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1.
Antibiotics (Basel) ; 11(6)2022 May 31.
Article in English | MEDLINE | ID: covidwho-1869451

ABSTRACT

Nonpharmaceutical interventions implemented during the COVID-19 pandemic (2020-2021) have provided a unique opportunity to understand their impact on the wholesale supply of antibiotics and incidences of infections represented by bacteremia due to common bacterial species in Hong Kong. The wholesale antibiotic supply data (surrogate indicator of antibiotic consumption) and notifications of scarlet fever, chickenpox, and tuberculosis collected by the Centre for Health Protection, and the data of blood cultures of patients admitted to public hospitals in Hong Kong collected by the Hospital Authority for the last 10 years, were tabulated and analyzed. A reduction in the wholesale supply of antibiotics was observed. This decrease coincided with a significant reduction in the incidence of community-onset bacteremia due to Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are encapsulated bacteria with respiratory transmission potential. This reduction was sustained during two pandemic years (period 2: 2020-2021), compared with eight pre-pandemic years (period 1: 2012-2019). Although the mean number of patient admissions per year (1,704,079 vs. 1,702,484, p = 0.985) and blood culture requests per 1000 patient admissions (149.0 vs. 158.3, p = 0.132) were not significantly different between periods 1 and 2, a significant reduction in community-onset bacteremia due to encapsulated bacteria was observed in terms of the mean number of episodes per year (257 vs. 58, p < 0.001), episodes per 100,000 admissions (15.1 vs. 3.4, p < 0.001), and per 10,000 blood culture requests (10.1 vs. 2.1, p < 0.001), out of 17,037,598 episodes of patient admissions with 2,570,164 blood culture requests. Consistent with the findings of bacteremia, a reduction in case notification of scarlet fever and airborne infections, including tuberculosis and chickenpox, was also observed; however, there was no reduction in the incidence of hospital-onset bacteremia due to Staphylococcus aureus or Escherichia coli. Sustained implementation of non-pharmaceutical interventions against respiratory microbes may reduce the overall consumption of antibiotics, which may have a consequential impact on antimicrobial resistance. Rebound of conventional respiratory microbial infections is likely with the relaxation of these interventions.

2.
Clin Infect Dis ; 74(9): 1623-1630, 2022 05 03.
Article in English | MEDLINE | ID: covidwho-1707925

ABSTRACT

BACKGROUND: Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as variants of concern (VOCs) or variants of interest (VOIs). Here we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1.617.1 (kappa variant) and P.3 (theta variant), which were first detected in India and the Philippines, respectively. METHODS: The neutralization susceptibility of the VOCs/VOIs (B.1.351, B.1.617.1, and P.3) and a non-VOC/VOI without RBD mutations (B.1.36.27) to convalescent sera from coronavirus disease 2019 (COVID-19) patients or BNT162b2 vaccinees was determined using a live virus microneutralization (MN) assay. Serum immunoglobulin G (IgG) binding to wild-type and mutant RBDs were determined using an enzyme immunoassay. RESULTS: The geometric mean neutralization titers (GMT) of B.1.351, P.3, and B.1.617.1 were significantly lower than that of B.1.36.27 for COVID-19 patients infected with non-VOCs/VOIs (3.4- to 5.7-fold lower) or individuals who have received 2 doses of BNT162b2 vaccine (4.4- to 7.3-fold lower). The GMT of B.1.351 or P.3 were lower than that of B.1.617.1. For the 4 patients infected with B.1.351 or B.1.617.1, the MN titer was highest for their respective lineage. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding. CONCLUSIONS: P.3 and B.1.617.1 escape serum neutralization induced by natural infection or vaccine. Infection with 1 variant does not confer cross-protection for heterologous lineages. Immunogenicity testing for second generation COVID-19 vaccines should include multiple variant and "nonvariant" strains.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/therapy , COVID-19 Vaccines , Humans , Immunization, Passive , Immunoglobulin G , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Vaccination
3.
J Virol Methods ; 299: 114333, 2022 01.
Article in English | MEDLINE | ID: covidwho-1525873

ABSTRACT

The increasing prevalence of N501Y variants of SARS-CoV-2 has kindled global concern due to their enhanced transmissibility. Genome sequencing is the gold standard method to identify the emerging variants of concern. But it is time-consuming and expensive, limiting the widespread deployment of genome surveillance in some countries. Health authorities surge the development of alternative assay to expand screening capacity with reduced time and cost. In this study, we developed an in-house TaqMan minor groove binder (MGB) probe-based one-step RT-qPCR assay to detect the presence of N501Y mutation in SARS-CoV-2. A total of 168 SARS-CoV-2 positive respiratory specimens were collected to determine diagnostic accuracy of the RT-qPCR assay. As a reference standard, PANGO lineages and the mutation patterns of all samples were characterised by whole-genome sequencing. The analytical sensitivity and the ability of the assay to detect low frequency of N501Y variants were also evaluated. A total of 31 PANGO lineages were identified from 168 SARS-CoV-2 positive cases, in which 34 samples belonged to N501Y variants, including B.1.1.7 (n = 20), B.1.351 (n = 12) and P.3 (n = 2). The N501Y RT-qPCR correctly identified all 34 samples as N501Y-positive and the other 134 samples as wildtype. The limit-of-detection of the assay consistently achieved 1.5 copies/µL on four different qPCR platforms. N501Y mutation was successfully detected at an allele frequency as low as 10 % in a sample with mixed SARS-CoV-2 lineage. The N501Y RT-qPCR is simple and inexpensive (US$1.6 per sample). It enables robust high-throughput screening for surveillance of SARS-CoV-2 variants of concern harbouring N501Y mutation.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Real-Time Polymerase Chain Reaction , Whole Genome Sequencing
4.
Clin Infect Dis ; 74(9): 1623-1630, 2022 05 03.
Article in English | MEDLINE | ID: covidwho-1324612

ABSTRACT

BACKGROUND: Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as variants of concern (VOCs) or variants of interest (VOIs). Here we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1.617.1 (kappa variant) and P.3 (theta variant), which were first detected in India and the Philippines, respectively. METHODS: The neutralization susceptibility of the VOCs/VOIs (B.1.351, B.1.617.1, and P.3) and a non-VOC/VOI without RBD mutations (B.1.36.27) to convalescent sera from coronavirus disease 2019 (COVID-19) patients or BNT162b2 vaccinees was determined using a live virus microneutralization (MN) assay. Serum immunoglobulin G (IgG) binding to wild-type and mutant RBDs were determined using an enzyme immunoassay. RESULTS: The geometric mean neutralization titers (GMT) of B.1.351, P.3, and B.1.617.1 were significantly lower than that of B.1.36.27 for COVID-19 patients infected with non-VOCs/VOIs (3.4- to 5.7-fold lower) or individuals who have received 2 doses of BNT162b2 vaccine (4.4- to 7.3-fold lower). The GMT of B.1.351 or P.3 were lower than that of B.1.617.1. For the 4 patients infected with B.1.351 or B.1.617.1, the MN titer was highest for their respective lineage. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding. CONCLUSIONS: P.3 and B.1.617.1 escape serum neutralization induced by natural infection or vaccine. Infection with 1 variant does not confer cross-protection for heterologous lineages. Immunogenicity testing for second generation COVID-19 vaccines should include multiple variant and "nonvariant" strains.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/therapy , COVID-19 Vaccines , Humans , Immunization, Passive , Immunoglobulin G , Mutation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Vaccination
5.
Microorganisms ; 9(5)2021 May 10.
Article in English | MEDLINE | ID: covidwho-1224073

ABSTRACT

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.

7.
Emerg Infect Dis ; 27(1): 196-204, 2021 01.
Article in English | MEDLINE | ID: covidwho-993249

ABSTRACT

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


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Disease Outbreaks , Adult , Aged , Aged, 80 and over , COVID-19/transmission , Cluster Analysis , Disease Hotspot , Evolution, Molecular , Female , Hong Kong/epidemiology , Humans , Male , Middle Aged , Mutation , Phylogeny , Phylogeography , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viroporin Proteins/genetics , Whole Genome Sequencing , Young Adult
9.
BMJ Open Qual ; 9(4)2020 11.
Article in English | MEDLINE | ID: covidwho-913773

ABSTRACT

Since the outbreak of COVID-19 in December 2019, there had been global shortage of personal protective equipment (PPE) supply due to the breakage of supply chain and also the forbidding of PPE exported by various countries. This situation had greatly affected the healthcare services in local hospitals of Hong Kong. To maintain the availability of PPE for healthcare workers in high-risk clinical settings, the cluster management of New Territories West Cluster, Hospital Authority, had implemented a bundle of interventions in controlling and managing the PPE consumption and ensuring its proper use. A Taskforce on Management of PPE was set up in February 2020 with the aim to monitor and manage the use of PPE in five local hospitals and eight general outpatient clinics of New Territories West Cluster, which were governed in a cluster basis, under the COVID-19 epidemic. Interventions including cutting down non-essential services, implementing telecare, monitoring PPE consumption at unit level and PPE stock at the Cluster Central Distribution Centre and forming mobile infection teams were implemented. The updated PPE standards and usage guidelines to clinical staff were promulgated through forums, newsletters and unit visits. The PPE consumption rates of individual unit were reviewed. Significant decrease in PPE consumption rates was noted when comparing with the baseline data. Comparing the data between 20 February and 1 June 2020, the overall PPE consumption rates were reduced by 64% (r=-0.841; p<0.001) while the PPE consumption rates in anaesthesia and operating theatres, and isolation and surveillance wards were reduced by 47% (r=-0.506; p=0.023) and 49% (r=-0.810; p<0.001), respectively. A bundled approach, including both administrative measures and staff education, is effective in managing PPE consumption during major infection outbreaks especially when PPE supply is at risk.


Subject(s)
Coronavirus Infections/prevention & control , Health Care Rationing/standards , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Pandemics/prevention & control , Personal Protective Equipment/supply & distribution , Pneumonia, Viral/prevention & control , Advisory Committees , Betacoronavirus , COVID-19 , Hong Kong , Hospitals/statistics & numerical data , Humans , SARS-CoV-2
10.
Int J Mol Sci ; 21(15)2020 Jul 29.
Article in English | MEDLINE | ID: covidwho-693630

ABSTRACT

To control the COVID-19 pandemic and prevent its resurgence in areas preparing for a return of economic activities, a method for a rapid, simple, and inexpensive point-of-care diagnosis and mass screening is urgently needed. We developed and evaluated a one-step colorimetric reverse-transcriptional loop-mediated isothermal amplification assay (COVID-19-LAMP) for detection of SARS-CoV-2, using SARS-CoV-2 isolate and respiratory samples from patients with COVID-19 (n = 223) and other respiratory virus infections (n = 143). The assay involves simple equipment and techniques and low cost, without the need for expensive qPCR machines, and the result, indicated by color change, is easily interpreted by naked eyes. COVID-19-LAMP can detect SARS-CoV-2 RNA with detection limit of 42 copies/reaction. Of 223 respiratory samples positive for SARS-CoV-2 by qRT-PCR, 212 and 219 were positive by COVID-19-LAMP at 60 and 90 min (sensitivities of 95.07% and 98.21%) respectively, with the highest sensitivities among nasopharyngeal swabs (96.88% and 98.96%), compared to sputum/deep throat saliva samples (94.03% and 97.02%), and throat swab samples (93.33% and 98.33%). None of the 143 samples with other respiratory viruses were positive by COVID-19-LAMP, showing 100% specificity. Samples with higher viral load showed shorter detection time, some as early as 30 min. This inexpensive, highly sensitive and specific COVID-19-LAMP assay can be useful for rapid deployment as mobile diagnostic units to resource-limiting areas for point-of-care diagnosis, and for unlimited high-throughput mass screening at borders to reduce cross-regional transmission.


Subject(s)
Betacoronavirus/genetics , Colorimetry/methods , Coronavirus Infections/diagnosis , Mass Screening/economics , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Betacoronavirus/isolation & purification , COVID-19 , Colorimetry/economics , Coronavirus Infections/virology , Humans , Limit of Detection , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , Pandemics , Pneumonia, Viral/virology , Point-of-Care Systems , RNA, Viral/metabolism , SARS-CoV-2 , Viral Load
11.
JBJS Case Connect ; 10(3): e2000288, 2020.
Article in English | MEDLINE | ID: covidwho-682759

ABSTRACT

CASE: Coronavirus disease 2019 (COVID-19) is a pandemic respiratory disease. Patients typically present with fever, cough, and radiological lung changes. However, a significant proportion of these patients are asymptomatic. To date, we have limited information on the operations performed on these patients. We report our experience of a relatively asymptomatic elderly patient who underwent surgery for a hip fracture and was confirmed postoperatively to have COVID-19. CONCLUSION: Meticulous hand hygiene and use of surgical mask in daily practice is crucial to protect against asymptomatic and undiagnosed patients.


Subject(s)
Asymptomatic Diseases , Betacoronavirus/isolation & purification , Coronavirus Infections , Delayed Diagnosis/prevention & control , Femoral Neck Fractures/diagnosis , Hemiarthroplasty/methods , Infection Control , Pandemics , Pneumonia, Viral , Aged, 80 and over , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/physiopathology , Female , Humans , Infection Control/methods , Infection Control/standards , Pneumonia, Viral/diagnosis , Pneumonia, Viral/physiopathology , Postoperative Period , SARS-CoV-2 , Treatment Outcome , Universal Precautions/methods
12.
Lancet ; 395(10238): 1695-1704, 2020 05 30.
Article in English | MEDLINE | ID: covidwho-232479

ABSTRACT

BACKGROUND: Effective antiviral therapy is important for tackling the coronavirus disease 2019 (COVID-19) pandemic. We assessed the efficacy and safety of combined interferon beta-1b, lopinavir-ritonavir, and ribavirin for treating patients with COVID-19. METHODS: This was a multicentre, prospective, open-label, randomised, phase 2 trial in adults with COVID-19 who were admitted to six hospitals in Hong Kong. Patients were randomly assigned (2:1) to a 14-day combination of lopinavir 400 mg and ritonavir 100 mg every 12 h, ribavirin 400 mg every 12 h, and three doses of 8 million international units of interferon beta-1b on alternate days (combination group) or to 14 days of lopinavir 400 mg and ritonavir 100 mg every 12 h (control group). The primary endpoint was the time to providing a nasopharyngeal swab negative for severe acute respiratory syndrome coronavirus 2 RT-PCR, and was done in the intention-to-treat population. The study is registered with ClinicalTrials.gov, NCT04276688. FINDINGS: Between Feb 10 and March 20, 2020, 127 patients were recruited; 86 were randomly assigned to the combination group and 41 were assigned to the control group. The median number of days from symptom onset to start of study treatment was 5 days (IQR 3-7). The combination group had a significantly shorter median time from start of study treatment to negative nasopharyngeal swab (7 days [IQR 5-11]) than the control group (12 days [8-15]; hazard ratio 4·37 [95% CI 1·86-10·24], p=0·0010). Adverse events included self-limited nausea and diarrhoea with no difference between the two groups. One patient in the control group discontinued lopinavir-ritonavir because of biochemical hepatitis. No patients died during the study. INTERPRETATION: Early triple antiviral therapy was safe and superior to lopinavir-ritonavir alone in alleviating symptoms and shortening the duration of viral shedding and hospital stay in patients with mild to moderate COVID-19. Future clinical study of a double antiviral therapy with interferon beta-1b as a backbone is warranted. FUNDING: The Shaw-Foundation, Richard and Carol Yu, May Tam Mak Mei Yin, and Sanming Project of Medicine.


Subject(s)
Coronavirus Infections/drug therapy , Interferon beta-1b/therapeutic use , Lopinavir/therapeutic use , Pneumonia, Viral/drug therapy , Ribavirin/therapeutic use , Ritonavir/therapeutic use , Adult , Betacoronavirus , COVID-19 , Drug Combinations , Drug Therapy, Combination , Female , Hong Kong , Hospitalization , Humans , Male , Middle Aged , Pandemics , SARS-CoV-2
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