through SARS-CoV-2 genome isolation and sequencing. Development and application of phylogenetic analyses from the Los Angeles population established connections between COVID-19 clusters locally and throughout the US.

Epidemiological Investigation of OHCWs with COVID-19

During the coronavirus disease 2019 (COVID-19) pandemic, there is an important risk of infection in health care workers, including oral health care workers (OHCWs), due to the characteristics of dental practice. In this retrospective study, data pertaining to the 31 OHCWs diagnosed with COVID-19 in Wuhan, Hubei Province, were retrieved and analyzed. Questionnaires were administered to the subjects over the Internet and telephone. Clinical and epidemiological characteristics and information on the use of personal protective equipment (PPE) were collected. There were 22 females and 9 males, with a median age of 39 y. Although the severity of most cases of COVID-19 (93.5%) was mild or moderate, 1 case was severe, and another case was critical, resulting in death. Fever was the main first symptom of COVID-19, followed by fatigue and myalgia. Most of the OHCWs routinely used PPE such as medical masks, gloves, caps, and work clothes while performing clinical work. N95 or KN95 masks were rarely available because of the scarcity of PPE during the outbreak. Nineteen OHCWs reported a contact history, among whom 7 worked in a fever clinic, 5 reported contact with dental patients suspected of having COVID-19, and 7 reported contact with family members with COVID-19–related symptoms at least 1 d earlier. Our findings indicated that there were few clusters of COVID-19 in dental settings. Since the outbreak, the Hospital of Stomatology, Wuhan University, has provided emergency dental treatment, and none of their staff were infected while providing dental service, which indicates that comprehensive measures such as the use of advanced PPE and environmental disinfection can prevent cross-infection in dental practice. The analysis of the procedures followed during the emergency treatments indicated that OHCWs preferred to recommend conservative treatment to patients, suggesting that attention should be paid to the psychological impact of COVID-19 on dental practitioners.

First Local Transmission Cluster of COVID-19 in Malaysia: Public Health Response

Introduction: Rapid public health response is important in controlling the transmission of coronavirus disease 2019 (COVID-19). In this study, we described the public health response taken by the Ministry of Health of Malaysia in managing the first local transmission cluster of COVID-19 related to mass-gathering and inter-state traveling to celebrate a festival. Methods: We summarized strategies implemented by the Malaysia Crisis Preparedness and Response Centre (CPRC) in managing the first local transmission of COVID-19. We collected information related to the epidemiological investigation of this cluster and described the inter-state network in managing the outbreak. Results: This first local transmission of COVID-19 in Malaysia had a history of contact with her older brother, the index case, who was the first Malaysian imported case. Only two positive cases were detected out of 59 contacts traced from the index case. Close contacts with infected person/s, inter-state movement, and public/family gatherings were identified as the sources of transmission. A large number of contacts were traced from inter-state traveling, and family gatherings during the festive season, and health consultations and treatment. Conclusion: Close contacts from inter-state movement and public/family gatherings were identified as the source of transmission. Family or public gatherings during festivals or religious events should be prohibited or controlled in COVID-19 prevalent areas. A structured surveillance system with rapid contact tracing is significant in controlling the transmission of COVID-19 in the community.

Analysis on the cluster epidemic of coronavirus disease 2019 in Guangdong Province

Objective: Analysis of clustering characteristics of coronavirus disease 2019 (COVID-19) in Guangdong Province. Methods: The COVID-19 cases in Guangdong Province onset from January 1 to February 29, 2020 were collected from Chinese information system for disease control and prevention and Emergency Public Reporting System. Obtain the epidemiological survey data of the cluster epidemic situation, and clarify the scale of cluster epidemic situation, the characteristics of the index cases, family and non-family subsequent cases. Calculate serial interval according to the onset time of the index cases and subsequent cases, secondary attack rate based on the close contacts tracking results, the characteristics of different cases in the clustered epidemic were compared. Results: A total of 283 cluster were collected, including 633 index cases, 239 subsequent cases. Families are mainly clustered, the total number involved in each cluster is in the range of 2-27, M (P25, P75) are 2.0 (2.0, 4.0). During January 15 to February 29, the secondary attack rate is 2.86% (239/8 363) in Guangdong Province, the family secondary attack rate was 4.84% (276/3 697), and the non-family secondary attack rate was 1.32% (61/4 632). According to the reporting trend of the number of cases in Guangdong Province, it can be divided into four stages, the rising stage, the high platform stage, the descending stage and the low level fluctuation period. The secondary attack rate of the four stages were 3.5% (140/3 987), 2.3% (55/2 399), 2.6% (37/1 435), 1.3% (7/542), respectively. The difference was statistically significant (P=0.003). Conclusion: COVID-19 cluster mainly occurs in families in Guangdong Province. The scale of the clustered epidemic was small; the serial interval was short; and the overall secondary attack rate was low.

Spatiotemporal pattern of COVID-19 and government response in South Korea (as of May 31, 2020)

ObjectivesThe aim of this study was to assess how coronavirus disease 2019 (COVID-19) clustered across districts in South Korea and to assess whether the pattern and duration of clusters changed following the country's containment strategy. MethodsA spatiotemporal analysis of COVID-19 daily confirmed cases by 250 districts in South Korea from January 20 to May 31, 2020, obtained from the Korea Centers for Disease Control and Prevention and each provincial website, was conducted. The global Moran's I statistic was used for spatial autocorrelation analysis, and the retrospective space-time scan statistic was used to analyze spatiotemporal clusters of COVID-19. ResultsThe geographical distribution showed strong spatial autocorrelation, with a global Moran's I coefficient of 0.784 (p=0.0001). Twelve statistically significant spatiotemporal clusters were identified by space–time scan statistic using a discrete Poisson model. The spatial pattern of clusters changed and the duration of clusters became shorter over time. ConclusionsThe results indicate that South Korea's containment strategy for COVID-19 was highly effective in both early detection and mitigation, with recent clusters being small in size and duration. Lessons from South Korea should spark a discussion on epidemic response.

Health Care Workers and Patients as Trojan Horses: a COVID19 ward outbreak

SummaryBackgroundTransmission in healthcare settings can result in significant infections in healthcare workers and patients. Understanding infection dynamics has important implications for methods employed in hospitals to prevent nosocomial transmission events.MethodsIn this case series report we describe a cluster of COVID-19 (Coronavirus disease 2019) in a tertiary care university hospital, in the early phases of the epidemic, after hospital visiting had been stopped and when the UK lockdown was in place.FindingsA 48 year old patient developed COVID-19 31 days post-admission and four days after admission to a medical ward from ITU. Infection was likely acquired from an asymptomatic or minimally symptomatic healthcare worker (HCW). Subsequent investigation over a 14 day period revealed symptoms in 23 staff members and five linked cases in patients on the same ward.Nine of the 23 affected staff members provided care for and had direct exposure with the index case. Four staff reported caring for the index case without use of personal protective equipment. One was coughed on directly by the patient 24 hours prior to the onset of symptoms.ConclusionSARS CoV2 infection can be introduced to a ward area by asymptomatic and minimally symptomatic healthcare workers. Staff members and patients can act as Trojan horses carrying infection into and around the hospital, setting up unexpected transmission events.Transmission of infection from pre-symptomatic, asymptomatic and minimally symptomatic individuals means that universal use of measures to prevent transmission is required for successful reduction of transmission events in the hospital setting.

Daily surveillance of COVID-19 using the prospective space-time scan statistic in the United States

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in late 2019 in Wuhan City, China. The virus may cause novel coronavirus disease 2019 (COVID-19) in symptomatic individuals. Since December of 2019, there have been over 7,000,000 confirmed cases and over 400,000 confirmed deaths worldwide. In the United States (U.S.), there have been over 2,000,000 confirmed cases and over 110,000 confirmed deaths. COVID-19 case data in the United States has been updated daily at the county level since the first case was reported in January of 2020. There currently lacks a study that showcases the novelty of daily COVID-19 surveillance using space-time cluster detection techniques. In this paper, we utilize a prospective Poisson space-time scan statistic to detect daily clusters of COVID-19 at the county level in the contiguous 48 U.S. and Washington D.C. As the pandemic progresses, we generally find an increase of smaller clusters of remarkably steady relative risk. Daily tracking of significant space-time clusters can facilitate decision-making and public health resource allocation by evaluating and visualizing the size, relative risk, and locations that are identified as COVID-19 hotspots.

COVID-19 and Kidney Disease Disparities in the United States

Racial, ethnic, socioeconomic, age, and sex-related health disparities in kidney disease are prominent in the United States. The Coronavirus Disease 2019 (COVID-19) pandemic has disproportionately affected marginalized populations. Older adults, people experiencing unstable housing, racial and ethnic minorities, and immigrants are potentially at increased risk for infection and severe complications from COVID-19. The direct and societal effects of the pandemic may increase risk of incident kidney disease and lead to worse outcomes for those with kidney disease. The rapid transition to telemedicine potentially limits access to care for older adults, immigrants, and people experiencing unstable housing. The economic impact of the pandemic has had a disproportionate effect on women, minorities, and immigrants, which may limit their ability to manage kidney disease and lead to complications or kidney disease progression. We describe the impact of COVID-19 on marginalized populations and highlight how the pandemic may exacerbate existing disparities in kidney disease.

Strongly Heterogeneous Transmission of COVID-19 in Mainland China: Local and Regional Variation.

Background: The outbreak of novel coronavirus disease 2019 (COVID-19) started in the city of Wuhan, China, with a period of rapid initial spread. Transmission on a regional and then national scale was promoted by intense travel during the holiday period of the Chinese New Year. We studied the variation in transmission of COVID-19, locally in Wuhan, as well as on a larger spatial scale, among different cities and even among provinces in mainland China.Methods: In addition to reported numbers of new cases, we have been able to assemble detailed contact data for some of the initial clusters of COVID-19. This enabled estimation of the serial interval for clinical cases, as well as reproduction numbers for small and large regions.Findings: We estimated the average serial interval was 4.8 days. For early transmission in Wuhan, any infectious case produced as many as four new cases, transmission outside Wuhan was less intense, with reproduction numbers below two. During the rapid growth phase of the outbreak the region of Wuhan city acted as a hot spot, generating new cases upon contact, while locally, in other provinces, transmission was low.Interpretation: COVID-19 is capable of spreading very rapidly. The sizes of outbreak in provinces of mainland China mainly depended on the numbers of cases imported from Wuhan as the local reproduction numbers were low. The COVID-19 epidemic should be controllable with appropriate interventions (suspension of public transportation, cancellation of mass gatherings, implementation of surveillance and testing, and promotion of personal hygiene and face mask use).

Rapid detection of COVID-19 clusters in the United States using a prospective space-time scan statistic

Novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic with 1,420,299 confirmed cases and 85,992 total deaths within the United States as of May 15th, 2020. As the number of cases continues to climb, detecting clusters of COVID-19 is critical to alleviate the strain on our public health system through improved resource allocation and decision-making. Here, we report on an analysis of daily case data at the county level using the prospective spatial-temporal scan statistic. In previous work, we performed the analysis for March 27th 2020 [1], and here we report updated results as of April 27th 2020, producing a new set of "active" and emerging clusters present. Our analysis resulted in sixteen significant space-time clusters of COVID-19 at the county level in the U.S. during the time span of March 22nd -- April 27th. The spacetime pattern of significant clusters mirrors active and emerging disease hot-spots at the end of our study period. The statistic can be rerun to support timely surveillance of COVID-19, as demonstrated here.

Rapid detection of COVID-19 clusters in the United States using a prospective space-time scan statistic

Novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic with 1,420,299 confirmed cases and 85,992 total deaths within the United States as of May 15th, 2020. As the number of cases continues to climb, detecting clusters of COVID-19 is critical to alleviate the strain on our public health system through improved resource allocation and decision-making. Here, we report on an analysis of daily case data at the county level using the prospective spatial-temporal scan statistic. In previous work, we performed the analysis for March 27th 2020 [1], and here we report updated results as of April 27th 2020, producing a new set of and emerging clusters present. Our analysis resulted in sixteen significant space-time clusters of COVID-19 at the county level in the U.S. during the time span of March 22nd -- April 27th. The spacetime pattern of significant clusters mirrors active and emerging disease hot-spots at the end of our study period. The statistic can be rerun to support timely surveillance of COVID-19, as demonstrated here.

Delivering Dialysis During the COVID-19 Outbreak: Strategies and Outcomes

Abstract Background Haemodialysis (HD) patients are at increased risk of COVID-19 infection. Although all dialysis patients meet government criteria for shielding, only those on home treatment can comply. Patients attending incentre HD units represent a large and vulnerable group, who are unable to rigorously adhere to this advice. The need to adopt strategies to protect these patients is of great importance. We report our experience of delivering dialysis during the COVID-19 outbreak, describing the interventions taken to try to protect patients from virus transmission whilst maintaining optimal treatment. Methods We implemented measures, including use of; a system of active triage and isolation of suspected cases, separate transportation, a dedicated COVID-19 HD unit, personal protective equipment, active repatriation of patients back to base units. We collected data from all COVID-19 positive HD patients in our cohort, between 14/03/2020 - 20/04/2020. Data were compared to national reports of other units, and values obtained from a dialysis-specific Susceptible-Infectious-Removed model which predicted the impact of COVID-19 on our cohort. Results Results showed 76/670 (11.3%) tested positive for COVID-19. The majority were male (61.8%) and from a minority background (61.8%). 7/76 (9.2%) patients died following infection. The model projections overestimated the incidence of COVID-19, 221 vs 76 total number of infections by 20/4/20. Our incidence of COVID-19 and mortality are lower compared to other units across London. Conclusion Implementation of measures to limit the spread of COVID-19, and optimise dialysis, could account for the low infection and mortality rates observed in our cohort of patients.

French Spine Surgery Society guidelines for management of spinal surgeries during COVID-19 pandemic.

Since the outbreak of coronavirus disease 2019 (COVID-19) in December 2019 in China, various measures have been adopted in order to attenuate the impact of the virus on the population. With regard to spine surgery, French physicians are devoted to take place in the national plan against COVID-19, the French Spine Surgery Society therefore decided to elaborate specific guidelines for management of spinal disorders during COVID-19 pandemic in order to prioritize management of patients. A three levels stratification was elaborated with Level I: Urgent surgical indications, Level II: Surgical indications associated to a potential loss of chance for the patient and Level III: Non-urgent surgical indications. We also report French experience in a COVID-19 cluster region illustrated by two clinical cases. We hope that the guidelines formulated by the French Spine Surgery Society and the experience of spine surgeons from a cluster region will be helpful in order optimizing the management of patients with urgent spinal conditions during the pandemic.

Inferring super-spreading from transmission clusters of COVID-19 in Hong Kong, Japan, and Singapore

SummarySuper-spreading events in an outbreak can change the nature of an epidemic. Therefore, it is useful for public health teams to determine whether an ongoing outbreak has any contribution from such events, which may be amenable to interventions. We estimated the basic reproductive number (R0) and the dispersion factor (k) from empirical data on clusters of epidemiologically linked coronavirus disease 2019 (COVID-19) cases in Hong Kong, Japan and Singapore. This allowed us to infer the presence or absence of super-spreading events during the early phase of these outbreaks. The relatively large values of k implied that large cluster sizes, compatible with super-spreading, were unlikely.

Spine Surgical Procedures during Coronavirus Disease 2019 Pandemic: Is It Still Possible to Take Care of Patients? Results of an Observational Study in the First Month of Confinement

Study DesignObservational study.PurposeThe actual sanitary crisis led to a massive mobilization of the sanitary system toward intensive care units and management of coronavirus disease 2019 (COVID-19) patients. However, some patients still require spinal interventions. The present study aimed to assess the impact of the COVID-19 pandemic on spine surgical in a moderate COVID-19 cluster region.Overview of LiteraturePrevious studies have reported screening and management of patients with spinal conditions during the COVID-19 pandemic. However, to date, knowledge, no observational study on spine surgeries during the pandemic has not been reported.MethodsBetween March 17, 2020 and April 17, 2020, information on spine surgical activity was prospectively collected at our institution. This surgical activity related to the first month of confinement in France was compared to the activity during the same period in 2019 to evaluate the impact of the COVID-19 pandemic on surgical activities.ResultsIn order to reduce the contamination rate of patients and medical staff during hospitalization, the spine department was completely reorganized. Non-urgent elective spine surgeries were cancelled. When considering the global amount of surgeries procedures during the first month of confinement, a decrease of almost 50% was observed in the number of surgical procedures. During the study period, 62 patients were eligible for spine surgery. The numbers of patients managed for tumor and infectious cases were stable, while a considerable reduction was observed in the number of trauma and degenerative cases. During the follow-up period, two patients were tested as COVID+ during the postoperative course, and no cases of medical or paramedical staff contamination were reported using polymerase chain reaction-testing.ConclusionsDuring the COVID-19 pandemic, it is possible to maintain spine surgical activity. Each surgical procedure must be discussed and organized with all the caregivers involved. Indications for surgery must be in line with the scientific guidelines and adapted to each healthcare facility.

COVID-19 cluster study at a teaching hospital

On Mar 11th, 2020, the World Health Organization (WHO) stated in its Situation Report - 51 Coronavirus disease 2019 (COVID-19) as a pandemic. In early April 2020, a teaching hospital underwent shutdown and quarantine due to an outbreak of infection in accordance with Section 6 of the Infection Protection Act (index patient and 5 infected nursing staff). The complete staff (physicians, nurses and nonmedical personnel [NMP]) underwent COVID-19 testing within two phases: (1) between Apr 3rd and 5th, 2020 [n=1170], followed by (2) between Apr 8th and 9th, 2020 [n=953] with COVID-19 silent carrier positivity rates in accordance to testing phases of (1) n=19 (1.6%) and (2) n=25 (2.6%). The cumulative infection rate for NMP (1.6%), doctors (3.8%) and nurses (9.7%) was connected to type and extent of COVID-19 patient contact. Despite COVID-19 positivity of 34.8% (46 of 132 beds), a risk-free management of hospital operation is possible to a certain extent if hygiene regulations and strict patient selection are followed. However, a COVID-19-free clinic cannot be expected due to silent carriers.

The role of community-wide wearing of face mask for control of coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2

BackgroundFace mask usage by the healthy population in the community to reduce risk of transmission of respiratory viruses remains controversial. We assessed the effect of community-wide mask usage to control coronavirus disease 2019 (COVID-19) in Hong Kong Special Administrative Region (HKSAR). MethodsPatients presenting with respiratory symptoms at outpatient clinics or hospital wards were screened for COVID-19 per protocol. Epidemiological analysis was performed for confirmed cases, especially persons acquiring COVID-19 during mask-off and mask-on settings. The incidence of COVID-19 per million population in HKSAR with community-wide masking was compared to that of non-mask-wearing countries which are comparable with HKSAR in terms of population density, healthcare system, BCG vaccination and social distancing measures but not community-wide masking. Compliance of face mask usage in the HKSAR community was monitored. FindingsWithin first 100 days (31 December 2019 to 8 April 2020), 961 COVID-19 patients were diagnosed in HKSAR. The COVID-19 incidence in HKSAR (129.0 per million population) was significantly lower (p<0.001) than that of Spain (2983.2), Italy (2250.8), Germany (1241.5), France (1151.6), U.S. (1102.8), U.K. (831.5), Singapore (259.8), and South Korea (200.5). The compliance of face mask usage by HKSAR general public was 96.6% (range: 95.7% to 97.2%). We observed 11 COVID-19 clusters in recreational ‘mask-off’ settings compared to only 3 in workplace ‘mask-on’ settings (p = 0.036 by Chi square test of goodness-of-fit). ConclusionCommunity-wide mask wearing may contribute to the control of COVID-19 by reducing the amount of emission of infected saliva and respiratory droplets from individuals with subclinical or mild COVID-19.

The important role of serology for COVID-19 control

The important role of serology for COVID-19 control

Connecting clusters of COVID-19: an epidemiological and serological investigation

BackgroundElucidation of the chain of disease transmission and identification of the source of coronavirus disease 2019 (COVID-19) infections are crucial for effective disease containment. We describe an epidemiological investigation that, with use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serological assays, established links between three clusters of COVID-19.MethodsIn Singapore, active case-finding and contact tracing were undertaken for all COVID-19 cases. Diagnosis for acute disease was confirmed with RT-PCR testing. When epidemiological information suggested that people might have been nodes of disease transmission but had recovered from illness, SARS-CoV-2 IgG serology testing was used to establish past infection.FindingsThree clusters of COVID-19, comprising 28 locally transmitted cases, were identified in Singapore; these clusters were from two churches (Church A and Church B) and a family gathering. The clusters in Church A and Church B were linked by an individual from Church A (A2), who transmitted SARS-CoV-2 infection to the primary case from Church B (F1) at a family gathering they both attended on Jan 25, 2020. All cases were confirmed by RT-PCR testing because they had active disease, except for A2, who at the time of testing had recovered from their illness and tested negative. This individual was eventually diagnosed with past infection by serological testing. ELISA assays showed an optical density of more than 1·4 for SARS-CoV-2 nucleoprotein and receptor binding domain antigens in titres up to 1/400, and viral neutralisation was noted in titres up to 1/320.InterpretationDevelopment and application of a serological assay has helped to establish connections between COVID-19 clusters in Singapore. Serological testing can have a crucial role in identifying convalescent cases or people with milder disease who might have been missed by other surveillance methods.FundingNational Research Foundation (Singapore), National Natural Science Foundation (China), and National Medical Research Council (Singapore).

A Territory-Wide Study of COVID-19 Cases and Clusters with Unknown Source in Hong Kong Community: A Clinical, Epidemiological and Phylogenomic Investigation

Background: Initial cases of coronavirus disease 2019 (COVID-19) reported in Hong Kong were mostly imported cases from Mainland China. However, most cases reported in February 2020 were local infections with unknown source, indicating local community transmissions. This study aimed to report the clinical, epidemiological and phylogenomic characteristics of the local cases of COVID-19 in our community. Methods: We extracted the demographic, clinical and epidemiological data from 50 COVID-19 patients, who accounted for 53·8% of the cases in Hong Kong by the end of February 2020. We used both Nanopore and Illumina platforms to perform whole-genome sequencing (WGS) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from these patients. Phylogenetic relatedness among these local cases and their placement in the global phylogeny were examined. The evolutionary rate and divergence time of transmission were also determined. Findings: Of these 50 patients, only three (6·0%) had visited Wuhan while 43 (86·0%) did not have recent travel records. The average interval from symptom onset to hospital admission was 8·5 days. The most common signs and symptoms on admission were cough (74·0%) and fever (58·0%). Radiographic abnormality was found in 46 (92·0%) patients. Three (6·0%) patients required ICU admission. Phylogenetic analysis concurred with epidemiological investigation that 42 (84·0%) cases could be grouped into six transmission clusters. Forty-four (88·0%) cases harboured a common mutation Orf3aG251V. Global phylogeny of SARS-CoV-2 revealed that most (88·0%) cases in Hong Kong were clustered in two subclades with the strains from other countries. The estimated time to the most recent common ancestor (tMRCA) of COVID-2019 outbreak in Hong Kong was December 24, 2019 with an evolutionary rate of 3.04×10-3 substitutions per site per year. The reproduction number value was 1·84 as of February 28, 2020 in Hong Kong. Interpretation: We provided a territory-wide overview of COVID-19 in Hong Kong, which has borders connecting to Mainland China. Transmission in closed settings especially during family and religious gatherings is a hallmark of the recently reported cases. The reproduction number value indicated an ongoing outbreak in the community. Rapid isolation of suspected or confirmed cases and their close contacts coupled with robust laboratory surveillance is crucial to the containment of COVID-19 transmission. Funding Statement: The project was supported by internal funds from the Faculty of Health and Social Science, and Department of Health Technology and Informatics of The Hong Kong Polytechnic University. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: This study was approved by the Institutional Review Boards of The Hong Kong Polytechnic University (RSA20021) and the public hospitals involved (HKECREC-20200014; KCC/KEC2020-0070).