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  1. Article ; Online: Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals

    Haogao Gu / Ahmed Abdul Quadeer / Pavithra Krishnan / Daisy Y. M. Ng / Lydia D. J. Chang / Gigi Y. Z. Liu / Samuel M. S. Cheng / Tommy T. Y. Lam / Malik Peiris / Matthew R. McKay / Leo L. M. Poon

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 14

    Abstract: There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough ... ...

    Abstract There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough infections in vaccinated individuals do not seem to increase non-silent mutations.
    Keywords Science ; Q
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022

    Haogao Gu / Daisy Y.M. Ng / Gigi Y.Z. Liu / Samuel S.M. Cheng / Pavithra Krishnan / Lydia D.J. Chang / Sammi S.Y. Cheuk / Mani M.Y. Hui / Tommy T.Y. Lam / Malik Peiris / Leo L.M. Poon

    Emerging Infectious Diseases, Vol 28, Iss 6, Pp 1276-

    2022  Volume 1278

    Abstract: We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021–February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5′ end of the spike gene in 2 ... ...

    Abstract We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021–February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5′ end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed.
    Keywords COVID-19 ; respiratory infections ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; SARS ; coronavirus disease ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Natural Reassortment of Eurasian Avian-Like Swine H1N1 and Avian H9N2 Influenza Viruses in Pigs, China

    Wanying Sun / Samuel S.M. Cheng / Kristy N.T. Lam / Tsz C. Kwan / Ricky W.K. Wong / Leo H.K. Lau / Gigi Y.Z. Liu / Leo L.H. Luk / John K.C. Li / Haogao Gu / Malik Peiris / Leo L.M. Poon

    Emerging Infectious Diseases, Vol 28, Iss 7, Pp 1509-

    2022  Volume 1512

    Abstract: Several zoonotic influenza A viruses detected in humans contain genes derived from avian H9N2 subtypes. We uncovered a Eurasian avian-like H1N1 swine influenza virus with polymerase basic 1 and matrix gene segments derived from the H9N2 subtype, ... ...

    Abstract Several zoonotic influenza A viruses detected in humans contain genes derived from avian H9N2 subtypes. We uncovered a Eurasian avian-like H1N1 swine influenza virus with polymerase basic 1 and matrix gene segments derived from the H9N2 subtype, suggesting that H9N2 viruses are infecting pigs and reassorting with swine influenza viruses in China.
    Keywords influenza ; Eurasian avian-like swine H1N1 virus ; avian H9N2 virus ; zoonotic influenza A viruses ; pigs ; China ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: SARS-CoV-2 Superspread in Fitness Center, Hong Kong, China, March 2021

    Daniel K.W. Chu / Haogao Gu / Lydia D.J. Chang / Sammi S.Y. Cheuk / Shreya Gurung / Pavithra Krishnan / Daisy Y.M. Ng / Gigi Y.Z. Liu / Carrie K.C. Wan / Dominic N.C. Tsang / Malik Peiris / Leo L.M. Poon

    Emerging Infectious Diseases, Vol 27, Iss 8, Pp 2230-

    2021  Volume 2232

    Abstract: To investigate a superspreading event at a fitness center in Hong Kong, China, we used genomic sequencing to analyze 102 reverse transcription PCR–confirmed cases of severe acute respiratory syndrome coronavirus 2 infection. Our finding highlights the ... ...

    Abstract To investigate a superspreading event at a fitness center in Hong Kong, China, we used genomic sequencing to analyze 102 reverse transcription PCR–confirmed cases of severe acute respiratory syndrome coronavirus 2 infection. Our finding highlights the risk for virus transmission in confined spaces with poor ventilation and limited public health interventions.
    Keywords 2019 novel coronavirus disease ; coronavirus disease ; COVID-19 ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; viruses ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Replication of SARS-CoV-2 Omicron BA.2 variant in ex vivo cultures of the human upper and lower respiratory tract

    Kenrie P.Y. Hui / Ka-Chun Ng / John C.W. Ho / Hin-Wo Yeung / Rachel H.H. Ching / Haogao Gu / Joseph C.K. Chung / Velda L.Y. Chow / Ko-Yung Sit / Michael K.Y. Hsin / Timmy W.K. Au / Leo L.M. Poon / Malik Peiris / John M. Nicholls / Michael C.W. Chan

    EBioMedicine, Vol 83, Iss , Pp 104232- (2022)

    2022  

    Abstract: Summary: Background: The Omicron BA.2 sublineage has replaced BA.1 worldwide and has comparable levels of immune evasion to BA.1. These observations suggest that the increased transmissibility of BA.2 cannot be explained by the antibody evasion. Methods: ...

    Abstract Summary: Background: The Omicron BA.2 sublineage has replaced BA.1 worldwide and has comparable levels of immune evasion to BA.1. These observations suggest that the increased transmissibility of BA.2 cannot be explained by the antibody evasion. Methods: Here, we characterized the replication competence and respiratory tissue tropism of three Omicron variants (BA.1, BA.1.1, BA.2), and compared these with the wild-type virus and Delta variant, in human nasal, bronchial and lung tissues cultured ex vivo. Findings: BA.2 replicated more efficiently in nasal and bronchial tissues at 33°C than wild-type, Delta and BA.1. Both BA.2 and BA.1 had higher replication competence than wild-type and Delta viruses in bronchial tissues at 37°C. BA.1, BA.1.1 and BA.2 replicated at a lower level in lung parenchymal tissues compared to wild-type and Delta viruses. Interpretation: Higher replication competence of Omicron BA.2 in the human upper airway at 33°C than BA.1 may be one of the reasons to explain the current advantage of BA.2 over BA.1. A lower replication level of the tested Omicron variants in human lung tissues is in line with the clinical manifestations of decreased disease severity of patients infected with the Omicron strains compared with other ancestral strains. Funding: This work was supported by US National Institute of Allergy and Infectious Diseases and the Theme-Based Research Scheme under University Grants Committee of Hong Kong Special Administrative Region, China.
    Keywords SARS-CoV-2 ; Omicron BA.2 ; Nasal tissue ; Bronchial tissue ; Transmission ; Pathogenicity ; Medicine ; R ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2022-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Monitoring International Travelers Arriving in Hong Kong for Genomic Surveillance of SARS-CoV-2

    Haogao Gu / Samuel S.M. Cheng / Pavithra Krishnan / Daisy Y.M. Ng / Lydia D.J Chang / Gigi Y.Z. Liu / Sammi S.Y. Cheuk / Mani M.Y. Hui / Mathew C.Y. Fan / Jacob H.L. Wan / Leo H.K. Lau / Daniel K.W. Chu / Vijaykrishna Dhanasekaran / Malik Peiris / Leo L.M. Poon

    Emerging Infectious Diseases, Vol 28, Iss 1, Pp 247-

    2022  Volume 250

    Abstract: We sequenced ≈50% of coronavirus disease cases imported to Hong Kong during March–July 2021 and identified 70 cases caused by Delta variants of severe acute respiratory syndrome coronavirus 2. The genomic diversity detected in Hong Kong was similar to ... ...

    Abstract We sequenced ≈50% of coronavirus disease cases imported to Hong Kong during March–July 2021 and identified 70 cases caused by Delta variants of severe acute respiratory syndrome coronavirus 2. The genomic diversity detected in Hong Kong was similar to global diversity, suggesting travel hubs can play a substantial role in surveillance.
    Keywords coronavirus disease ; COVID-19 ; public health surveillance ; respiratory infections ; SARS-CoV-2 ; severe acute respiratory syndrome coronavirus 2 ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021

    Haogao Gu / Pavithra Krishnan / Daisy Y.M. Ng / Lydia D.J Chang / Gigi Y.Z. Liu / Samuel S.M. Cheng / Mani M.Y. Hui / Mathew C.Y. Fan / Jacob H.L. Wan / Leo H.K. Lau / Benjamin J. Cowling / Malik Peiris / Leo L.M. Poon

    Emerging Infectious Diseases, Vol 28, Iss 2, Pp 460-

    2022  Volume 462

    Abstract: We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler in a quarantine hotel in Hong Kong, China. The Omicron variant was also detected in a fully vaccinated ... ...

    Abstract We report detection of severe acute respiratory syndrome coronavirus 2 Omicron variant (B.1.1.529) in an asymptomatic, fully vaccinated traveler in a quarantine hotel in Hong Kong, China. The Omicron variant was also detected in a fully vaccinated traveler staying in a room across the corridor from the index patient, suggesting transmission despite strict quarantine precautions.
    Keywords COVID-19 ; coronavirus disease ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; coronaviruses¸ viruses ; respiratory infections ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Centers for Disease Control and Prevention
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

    Ruopeng Xie / Kimberly M. Edwards / Dillon C. Adam / Kathy S. M. Leung / Tim K. Tsang / Shreya Gurung / Weijia Xiong / Xiaoman Wei / Daisy Y. M. Ng / Gigi Y. Z. Liu / Pavithra Krishnan / Lydia D. J. Chang / Samuel M. S. Cheng / Haogao Gu / Gilman K. H. Siu / Joseph T. Wu / Gabriel M. Leung / Malik Peiris / Benjamin J. Cowling /
    Leo L. M. Poon / Vijaykrishna Dhanasekaran

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 11

    Abstract: Abstract Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high ... ...

    Abstract Abstract Hong Kong experienced a surge of Omicron BA.2 infections in early 2022, resulting in one of the highest per-capita death rates of COVID-19. The outbreak occurred in a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures (PHSMs). By analyzing genome sequences and epidemiological data, we reconstructed the epidemic trajectory of BA.2 wave and found that the initial BA.2 community transmission emerged from cross-infection within hotel quarantine. The rapid implementation of PHSMs suppressed early epidemic growth but the effective reproduction number (R e ) increased again during the Spring festival in early February and remained around 1 until early April. Independent estimates of point prevalence and incidence using phylodynamics also showed extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. Discordant inferences based on genomic and epidemiological data underscore the need for research to improve near real-time epidemic growth estimates by combining multiple disparate data sources to better inform outbreak response policy.
    Keywords Science ; Q
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Evidence-Based interventions of Norovirus outbreaks in China

    Tianmu Chen / Haogao Gu / Ross Ka-Kit Leung / Ruchun Liu / Qiuping Chen / Ying Wu / Yaman Li

    BMC Public Health, Vol 16, Iss 1, Pp 1-

    2016  Volume 9

    Abstract: Abstract Background In resource-limited settings where laboratory capacity is limited and response strategy is non-specific, delayed or inappropriate intervention against outbreaks of Norovirus (NoV) are common. Here we report interventions of two ... ...

    Abstract Abstract Background In resource-limited settings where laboratory capacity is limited and response strategy is non-specific, delayed or inappropriate intervention against outbreaks of Norovirus (NoV) are common. Here we report interventions of two norovirus outbreaks, which highlight the importance of evidence-based modeling and assessment to identify infection sources and formulate effective response strategies. Methods Spatiotemporal scanning, mathematical and random walk modeling predicted the modes of transmission in the two incidents, which were supported by laboratory results and intervention outcomes. Results Simulation results indicated that contaminated water was 14 to 500 fold more infectious than infected individuals. Asymptomatic individuals were not effective transmitters. School closure for up to a week still could not contain the outbreak unless the duration was extended to 10 or more days. The total attack rates (TARs) for waterborne NoV outbreaks reported in China (n = 3, median = 4.37) were significantly (p < 0.05) lower than worldwide (n = 14, median = 41.34). The low TARs are likely due to the high number of the affected population. Conclusions We found that school closure alone could not contain Norovirus outbreaks. Overlooked personal hygiene may serve as a hotbed for infectious disease transmission. Our results reveal that evidence-based investigations can facilitate timely interventions of Norovirus transmission.
    Keywords Mathematical model ; Norovirus ; Outbreak ; Water disinfection ; Public aspects of medicine ; RA1-1270
    Language English
    Publishing date 2016-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Meteorological Factors for Dengue Fever Control and Prevention in South China

    Haogao Gu / Ross Ka-Kit Leung / Qinlong Jing / Wangjian Zhang / Zhicong Yang / Jiahai Lu / Yuantao Hao / Dingmei Zhang

    International Journal of Environmental Research and Public Health, Vol 13, Iss 9, p

    2016  Volume 867

    Abstract: Dengue fever (DF) is endemic in Guangzhou and has been circulating for decades, causing significant economic loss. DF prevention mainly relies on mosquito control and change in lifestyle. However, alert fatigue may partially limit the success of these ... ...

    Abstract Dengue fever (DF) is endemic in Guangzhou and has been circulating for decades, causing significant economic loss. DF prevention mainly relies on mosquito control and change in lifestyle. However, alert fatigue may partially limit the success of these countermeasures. This study investigated the delayed effect of meteorological factors, as well as the relationships between five climatic variables and the risk for DF by boosted regression trees (BRT) over the period of 2005–2011, to determine the best timing and strategy for adapting such preventive measures. The most important meteorological factor was daily average temperature. We used BRT to investigate the lagged relationship between dengue clinical burden and climatic variables, with the 58 and 62 day lag models attaining the largest area under the curve. The climatic factors presented similar patterns between these two lag models, which can be used as references for DF prevention in the early stage. Our results facilitate the development of the Mosquito Breeding Risk Index for early warning systems. The availability of meteorological data and modeling methods enables the extension of the application to other vector-borne diseases endemic in tropical and subtropical countries.
    Keywords dengue fever ; boosted regression trees ; meteorological effects ; Medicine ; R
    Language English
    Publishing date 2016-08-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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