Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics.

Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.

Social Determinants of Cardiovascular Risk Factors Among Asian American Subgroups.

BACKGROUND: Social determinants of health (SDOH) play a significant role in the development of cardiovascular risk factors. We investigated SDOH associations with cardiovascular risk factors among Asian American subgroups. METHODS AND RESULTS: We utilized the National Health Interview Survey, a nationally representative survey of US adults, years 2013 to 2018. SDOH variables were categorized into economic stability, neighborhood and social cohesion, food security, education, and health care utilization. SDOH score was created by categorizing 27 SDOH variables as 0 (favorable) or 1 (unfavorable). Self-reported cardiovascular risk factors included diabetes, high cholesterol, high blood pressure, obesity, insufficient physical activity, suboptimal sleep, and nicotine exposure. Among 6395 Asian adults aged ≥18 years, 22.1% self-identified as Filipino, 21.6% as Asian Indian, 21.0% as Chinese, and 35.3% as other Asian. From multivariable-adjusted logistic regression models, each SD increment of SDOH score was associated with higher odds of diabetes among Chinese (odds ratio [OR], 1.45; 95% CI, 1.04-2.03) and Filipino (OR, 1.24; 95% CI, 1.02-1.51) adults; high blood pressure among Filipino adults (OR, 1.28; 95% CI, 1.03-1.60); insufficient physical activity among Asian Indian (OR, 1.42; 95% CI, 1.22-1.65), Chinese (OR, 1.58; 95% CI, 1.33-1.88), and Filipino (OR, 1.24; 95% CI, 1.06-1.46) adults; suboptimal sleep among Asian Indian adults (OR, 1.20; 95% CI, 1.01-1.42); and nicotine exposure among Chinese (OR, 1.56; 95% CI, 1.15-2.11) and Filipino (OR, 1.50; 95% CI, 1.14-1.97) adults. CONCLUSIONS: Unfavorable SDOH are associated with higher odds of cardiovascular risk factors in Asian American subgroups. Culturally specific interventions addressing SDOH may help improve cardiovascular health among Asian Americans.

Prevalence and Outcomes of Infections in Critically-ill Paediatric Oncology Patients: A Retrospective Observation Study.

PURPOSE: The survival of paediatric oncology patients has improved substantially in the past decades due to advances in the field of oncology. Modern cancer treatments often come with life-threatening complications, of which infection is one of the most common causes in this patient population. This study aims to investigate the prevalence and outcomes of common infections in haemato-oncology patients during their stay in paediatric intensive care unit (PICU) and to identify any factors associated with these infections. METHODS: A retrospective observational study was conducted on all children with a haemato-oncology diagnosis or who underwent haematopoietic stem cell transplantation (HSCT) and who were admitted to the Hong Kong Children's Hospital PICU over a one-year period. Infection characteristics and patient outcomes were evaluated and compared between different sub-groups. Univariable and multi-variable analyses were employed to identify risk factors associated with the development of active infection. RESULTS: Forty-five (36.3%) of 124 critically ill haemato-oncology admissions to PICU were associated with infections, of which 31 (25%) admissions involved bacterial infections, 26 (20.9%) involved viral infections and 6 (4.8%) involved fungal infections. Bloodstream infection was the most common type of infection. More than half (61.3%) of the bacterial infections were due to an antibiotic-resistant strain. After adjusting for confounding variables, post-HSCT status and neutropenia were significantly associated with active infections. CONCLUSION: Infections in critically-ill haemato-oncological patients are associated with post haematopoietic stem cell transplant status and neutropenia. Further study is warranted to review effective strategies that may mitigate the likelihood of infection in this patient population.

2024 Heart Disease and Stroke Statistics: A Report of US and Global Data From the American Heart Association.

BACKGROUND: The American Heart Association (AHA), in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, nutrition, sleep, and obesity) and health factors (cholesterol, blood pressure, glucose control, and metabolic syndrome) that contribute to cardiovascular health. The AHA Heart Disease and Stroke Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, brain health, complications of pregnancy, kidney disease, congenital heart disease, rhythm disorders, sudden cardiac arrest, subclinical atherosclerosis, coronary heart disease, cardiomyopathy, heart failure, valvular disease, venous thromboembolism, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS: The AHA, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States and globally to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2024 AHA Statistical Update is the product of a full year's worth of effort in 2023 by dedicated volunteer clinicians and scientists, committed government professionals, and AHA staff members. The AHA strives to further understand and help heal health problems inflicted by structural racism, a public health crisis that can significantly damage physical and mental health and perpetuate disparities in access to health care, education, income, housing, and several other factors vital to healthy lives. This year's edition includes additional global data, as well as data on the monitoring and benefits of cardiovascular health in the population, with an enhanced focus on health equity across several key domains. RESULTS: Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS: The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.

Epidemiology of Diabetes and Atherosclerotic Cardiovascular Disease Among Asian American Adults: Implications, Management, and Future Directions: A Scientific Statement From the American Heart Association.

Asian American individuals make up the fastest growing racial and ethnic group in the United States. Despite the substantial variability that exists in type 2 diabetes and atherosclerotic cardiovascular disease risk among the different subgroups of Asian Americans, the current literature, when available, often fails to examine these subgroups individually. The purpose of this scientific statement is to summarize the latest disaggregated data, when possible, on Asian American demographics, prevalence, biological mechanisms, genetics, health behaviors, acculturation and lifestyle interventions, pharmacological therapy, complementary alternative interventions, and their impact on type 2 diabetes and atherosclerotic cardiovascular disease. On the basis of available evidence to date, we noted that the prevalences of type 2 diabetes and stroke mortality are higher in all Asian American subgroups compared with non-Hispanic White adults. Data also showed that atherosclerotic cardiovascular disease risk is highest among South Asian and Filipino adults but lowest among Chinese, Japanese, and Korean adults. This scientific statement discusses the biological pathway of type 2 diabetes and the possible role of genetics in type 2 diabetes and atherosclerotic cardiovascular disease among Asian American adults. Challenges to provide evidence-based recommendations included the limited data on Asian American adults in risk prediction models, national surveillance surveys, and clinical trials, leading to significant research disparities in this population. The large disparity within this population is a call for action to the public health and clinical health care community, for whom opportunities for the inclusion of the Asian American subgroups should be a priority. Future studies of atherosclerotic cardiovascular disease risk in Asian American adults need to be adequately powered, to incorporate multiple Asian ancestries, and to include multigenerational cohorts. With advances in epidemiology and data analysis and the availability of larger, representative cohorts, furthering refining the Pooled Cohort Equations, in addition to enhancers, would allow better risk estimation in segments of the population. Last, this scientific statement provides individual- and community-level intervention suggestions for health care professionals who interact with the Asian American population.

Probable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China.

Between January 2015 and October 2022, 38 patients with culture-confirmed melioidosis were identified in the Kowloon West (KW) Region, Hong Kong. Notably, 30 of them were clustered in the Sham Shui Po (SSP) district, which covers an estimated area of 2.5 km2. Between August and October 2022, 18 patients were identified in this district after heavy rainfall and typhoons. The sudden upsurge in cases prompted an environmental investigation, which involved collecting 20 air samples and 72 soil samples from residential areas near the patients. A viable isolate of Burkholderia pseudomallei was obtained from an air sample collected at a building site five days after a typhoon. B. pseudomallei DNA was also detected in 21 soil samples collected from the building site and adjacent gardening areas using full-length 16S rRNA gene sequencing, suggesting that B. psuedomallei is widely distributed in the soil environment surrounding the district. Core genome-multilocus sequence typing showed that the air sample isolate was phylogenetically clustered with the outbreak isolates in KW Region. Multispectral satellite imagery revealed a continuous reduction in vegetation region in SSP district by 162,255 m2 from 2016 to 2022, supporting the hypothesis of inhalation of aerosols from the contaminated soil as the transmission route of melioidosis during extreme weather events. This is because the bacteria in unvegetated soil are more easily spread by winds. In consistent with inhalational melioidosis, 24 (63.2%) patients had pneumonia. Clinicians should be aware of melioidosis during typhoon season and initiate appropriate investigation and treatment for patients with compatible symptoms.

Heart Disease and Stroke Statistics-2023 Update: A Report From the American Heart Association.

BACKGROUND: The American Heart Association, in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, diet, and weight) and health factors (cholesterol, blood pressure, and glucose control) that contribute to cardiovascular health. The Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, venous disease, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS: The American Heart Association, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2023 Statistical Update is the product of a full year's worth of effort in 2022 by dedicated volunteer clinicians and scientists, committed government professionals, and American Heart Association staff members. The American Heart Association strives to further understand and help heal health problems inflicted by structural racism, a public health crisis that can significantly damage physical and mental health and perpetuate disparities in access to health care, education, income, housing, and several other factors vital to healthy lives. This year's edition includes additional COVID-19 (coronavirus disease 2019) publications, as well as data on the monitoring and benefits of cardiovascular health in the population, with an enhanced focus on health equity across several key domains. RESULTS: Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS: The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.

Prevalence and Predictors of Premature Coronary Heart Disease Among Asians in the United States: A National Health Interview Survey Study.

Identifying Asian subgroups with higher risk of premature coronary heart disease (CHD) can help implement targeted strategies to prevent future CHD events. We conducted this National Health Interview Survey study from 2006 to 2015 among participants with history of CHD to compare the risk of premature CHD (<65 for women and <55 years old for men) across Whites, Chinese, Asian Indians, Filipinos, and "other Asians" (Japanese, Korean, and Vietnamese individuals) using univariate and multi-variable logistic regression models. A total of 17,266 participants with history of CHD (mean age, 66.0 ± 0.2; 39% women) were included. Risk of premature CHD was higher among Asian Indians (OR = 1.77, 1.05-2.97) and "other Asians" (OR = 1.68, 1.17-2.42) than Whites adults. Compared with Chinese, the risk of premature CHD was significantly higher for Asian Indians in the unadjusted models (OR = 2.72, 1.19-6.3). "Other Asians" exhibited significantly higher risk in crude (OR = 2.88, 1.32-6.27) and adjusted models (aOR = 2.29, 1.01-5.18). Among younger adults (<50 years) with CHD, Asian Indian adults (aOR = 2.43, 1.26-4.70) and other Asian adults (aOR = 1.86, 1.14-3.02) showed higher odds of premature CHD compared with White adults. The risk of premature CHD varies across Asian populations. More studies with an adequate sampling of Asian subgroups are needed to identify the risk and determinants of premature CHD.

Association of Acculturation with Cardiovascular Risk Factors in Asian-American Subgroups.

Objective: This cross-sectional study aims to better understand the heterogeneous associations of acculturation level on CV risk factors among disaggregated Asian subgroups. We hypothesize that the association between acculturation level and CV risk factors will differ significantly by Asian subgroup. Methods: We used the National Health Interview Survey (NHIS), a nationally representative US survey, years 2014-18. Acculturation was defined using: (a) years in the US, (b) US citizenship status, and (c) level of English proficiency. We created an acculturation index, categorized into low vs. high (scores of 0-3 and 4, respectively). Self-reported CV risk factors included diabetes, high cholesterol, hypertension, obesity, tobacco use, and sufficient physical activity. Rao-Scott Chi Square was used to compare age-standardized, weighted prevalence of CV risk factors between Asian subgroups. We used logistic regression analysis to assess associations between acculturation and CV risk factors, stratified by Asian subgroup. Results: The study sample consisted of 6,051 adults ≥ 18 years of age (53.9% female; mean age 46.6 [SE 0.33]). The distribution by race/ethnicity was Asian Indian 26.9%, Chinese 22.8%, Filipino 18.1%, and other Asian 32.3%. The association between acculturation and CV risk factors differed by Asian subgroups. From multivariable adjusted models, high vs. low acculturation was associated with: high cholesterol amongst Asian Indian (OR=1.57, 95% CI: 1.11, 2.37) and other Asian (OR=1.48, 95% CI: 1.10, 2.01) adults, obesity amongst Filipino adults (OR= 1.62, 95% CI: 1.07, 2.45), and sufficient physical activity amongst Chinese (OR= 1.54, 95% CI: 1.09, 2.19) and Filipino adults (OR=1.58, 95% CI: 1.10, 2.27). Conclusion: This study demonstrates that acculturation is heterogeneously associated with higher prevalence of CV risk factors among Asian subgroups. More studies are needed to better understand these differences that can help to inform targeted, culturally specific interventions.

Prediction of frozen virus stability based on degradation mechanisms, real-time data and modeling.

Aim: Critical virus reagents in regulated bioanalytical assays require stability monitoring. Although stability at ultra-low frozen temperatures is generally assumed, published data are limited and real-time studies are time consuming. Materials & methods: The authors reviewed literature data, typical mechanisms of molecular degradation, glass transition temperatures of commonly used buffers and available real-time storage data to model frozen virus reagent stability. Results: Storage at ultra-low temperatures below the glass transition temperature was critical for virus stability. Modeling of real-time data suggested that virus potency remained within 0.5 log10 of its starting potency at a probability of >99, 90 and 73% after 10, 20 and 30 years, respectively. Conclusion: The study supports the practice of virus storage at -70°C or below for 20-30 years.

Association of U.S. birth, duration of residence in the U.S., and atherosclerotic cardiovascular disease risk factors among Asian adults.

Introduction: Prior studies have shown a direct association between U.S. birth and duration of residence with atherosclerotic cardiovascular disease (ASCVD) though, few have specifically focused on Asian Americans. Methods: We utilized cross-sectional data from the 2006 to 2015 National Health Interview Survey. We compared prevalent cardiovascular risk factors and ASCVD among Asian American individuals by U.S. birth and duration of time spent in the U.S. Results: The study sample consisted of 18,150 Asian individuals of whom 20.5 % were Asian Indian, 20.5 % were Chinese, 23.4 % were Filipino, and 35.6 % were of other Asian ethnic groups. The mean (standard error) age was 43.8 (0.21) years and 53 % were women. In multivariable-adjusted logistic regression models, U.S. birth was associated with a higher prevalence odds ratio (95 % confidence interval) of current smoking 1.31 (1.07,1.60), physical inactivity 0.62 (0.54,0.72), obesity 2.26 (1.91,2.69), hypertension 1.33 (1.12,1.58), and CAD 1.96 (1.24,3.11), but lower prevalence of stroke 0.28 (0.11,0.71). Spending greater than 15 years in the U.S. was associated with a higher prevalence of current smoking 1.65 (1.24,2.21), obesity 2.33 (1.57,3.47), diabetes 2.68 (1.17,6.15), and hyperlipidemia 1.72 (1.09,2.71). Conclusion: Heterogeneity exists in cardiovascular risk factor burden among Asian Americans according to Asian ethnicity, U.S. birth, and duration of time living in the U.S.

High attack rate in a Tong Lau house outbreak of COVID-19 with subdivided units in Hong Kong.

Poor housing conditions are known to be associated with infectious diseases such as high Coronavirus disease 2019 (COVID-19) incidences. Transmission causes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in poor housing conditions can be complex. An understanding of the exact mechanism of transmission can help to pinpoint contributing environmental issues. Here, we investigated a Hong Kong COVID-19 outbreak in early 2021 in four traditional Tong Lau houses with subdivided units. There are more than 80 subdivided units of less than 20 m2 floor area each on average. With a total of 34 confirmed COVID-19 cases, the outbreak had an attack rate of 25.4%, being one of the highest attack rates observed in Hong Kong, and ranked among the highest attack rates in reported outbreaks internationally. Tracer gas leakage and decay measurements were performed in the drainage system and in the subdivided units to determine the transport of infectious aerosols by the owner-modified sophisticated wastewater drainage pipe networks and the poor ventilation conditions in some subdivided units. The results show that the outbreak was probably due to multiple transmission routes, i.e. by the drainage pipe spread of stack aerosols, which is enhanced by poor ventilation in the subdivided units.

Spread of SARS-CoV-2 aerosols via two connected drainage stacks in a high-rise housing outbreak of COVID-19.

Vertical transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) along a vertical column of flats has been documented in several outbreaks of coronavirus disease 2019 (COVID-19) in Guangdong and Hong Kong. We describe an outbreak in Luk Chuen House, involving two vertical columns of flats associated with an unusually connected two-stack drainage system, in which nine individuals from seven households were infected. The index case resided in Flat 812 (8th floor, Unit 12), two flats (813, 817) on its opposite side reported one case each (i.e., a horizontal sub-cluster). All other flats with infected residents were vertically associated, forming a vertical sub-cluster. We injected tracer gas (SF6) into drainage stacks via toilet or balcony of Flat 812, monitored gas concentrations in roof vent, toilet, façade, and living room in four of the seven flats with infected residents and four flats with no infected residents. The measured gas concentration distributions agreed with the observed distribution of affected flats. Aerosols leaking into drainage stacks may generate the vertical sub-cluster, whereas airflow across the corridor probably caused the horizontal sub-cluster. Sequencing and phylogenetic analyses also revealed a common point-source. The findings provided additional evidence of probable roles of drainage systems in SARS-CoV-2 transmission.

Aerosol transmission of SARS-CoV-2 due to the chimney effect in two high-rise housing drainage stacks.

Stack aerosols are generated within vertical building drainage stacks during the discharge of wastewater containing feces and exhaled mucus from toilets and washbasins. Fifteen stack aerosol-related outbreaks of coronavirus disease 2019 (COVID-19) in high-rise buildings have been observed in Hong Kong and Guangzhou. Currently, we investigated two such outbreaks of COVID-19 in Hong Kong, identified the probable role of chimney effect-induced airflow in a building drainage system in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We injected tracer gas (SF6) into the drainage stacks via the water closet of the index case and monitored tracer gas concentrations in the bathrooms and along the facades of infected and non-infected flats and in roof vents. The air temperature, humidity, and pressure in vertical stacks were also monitored. The measured tracer gas distribution agreed with the observed distribution of the infected cases. Phylogenetic analysis of the SARS-CoV-2 genome sequences demonstrated clonal spread from a point source in cases along the same vertical column. The stack air pressure and temperature distributions suggested that stack aerosols can spread to indoors through pipe leaks which provide direct evidence for the long-range aerosol transmission of SARS-CoV-2 through drainage pipes via the chimney effect.

Hepatitis E Virus Species C Infection in Humans, Hong Kong.

BACKGROUND: Hepatitis E virus (HEV) variants belonging to Orthohepevirus species A (HEV-A) are the primary cause of human hepatitis E. However, we previously reported that Orthohepevirus species C genotype 1 (HEV-C1), a divergent HEV variant commonly found in rats, also causes hepatitis in humans. Here, we present a clinical-epidemiological investigation of human HEV-C1 infections detected in Hong Kong, with an emphasis on outcomes in immunocompromised individuals. METHODS: A surveillance system for detecting human HEV-C1 infections was established in Hong Kong. Epidemiological and clinical characteristics of HEV-C1 cases identified via this system between 1 August 2019 and 31 December 2020 were retrieved. Phylogenetic analysis of HEV-C1 strain sequences was performed. Infection outcomes of immunocompromised individuals with HEV-A and HEV-C1 infections were analyzed. RESULTS: HEV-C1 accounted for 8 of 53 (15.1%) reverse-transcription polymerase chain reaction (RT-PCR)-confirmed HEV infections in Hong Kong during the study period, raising the total number of HEV-C1 infections detected in the city to 16. Two distinct HEV-C1 strain groups caused human infections. Patients were elderly and/or immunocompromised; half tested negative for HEV immunoglobulin M. Cumulatively, HEV-C1 accounted for 9 of 21 (42.9%) cases of hepatitis E recorded in immunocompromised patients in Hong Kong. Immunocompromised HEV-C1 patients progressed to persistent hepatitis at similar rates (7/9 [77.8%]) as HEV-A patients (10/12 [75%]). HEV-C1 patients responded to oral ribavirin, although response to first course was sometimes poor or delayed. CONCLUSIONS: Dedicated RT-PCR-based surveillance detected human HEV-C1 cases that evade conventional hepatitis E diagnostic testing. Immunosuppressed HEV-C1-infected patients frequently progress to persistent HEV-C1 infection, for which ribavirin is a suitable treatment option.

A Sensitive and Specific Competitive Enzyme-Linked Immunosorbent Assay for Serodiagnosis of COVID-19 in Animals.

In addition to human cases, cases of COVID-19 in captive animals and pets are increasingly reported. This raises the concern for two-way COVID-19 transmission between humans and animals. Here, we developed a SARS-CoV-2 nucleocapsid protein-based competitive enzyme-linked immunosorbent assay (cELISA) for serodiagnosis of COVID-19 which can theoretically be used in virtually all kinds of animals. We used 187 serum samples from patients with/without COVID-19, laboratory animals immunized with inactive SARS-CoV-2 virions, COVID-19-negative animals, and animals seropositive to other betacoronaviruses. A cut-off percent inhibition value of 22.345% was determined and the analytical sensitivity and specificity were found to be 1:64-1:256 and 93.9%, respectively. Evaluation on its diagnostic performance using 155 serum samples from COVID-19-negative animals and COVID-19 human patients showed a diagnostic sensitivity and specificity of 80.8% and 100%, respectively. The cELISA can be incorporated into routine blood testing of farmed/captive animals for COVID-19 surveillance.

Genome Sequences of Three SARS-CoV-2 ORF7a Deletion Variants Obtained from Patients in Hong Kong.

We report the genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from the clinical samples of three coronavirus disease 2019 (COVID-19) patients in Hong Kong. All the genome sequences showed a 370-nucleotide deletion resulting in the complete loss of ORF7a.

Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.

BACKGROUND: Viral genomic surveillance is vital for understanding the transmission of COVID-19. In Hong Kong, breakthrough outbreaks have occurred in July (third wave) and November (fourth wave) 2020. We used whole viral genome analysis to study the characteristics of these waves. METHODS: We analyzed 509 SARS-CoV-2 genomes collected from Hong Kong patients between 22nd January and 29th November, 2020. Phylogenetic and phylodynamic analyses were performed, and were interpreted with epidemiological information. FINDINGS: During the third and fourth waves, diverse SARS-CoV-2 genomes were identified among imported infections. Conversely, local infections were dominated by a single lineage during each wave, with 96.6% (259/268) in the third wave and 100% (73/73) in the fourth wave belonging to B.1.1.63 and B.1.36.27 lineages, respectively. While B.1.1.63 lineage was imported 2 weeks before the beginning of the third wave, B.1.36.27 lineage has circulated in Hong Kong for 2 months prior to the fourth wave. During the fourth wave, 50.7% (37/73) of local infections in November was identical to the viral genome from an imported case in September. Within B.1.1.63 or B.1.36.27 lineage in our cohort, the most common non-synonymous mutations occurred at the helicase (nsp13) gene. INTERPRETATION: Although stringent measures have prevented most imported cases from spreading in Hong Kong, a single lineage with low-level local transmission in October and early November was responsible for the fourth wave. A superspreading event or lower temperature in November may have facilitated the spread of the B.1.36.27 lineage.

Emergence of a Severe Acute Respiratory Syndrome Coronavirus 2 Virus Variant With Novel Genomic Architecture in Hong Kong.

Throughout the coronavirus disease 2019 (COVID-19) pandemic, divergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages have emerged continuously, mostly through the genomic accumulation of substitutions. We report the discovery of a SARS-CoV-2 variant with a novel genomic architecture characterized by absent ORF7a, ORF7b, and ORF8, and a C-terminally modified ORF6 product resulting from partial 5'-untranslated region (UTR) duplication and transposition.