Development and Evaluation of an In-House Real-Time Rt-Pcr Targeting nsp10 Gene for SARS-CoV-2 Detection (preprint)

The emergence of SARS-CoV-2 mutations pose significant challenges to diagnostic tests as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified a novel diagnostic target, nsp10 gene, using nanopore sequencing. Firstly, we determined the analytical sensitivity and specificity of our COVID-19-nsp10 assay. The COVID-19-nsp10 assay had the limit of detection of 74 copies/mL (95% confidence interval: 48-299 copies/mL) and did not show cross-reactivity with other respiratory viruses. Next, we determined the diagnostic performance of the COVID-19-nsp10 assay using 261 respiratory specimens, including 147 SARS-CoV-2-positive specimens belonging to ancestral strain and Alpha, Beta, Gamma, Delta, Mu, Eta, Kappa, Theta and Omicron lineages. Using the LightMix E-gene RT-PCR assay as the reference method, the diagnostic sensitivity and specificity of the COVID-19-nsp10 assay were 100%. The median Cp values for the LightMix E-gene RT-PCR and our COVID-19-nsp10 RT-PCR were 22.48 (range: 12.95-36.60) and 25.94 (range 16.37-36.87), respectively. The Cp values of the COVID-19-nsp10 RT-PCR assay correlated well with those of the LightMix E-gene RT-PCR assay (Spearman’s ρ = 0.968; P<0.0001). In conclusion, nsp10 is a suitable target for SARS-CoV-2 RT-PCR assay.

Inpatient Antibacterial Drug Prescribing for Patients with COVID-19 in Hong Kong (preprint)

Background: Hong Kong experienced four epidemic waves caused by the ancestral strain of SARS-CoV-2 in 2020-2021 and a large Omicron wave in 2022. Few studies have assessed antibacterial drug prescribing for COVID-19 inpatients throughout the pandemic. Objectives: To describe inpatient antibacterial drug prescribing for COVID-19 patients throughout the pandemic and to determine factors associated with their prescription. Methods: This cohort study used electronic health records of COVID-19 cases admitted to public hospitals in Hong Kong from 21 January 2020 to 30 September 2022. We assessed the prevalence and rates of inpatient antibacterial drug use, using days of therapy/1000 patient days (DOT/1000PD), and examined the association of baseline factors and disease severity with receipt of an inpatient antibacterial drug prescription. Results: Among 65,810 inpatients, 54.0% were prescribed antibacterial drugs at a rate of 550.5 DOT/1000PD. Antibacterial use was lowest during wave 4 (28.0%; 246.9 DOT/1000PD), peaked in early wave 5 (64.6%; 661.2 DOT/1000PD), and then modestly declined in late wave 5 (43.2%; 464.1 DOT/1000PD) starting on 23 May 2022. Older age, increased disease severity, and residing in an elderly care home were strongly associated with increased odds of prescription, while receiving [≥] 2 doses of COVID-19 vaccines and pre-admission use of coronavirus antivirals were associated with lower odds. Conclusions: The rate of inpatient antibacterial prescribing initially declined during the pandemic, but increased during the Omicron wave when hospital capacity was overwhelmed. Despite the availability of COVID-19 vaccines and antiviral drugs, antibacterial drug use among COVID-19 inpatients remained high into late 2022.

Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong (preprint)

Monitoring population protective immunity against SARS-CoV-2 variants is critical for risk assessment. In this serosurveillance study, older adults show much lower seropositive rates of neutralizing antibody (NAb) against ancestral virus than the younger population. The increase in NAb seopositive rate generally follows the population vaccination uptake rate, but older adults have a much lower NAb seropositive rate than vaccination uptake rate. For all age groups, the seropositive rates of NAb against Omicron variant are much lower than those against the ancestral virus. During the fifth wave of COVID-19 in Hong Kong which is dominated by Omicron sublineage BA.2, the case-fatality rate is exceptionally high in the ≥80 year-old age group (9.2%). Our study suggests that the severe BA.2 outbreak in Hong Kong can be attributed by the lack of protective immunity in the population, especially among the vulnerable older adults, and highlights the importance of continual surveillance of protective immunity against emerging variants of SARS-CoV-2.

Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients (preprint)

ABSTRACT Background The SARS-CoV-2 Omicron variant, designated as a Variant of Concern(VOC) by the World Health Organization, carries numerous spike protein mutations which have been found to evade neutralizing antibodies elicited by COVID-19 vaccines. The susceptibility of Omicron variant by vaccine-induced neutralizing antibodies are urgently needed for risk assessment. Methods Omicron variant strains HKU691 and HKU344-R346K were isolated from patients using TMPRSS2-overexpressing VeroE6 cells. Whole genome sequence was determined using nanopore sequencing. Neutralization susceptibility of ancestral lineage A virus and the Omicron, Delta and Beta variants to sera from 25 BNT162b2 and 25 Coronavac vaccine recipients was determined using a live virus microneutralization assay. Results The Omicron variant strain HKU344-R346K has an additional spike R346K mutation, which is present in 8.5% of strains in GISAID database. Only 20% and 24% of BNT162b2 recipients had detectable neutralizing antibody against the Omicron variant HKU691 and HKU344-R346K, respectively, while none of the Coronavac recipients had detectable neutralizing antibody titer against either Omicron isolates. For BNT162b2 recipients, the geometric mean neutralization antibody titers(GMT) of the Omicron variant isolates(5.43 and 6.42) were 35.7-39.9-fold lower than that of the ancestral virus(229.4), and the GMT of both omicron isolates were significantly lower than those of the beta and delta variants. There was no significant difference in the GMT between HKU691 and HKU344-R346K. Conclusions Omicron variant escapes neutralizing antibodies elicited by BNT162b2 or CoronaVac. The additional R346K mutation did not affect the neutralization susceptibility. Our data suggest that the Omicron variant may be associated with lower COVID-19 vaccine effectiveness.

Neurosensory Rehabilitation and Olfactory Network Recovery in COVID-19-related Olfactory Dysfunction (preprint)

Background: Non-conductive olfactory dysfunction (OD) is an important extra-pulmonary manifestation of coronavirus disease 2019 (COVID-19). Prolonged COVID-19-related OD is a serious neurosensory disability. Treatment for the restoration of smell is urgently needed. Case presentation Two patients presenting with prolonged COVID-19-related OD underwent structural and resting-state functional magnetic resonance imaging (rs-fMRI) brain scans. Two healthy controls were recruited for radiological comparison. One patient received olfactory treatment (OT) by the combination of oral vitamin A and smell training via the novel electronic portable aromatic rehabilitation (EPAR) diffusers. After four-weeks of OT, clinical recuperation of smell was correlated with interval increase of bilateral OB volumes [right: 22.5mm 3 to 49.5mm 3 (120%), left: 37.5mm 3 to 42mm 3 (12%)] and the enhancement of mean olfactory functional connectivity [0.09 to 0.15 (66.6%)]. Conclusions: Olfactory network functional defects and OB volume loss were identified in patients presenting with prolonged COVID-19-related OD. Preliminary evidence demonstrated that the combination of oral vitamin A and smell training may induce neurogenesis at the olfactory apparatus and achieve olfactory neurosensory rehabilitation. This observation should be validated in large scale randomized–controlled trials.

Perceived Challenges of COVID-19 Infection Prevention and Control Preparedness: A Multinational Survey (preprint)

Objectives Implementation of effective infection prevention and control (IPC) measures is needed to support global capacity building to limit transmission of coronavirus disease 2019 (COVID-19) and mitigate its impact on health systems. We assessed the perceptions of healthcare workers on the current global IPC preparedness measures for COVID-19. Methods A cross-sectional survey using an electronic survey was circulated between February 26, 2020, and March 20, 2020, to IPC professionals during COVID-19 pandemic. The survey addressed the presence of COVID-19 guidelines as well as specific IPC preparedness activities in response to the outbreak. Findings In total, 339 IPC professionals spanning 63 countries in all 6 World Health Organization (WHO) regions, mostly from tertiary care centres participated. Of all participants, 66{middle dot}6% were aware of the existence of national guidelines to prevent COVID-19. A shortage of PPE supplies was reported by 48% (ranging from 64{middle dot}2% in low-income countries to 27{middle dot}4% in high-income countries); 41{middle dot}5% of respondents considered that the media had an impact on guideline development and 63{middle dot}6% believed that guidelines were based on maximum security rather than on evidence-based analyses. 58{middle dot}5% and 72{middle dot}7% of participants believed that healthcare facilities and community settings respectively were not sufficiently prepared. Conclusion Results revealed lack of guidelines and concerns over insufficient PPE supply in both high- and low-income countries. Our findings should alert national health authorities to ramp up the implementation of IPC measures and focus on long-term preparedness and readiness for future pandemics, likely requiring government funds rather than reliance on healthcare institutions.