The distinct microbial community patterns and pathogen transmission routes in intensive care units

While the microbiome in indoor environments such as hospitals has drawn increasing attention, the transmission routes especially for pathogens in ICUs remain largely unexamined. In this study, we have explored the distinct bacterial communities of ICU compared with Non-ICU in hospital wards. We have then clarified their different transmission patterns by means of microbial source tracking, with results suggesting that bedrail and inside floor were hubs in two wards, respectively. Streptococcus, Staphylococcus were identified as "Transfer-Easy taxa" that were found in both ICU and Non-ICU settings, with potential pathogenicity and cases recorded. We have also detected another 15 pathogenic genera in hospital environment, including Pseudomonas and Acinetobacter, and charted how these pathogenic microorganisms affect patients, demonstrating that there were far more strong routes for pathogens transmitted from environment to patients in ICU. In summary, this work investigates patterns of bacterial transmission in hospital settings, highlights pathogenic genera that are likely to transfer from the environment to humans and cause nosocomial infection, which could provide guidance for healthcare system monitoring and co-infection avoidance.

Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data.

BACKGROUND: As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. METHODS: For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID's EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. RESULTS: As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia's daily infections during the period of March-May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. CONCLUSIONS: SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential.

Testing volatility spillovers using GARCH models in the Japanese stock market during COVID-19

This paper investigates volatility spillovers in the stock market in Japan during the COVID-19 pandemic by using GARCH family models. The empirical analysis is focused on the dynamics of the NIKKEI 225 stock market index during the sample period from July 30, 1998, to January 24, 2022. In other words, the sample period covers both the period of the global financial crisis (GFC) and the COVID-19 pandemic. The econometrics includes GARCH (1,1), GJR (1,1), and EGARCH (1,1) models. By applying GARCH family models, this empirical study also examines the long-term behavior of the Japanese stock market. The Japanese stock market is much more stable and efficient than emerging or frontier markets characterized by higher volatility and lower liquidity. The paper establishes that NIKKEI 225 index dynamics is different in intensity in the case of the two most recent extreme events analyzed, namely the global financial crisis (GFC)of 2007-2008 and the COVID-19 pandemic. The findings confirmed the presence of the leverage effect during the sample period. Moreover, the empirical results identified the presence of high volatility in the sample returns of the selected stock market. Nevertheless, the econometric framework showed that the negative implications of the GFC were much more severe and caused more significant contractions compared to the COVID-19 pandemic for the Japanese stock market. This study contributes to the existing literature by providing additional empirical evidence on the long-term behavior of the stock market in Japan, especially in the context of extreme events. © 2022 LLC CPC Business Perspectives. All rights reserved.

Reporting of Infectious Diseases in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic.

Reporting of infectious diseases other than COVID-19 has been greatly decreased throughout the COVID-19 pandemic. We find this decrease varies by routes of transmission, reporting state, and COVID-19 incidence at the time of reporting. These results underscore the need for continual investment in routine surveillance efforts despite pandemic conditions.

Uncovering transmission patterns of COVID-19 outbreaks: A region-wide comprehensive retrospective study in Hong Kong.

BACKGROUND: Given the dynamism and heterogeneity of COVID-19 transmission patterns, determining the most effective yet timely strategies for specific regions remains a severe challenge for public health decision-makers. METHODS: In this work, we proposed a spatiotemporal connectivity analysis method for discovering transmission patterns across geographic locations and age-groups throughout different COVID-19 outbreak phases. First, we constructed the transmission networks of the confirmed cases during different phases by considering the spatiotemporal connectivity of any two cases. Then, for each case and those cases immediately pointed from it, we characterized the corresponding cross-district/population transmission pattern by counting their district-to-district and age-to-age occurrences. By summating the cross-district/population transmission patterns of all cases during a given period, we obtained the aggregated cross-district and cross-population transmission patterns. FINDINGS: We conducted a region-wide comprehensive retrospective study in Hong Kong based on the complete data report of COVID-19 cases, covering all 18 districts between January 23, 2020, and January 8, 2021 (https://data.gov.hk/en-data/dataset/hk-dh-chpsebcddr-novel-infectious-agent). The spatiotemporal connectivity analysis clearly unveiled the quantitative differences among various outbreak waves in their transmission scales, durations, and patterns. Moreover, for the statistically similar waves, their cross-district/population transmission patterns could be quite different (e.g., the cross-district transmission of the fourth wave was more diverse than that of the third wave, while the transmission over age-groups of the fourth wave was more concentrated than that of the third wave). At an overall level, super-spreader individuals (highly connected cases in the transmission networks) were usually concentrated in only a few districts (2 out of 18 in our study) or age-groups (3 out of 11 in our study). INTERPRETATION: With the discovered cross-district or cross-population transmission patterns, all of the waves of COVID-19 outbreaks in Hong Kong can be systematically scrutinized. Among all districts, quite a few (e.g., the Yau Tsim Mong district) were instrumental in spreading the virus throughout the pandemic. Aside from being exceptionally densely populated, these districts were also social-economic centers. With a variety of situated public venues, such as restaurants and singing/dancing clubs, these districts played host to all kinds of social gathering events, thereby providing opportunities for widespread and rapid transmission of the virus. Thus, these districts should be given the highest priority when deploying district-specific social distancing or intervention strategies, such as lockdown and stringent mandatory coronavirus testing for identifying and obstructing the chain of transmission. We also observed that most of the reported cases and the highly connected cases were middle-aged and elderly people (40- to 69-year-olds). People in these age-groups were active in various public places and social activities, and thus had high chances of being infected by or infecting others. FUNDING: General research fund of the Hong Kong research grants council.

Epidemiological and clinical characteristics of 214 families with COVID-19 in Wuhan, China.

OBJECTIVE: To investigate the epidemiological dynamics, transmission patterns, and the clinical outcomes of Coronavirus disease 2019 (COVID-19) in familial cluster patients in Wuhan, China. METHODS: Between January 22, 2020, and February 4, 2020, we enrolled 214 families for this retrospective study. The COVID-19 cases were diagnosed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). The number of COVID-19 subjects in a family, their relationship with index patients, the key time-to-event, exposure history, and the clinical outcomes were obtained through telephone calls. RESULTS: Overall, 96 families (44.9%) met the criteria of a familial cluster, which is at least one confirmed case in addition to the index patient in the same household. The secondary attack rate was 42.9%, and nearly 95% of index patients transmitted the infection to ≤2 other family members. High transmission pattern was noted between couples (51.0%) and among multi-generations (27.1%). The median serial interval distribution in familial clusters was 5 days (95% CI, 4 to 6). The case fatality rate was 8.7% in index patients and 1.7% in non-familial clusters patients (p = 0.023). CONCLUSIONS: There is a related higher attack rate and worse clinical outcomes in COVID-19 family clusters.

What are the underlying transmission patterns of COVID-19 outbreak? An age-specific social contact characterization.

BACKGROUND: COVID-19 has spread to 6 continents. Now is opportune to gain a deeper understanding of what may have happened. The findings can help inform mitigation strategies in the disease-affected countries. METHODS: In this work, we examine an essential factor that characterizes the disease transmission patterns: the interactions among people. We develop a computational model to reveal the interactions in terms of the social contact patterns among the population of different age-groups. We divide a city's population into seven age-groups: 0-6 years old (children); 7-14 (primary and junior high school students); 15-17 (high school students); 18-22 (university students); 23-44 (young/middle-aged people); 45-64 years old (middle-aged/elderly people); and 65 or above (elderly people). We consider four representative settings of social contacts that may cause the disease spread: (1) individual households; (2) schools, including primary/high schools as well as colleges and universities; (3) various physical workplaces; and (4) public places and communities where people can gather, such as stadiums, markets, squares, and organized tours. A contact matrix is computed to describe the contact intensity between different age-groups in each of the four settings. By integrating the four contact matrices with the next-generation matrix, we quantitatively characterize the underlying transmission patterns of COVID-19 among different populations. FINDINGS: We focus our study on 6 representative cities in China: Wuhan, the epicenter of COVID-19 in China, together with Beijing, Tianjin, Hangzhou, Suzhou, and Shenzhen, which are five major cities from three key economic zones. The results show that the social contact-based analysis can readily explain the underlying disease transmission patterns as well as the associated risks (including both confirmed and unconfirmed cases). In Wuhan, the age-groups involving relatively intensive contacts in households and public/communities are dispersedly distributed. This can explain why the transmission of COVID-19 in the early stage mainly took place in public places and families in Wuhan. We estimate that Feb. 11, 2020 was the date with the highest transmission risk in Wuhan, which is consistent with the actual peak period of the reported case number (Feb. 4-14). Moreover, the surge in the number of new cases reported on Feb. 12 and 13 in Wuhan can readily be captured using our model, showing its ability in forecasting the potential/unconfirmed cases. We further estimate the disease transmission risks associated with different work resumption plans in these cities after the outbreak. The estimation results are consistent with the actual situations in the cities with relatively lenient policies, such as Beijing, and those with strict policies, such as Shenzhen. INTERPRETATION: With an in-depth characterization of age-specific social contact-based transmission, the retrospective and prospective situations of the disease outbreak, including the past and future transmission risks, the effectiveness of different interventions, and the disease transmission risks of restoring normal social activities, are computationally analyzed and reasonably explained. The conclusions drawn from the study not only provide a comprehensive explanation of the underlying COVID-19 transmission patterns in China, but more importantly, offer the social contact-based risk analysis methods that can readily be applied to guide intervention planning and operational responses in other countries, so that the impact of COVID-19 pandemic can be strategically mitigated. FUNDING: General Research Fund of the Hong Kong Research Grants Council; Key Project Grants of the National Natural Science Foundation of China.