Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

Residential Clustering of Coronavirus Disease 2019 Cases and Efficiency of Building-Wide Compulsory Testing Notices as a Transmission Control Measure in Hong Kong

We described the frequency of residential case clusters and the efficiency of compulsory testing in identifying cases using buildings targeted in compulsory testing and locally infected coronavirus disease 2019 (COVID-19) cases matched by residence in Hong Kong. Most of the buildings (4246 of 7688, 55.2%) with COVID-19 cases identified had only 1 reported case, and 13% of the daily reported cases were detected through compulsory testing. Compulsory testing notices could be essential in attempting to eliminate infections ("zero COVID") and have an impact early in an epidemic, but they appear to be relatively inefficient in response to sustained community transmission.

Investigation of the Molecular Epidemiology and Evolution of Circulating Severe Acute Respiratory Syndrome Coronavirus 2 in Thailand from 2020 to 2022 via Next-Generation Sequencing

Coronavirus disease 2019 (COVID-19) is an infectious condition caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which surfaced in Thailand in early 2020. The current study investigated the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history. Complete genome sequencing of 210 SARS-CoV-2 samples collected from collaborating hospitals and the Institute of Urban Disease Control and Prevention over two years, from December 2020 to July 2022, was performed using next-generation sequencing technology. Multiple lineage introductions were observed before the emergence of the B.1.1.529 omicron variant, including B.1.36.16, B.1.351, B.1.1, B.1.1.7, B.1.524, AY.30, and B.1.617.2. The B.1.1.529 omicron variant was subsequently detected between January 2022 and June 2022. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated to be between 0.87 and 1.71 × 10^-3 substitutions per site per year. There was a substantial prevalence of the predominant mutations C25672T (L94F), C25961T (T190I), and G26167T (V259L) in the ORF3a gene during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes in viral genomes, which is crucial to ensuring that vaccine strains are protective against worldwide outbreaks.

Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

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 (Re) 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.

Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals

Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.

Evaluating Data Sharing of SARS-CoV-2 Genomes for Molecular Epidemiology across the COVID-19 Pandemic

Following the emergence of COVID-19 in December 2019, caused by the coronavirus SARS-CoV-2, the disease spread dramatically worldwide. The use of genomics to trace the dissemination of the virus and the identification of novel variants was essential in defining measures for containing the disease. We aim to evaluate the global effort to genomically characterize the circulating lineages of SARS-CoV-2, considering the data deposited in GISAID, the major platform for data sharing in a massive worldwide collaborative undertaking. We contextualize data for nearly three years (January 2020-October 2022) for the major contributing countries, percentage of characterized isolates and time for data processing in the context of the global pandemic. Within this collaborative effort, we also evaluated the early detection of seven major SARS-CoV-2 lineages, G, GR, GH, GK, GV, GRY and GRA. While Europe and the USA, following an initial period, showed positive results across time in terms of cases sequenced and time for data deposition, this effort is heterogeneous worldwide. Given the current immunization the major threat is the appearance of variants that evade the acquired immunity. In that scenario, the monitoring of those hypothetical variants will still play an essential role.

Risk of within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong: an epidemiological and phylogenomic investigation

Background

On-arrival quarantine has been one of the primary measures to prevent the introduction of SARS-CoV-2 into Hong Kong since the start of the pandemic. Most on-arrival quarantines have been done in hotels, with the duration of quarantine and testing frequency during quarantine modified over time along with other pandemic control measures. However, hotels are not designed with infection control in mind. We aimed to systematically study the potential risk of acquisition of SARS-CoV-2 infection among individuals undergoing hotel quarantine.

Methods

We examined data on each laboratory-confirmed COVID-19 case identified in on-arrival quarantine in a hotel in Hong Kong between 1 May 2020 and 31 January 2022. We sequenced the whole genomes of viruses from cases that overlapped with other confirmed cases in terms of the hotel of stay, date of arrival and date of testing positive. By combining multiple sources of evidence, we identify probable and plausible transmission events and calculate the overall risk of transmission.

Findings

Among 221 imported cases that overlapped with other cases detected during hotel quarantine with available sequence data, phylogenomic analyses identified five probable and two plausible clusters of within-hotel transmission. Only two of these clusters were recognised at the time. Including other clusters reported in Hong Kong, we estimate that 8-11 per 1000 cases identified in hotel quarantine may be infected by another unlinked case during quarantine, or 2-3 per 100,000 overseas arrivals.

Interpretation

We have identified additional undetected occurrences of COVID-19 transmission within hotel quarantine in Hong Kong. Although hotels provide suboptimal infection control as improvised quarantine facilities, the risk of contracting infection whilst in quarantine is low. However, these unlikely events could have high consequences by allowing the virus to spread into immunologically naïve communities. Additional vigilance should be taken in the absence of improved controls to identify such events. If on-arrival quarantine is expected to be used for a long time, quarantine facilities could be purpose-built to minimise the risk of transmission.

Funding

Health and Medical Research Fund, Hong Kong.

The origins of COVID-19 pandemic: A brief overview

The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.

COVID-19 pandemic fatigue and its sociodemographic and psycho-behavioral correlates: a population-based cross-sectional study in Hong Kong

Pandemic fatigue is a growing public health concern of the lingering COVID-19 pandemic. Despite its widespread mass media coverage, systematic empirical investigations are scarce. Under the Hong Kong Jockey Club SMART Family-Link Project, we conducted online and telephone surveys amid the pandemic in February to March 2021 to assess self-reported pandemic fatigue (range 0-10) in Hong Kong adults (N = 4726) and its associations with sociodemographic and psycho-behavioral (high vs low to moderate) variables. Data were weighted by sex, age, and education of the general population. Binary logistic regression models yielded adjusted odds ratios (aORs) for high pandemic fatigue (score ≥ 7) for sociodemographic and psycho-behavioral variables. 43.7% reported high pandemic fatigue. It was less common in older people (55-64 years: aOR 0.56, 95% CI 0.39-0.82; 65 + years: 0.33, 0.21-0.52) versus age group 18-24 years, but more common in those with tertiary education (1.36, 1.15-1.62) versus secondary or below. High pandemic fatigue was positively associated with depressive symptoms (aOR 1.83, 95% CI 1.55-2.17), anxiety symptoms (1.87, 1.58-2.20), loneliness (1.75, 1.32-2.31), personal fear of COVID-19 (2.61, 2.12-3.23), family fear of COVID-19 (2.03, 1.67-2.47), and current alcohol use (1.16, 1.00-1.33), but negatively associated with self-rated health (0.79, 0.68-0.92), personal happiness (0.63, 0.55-0.72), personal adversity coping capability (0.71, 0.63-0.81), family adversity coping capability (0.79, 0.69-0.90), family well-being (0.84, 0.73-0.97), family communication quality (0.86, 0.75-0.98), and frequent home exercise (0.82, 0.69-0.96; versus less frequent). We first used a single-item tool to measure COVID-19 pandemic fatigue, showing that it was common and associated with worse mental health, lower levels of personal and family well-being and alcohol use.

Adversity coping capability and its associations with mental health and family wellbeing amid the COVID-19 pandemic in Hong Kong

BACKGROUND

Adversity coping capability (ACC) is important amid the COVID-19 pandemic. We examined the associations of ACC as measured by our one-item ACC scale (ACC-1) with mental health, family well-being and validity of ACC-1 in Hong Kong.

METHODS

A cross-sectional survey was conducted on Hong Kong Chinese adults aged ≥ 18 years by landline, mobile phone, and online survey from February to March 2021, when the fourth wave of COVID-19 was under control. ACC-1 consisted of the question: "How do you rate your capability to cope with adversities?" with higher scores (0-10) indicating stronger ACC. The associations of ACC with socioeconomic characteristics, resilience, mental health, and family wellbeing were examined by linear regression coefficients (βs). Data were weighted by sex, age, and education of the general population.

RESULTS

Of 7441 respondents, after weighing, 52.2% were female and 79.1% were aged 18 to 64 years. ACC-1 showed good construct validity, with higher ACC being associated with higher levels of resilience (adjusted β = 0.29), personal happiness (0.55), family happiness (0.42), family wellbeing (0.41), and family communication quality (0.41), and lower levels of depressive symptoms (-0.30), anxiety (-0.30), loneliness (-0.15); incremental validity with additional contributions of ACC to mental health and family wellbeing; and known-group validity with older age and favorable socioeconomic characteristics showing higher ACC (all P < 0.02). Females (mean ± standard deviation: 6.04 ± 1.82 vs 6.15 ± 1.96 [male]) and unemployed respondents (5.30 ± 1.99 vs 6.11 ± 2.03 [in paid employment]) had lower ACC (all P ≤ 0.02).

CONCLUSIONS

We have first shown that stronger ACC was associated with better mental health and family wellbeing, and the results support ACC-1 as a simple and valid measure of ACC.

Within-host diversity of SARS-CoV-2 lineages and effect of vaccination

Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.

Natural Reassortment of Eurasian Avian-Like Swine H1N1 and Avian H9N2 Influenza Viruses in Pigs, China

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.

The ethics behind mandatory COVID-19 vaccination post-Omicron: The South African context

The legitimacy of mandatory vaccine policies is underscored by a public health ethics framework based on the principles of limited autonomy, social justice and the common good. Ideally, vaccine uptake ought to occur on a voluntary basis as an act of solidarity to ensure that everyone is protected. Given that the altruistic approach has failed and vaccine uptake remains sub-optimal in South Africa, in this paper, I argue for vaccine mandates, in a post-Omicron context. This viewpoint is substantiated by several considerations. Healthcare workers are fatigued after 2 years of treating COVID-19 and many are still treating patients with post-viral syndromes, mental health conditions and cardiovascular complications. Health systems remain under pressure as people with non-COVID diseases, neglected during the pandemic, are also now presenting to medical practices and hospitals. Although South Africa has emerged from a relatively less severe fourth wave of COVID-19, there have been many deaths. Vaccine and natural immunity in a relatively young general population has been advantageous. However, the country has a high prevalence of HIV and those who are untreated may not be able to clear the coronavirus easily. Similarly chronic illnesses place many at risk for severe disease from COVID variants, especially if unvaccinated. The future is shrouded in uncertainty. The next variant could be similar to or less severe than Omicron, yet still impact negatively on health systems, education and the economy. Physical distancing is not ideal in many low socio-economic settings, making vaccines an important component of our prevention toolbox. Our safest option now is to ensure that as many South Africans as possible are vaccinated and receive boosters. Vaccine mandates work to achieve this end.

Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission

Many locations around the world have used real-time estimates of the time-varying effective reproductive number (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}_{t}$$\end{document}Rt) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}_{t}$$\end{document}Rt are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the latent period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral loads among confirmed cases can provide insights into epidemic trajectory. Here, we analyzed viral load data on confirmed cases during two local epidemics in Hong Kong, identifying a strong correlation between temporal changes in the distribution of viral loads (measured by RT-qPCR cycle threshold values) and estimates of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}_{t}$$\end{document}Rt based on case counts. We demonstrate that cycle threshold values could be used to improve real-time \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${R}_{t}$$\end{document}Rt estimation, enabling more timely tracking of epidemic dynamics.

The time-varying effective reproductive number (Rt) is useful for monitoring transmission of infections such as COVID-19, but reporting delays impact case count-based estimation methods. Here, the authors demonstrate and validate a method for estimation of Rt based on viral load data from Hong Kong that does not require accurate daily counts.