Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge (preprint)

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

TREM-1, TREM-2 and their association with disease severity in patients with COVID-19 (preprint)

Background Delayed diagnosis and inadequate treatment caused by limited biomarkers were associated with outcomes of COVID-19 patients. It is necessary to find other promising biomarkers and candidate targets for defining dysregulated inflammatory state besides the typical biomarkers and drug targets have been used clinically.Methods In a cohort of hospitalized COVID-19 patients with varying degrees of illness severity, we characterized TREM-1 and TREM-2 expression in plasma and on the surface of cell subpopulations using ELISA and flow cytometry, respectively. And their correlations with disease severity and contrast with main clinical indicators were evaluated.Results We found the increased expression of soluble TREM-1 and TREM-2 in plasma from COVID-19 patients compared to the control group. Moreover, membrane-bound TREM-1 and TREM-2 expression was also upregulated on the cell surface of circulating blood T cells from COVID-19 patients. Correlation analysis results showed the sTREM-2 level was negatively correlated with PaO2/FiO2, but positively correlated with CRP, PCT and IL-6 level. Receiver operating characteristic (ROC) curves presented that TREM-1 and TREM-2 exhibited strong predictive abilities, and their expression was equal to CRP and IL-6, and better than leukocytes or neutrophil absolute count and PCT in distinguishing disease severity.Conclusion These results highlighted the important role of TREM-1 and TREM-2 in viral infection. TREM-2 and TREM-1 were critical host immune factors in response to SARS-COV-2 infection and could serve as potential diagnostic and therapeutic biomarkers of COVID-19.

A longitudinal study of COVID-19 preventive behavior fatigue in Hong Kong: a city with previous pandemic experience.

BACKGROUND: In addition to high vaccination levels, COVID-19 control requires uptake and continued adherence to personal hygiene and social distancing behaviors. It is unclear whether residents of a city with successive experience in worldwide pandemics such as SARS, would quickly adopt and maintain preventive behaviors. METHODS: A population-based, longitudinal telephone survey was conducted between in first local wave of the COVID-19 pandemic (April 2020) and third local wave (December 2020) (n = 403). The study examined factors associated with personal hygiene and social distancing behavior fatigue, as measured by reduced adherence. RESULTS: Over 9 months, face mask use increased (96.5-100%, p < 0.001). Although habitual hand hygiene remained unchanged (92.0%), blue collar workers and non-working individuals showed higher risk of hand hygiene fatigue. There was a decline (p < 0.05) in avoidance of social gatherings (81.1 to 70.7%), avoidance of public places (52.9-27.5%) and avoidance of international travel (81.9-77.4%) even with rising caseloads. Lowered perception of COVID-19 disease severity was associated with decreased avoidance of social gatherings and public places while lower education was associated with decline in avoidance of social gatherings. CONCLUSION: Even in regions with past pandemic experience, maintaining social distancing behaviors during a protracted pandemic remains a major public health challenge.

Disciplinary differences in the experience of online education among teachers and students in Chinese universities during COVID-19

Online education has advantages during COVID-19, but it also has problems related to hardware support and user experience. Focusing on teaching quality by discipline is an effective way to improve teaching quality in universities. To investigate the online education experience from the perspective of different academic disciplines, we evaluated 251,929 student questionnaires and 13,695 teacher questionnaires from 334 universities in China. The main finding was a difference in teaching preparation, experience, feedback, and improvement processes by disciplines. Teachers and students had obvious disciplinary differences in preparation, school support, and teaching constraints. However, disciplinary differences were minor for pedagogical issues such as participation, assignments, and grading, as well as for evaluation of platform technical support and views on the continuation of online learning. The research results analyzed the teaching psychology of teachers and students in different disciplines during the pandemic. Therefore, it explained the impact and role of discipline differences on students’ learning psychology during COVID-19. This research will benefit educators, researchers, and policy makers to help them with the improvement of online education.

The way forward to achieve high COVID-19 vaccination and revaccination coverage in a city amid a period of tranquility

Background Amid the current COVID-19 pandemic, there is an urgent need for both vaccination and revaccination (“boosting”). This study aims to identify factors associated with the intention to receive a booster dose of the coronavirus (COVID-19) vaccine among individuals vaccinated with two doses and characterize their profiles in Hong Kong, a city with a low COVID-19 incidence in the initial epidemic waves. Among the unvaccinated, vaccination intention is also explored and their profiles are investigated. Methods From December 2021 - January 2022, an online survey was employed to recruit 856 Hong Kong residents aged 18 years or over from an established population-based cohort. Latent class analysis and multivariate logistic regression modeling approaches were used to characterize boosting intentions. Results Of 638 (74.5%) vaccinated among 856 eligible subjects, 42.2% intended to receive the booster dose. Four distinct profiles emerged with believers having the highest intention, followed by apathetics, fence-sitters and skeptics. Believers were older and more likely to have been vaccinated against influenza. Older age, smoking, experiencing no adverse effects from a previous COVID-19 vaccination, greater confidence in vaccines and collective responsibility, and fewer barriers in accessing vaccination services were associated with higher intentions to receive the booster dose. Of 218 unvaccinated, most were fence-sitters followed by apathetics, skeptics, and believers. Conclusion This study foretells the booster intended uptake lagging initial vaccination across different age groups and can help refine the current or future booster vaccination campaign. Given the fourth COVID-19 vaccine dose may be offered to all adults, strategies for improving boosting uptake include policies targeting young adults, individuals who experienced adverse effects from previous doses, fence-sitters, apathetics, and the general public with low trust in the health authorities.

Effect of sampling positions in nucleic acid test on the test result: a report from 47 confirmed COVID-19 cases in Jinan City

Objective: To investigate the effect of sampling positions in nucleic acid test for COVID-19 on test results.

Challenges of Data Availability and Use in Conducting Health-EDRM Research in a Post-COVID-19 World.

Disasters disrupt communication channels, infrastructure, and overburden health systems. This creates unique challenges to the functionality of surveillance tools, data collection systems, and information sharing platforms. The WHO Health Emergency and Disaster Risk Management (Health-EDRM) framework highlights the need for appropriate data collection, data interpretation, and data use from individual, community, and global levels. The COVID-19 crisis has evolved the way hazards and risks are viewed. No longer as a linear event but as a protracted hazard, with cascading and compound risks that affect communities facing complex risks such as climate-related disasters or urban growth. The large-scale disruptions of COVID-19 show that disaster data must evolve beyond mortality and frequency of events, in order to encompass the impact on the livelihood of communities, differentiated between population groups. This includes relative economic losses and psychosocial damage. COVID-19 has created a global opportunity to review how the scientific community classifies data, and how comparable indicators are selected to inform evidence-based resilience building and emergency preparedness. A shift into microlevel data, and regional-level information sharing is necessary to tailor community-level interventions for risk mitigation and disaster preparedness. Real-time data sharing, open governance, cross-organisational, and inter-platform collaboration are necessary not just in Health-EDRM and control of biological hazards, but for all natural hazards and man-made disasters.

Anti-microbial properties of a multi-component alloy (preprint)

High traffic touch surfaces such as doorknobs, countertops, and handrails can be transmission points for the spread of pathogens, emphasizing the need to develop materials that actively self-sanitize. Metals are frequently used for these surfaces due to their durability, but many metals also possess antimicrobial properties which function through a variety of mechanisms. This work investigates metallic alloys comprised of several bioactive metals with the target of achieving broad-spectrum, rapid bioactivity through synergistic activity. An entropy-motivated stabilization paradigm is proposed to prepare scalable alloys of copper, silver, nickel and cobalt. Using combinatorial sputtering, thin-film alloys were prepared on 100 mm wafers with 50% compositional grading of each element across the wafer. The films were then annealed and investigated for alloy stability. Bioactivity testing was performed on both the as-grown alloys and the annealed films using four microorganisms -- Phi6, MS2, Bacillus subtilis and Escherichia coli -- as surrogates for human viral and bacterial pathogens. Testing showed that after 30 s of contact with some of the test alloys, Phi6, an enveloped, single-stranded RNA bacteriophage that serves as a SARS-CoV 2 surrogate, was reduced up to 6.9 orders of magnitude (>99.9999%). Additionally, the non-enveloped, double-stranded DNA bacteriophage MS2, and the Gram-negative E. coli and Gram-positive B. subtilis bacterial strains showed a 5.0, 6.4, and 5.7 log reduction in activity after 30, 20 and 10 minutes, respectively. Bioactivity in the alloy samples showed a strong dependence on the composition, with the log reduction scaling directly with the Cu content. Concentration of Cu by phase separation after annealing improved activity in some of the samples. The results motivate a variety of themes which can be leveraged to design ideal bioactive surfaces.

Consumption of home-prepared meal at workplace as a predictor of glycated haemoglobin among people with type 2 diabetes in Hong Kong: a mixed-methods study.

OBJECTIVES: There is increasing attention on association between eating patterns and diabetes control following global changes in eating patterns. There had been very limited research on the eating patterns of diabetic patients with employment, although working age population has seen the highest increase in diabetes incidence. This study aimed to identify workplace eating patterns in relation to glycaemic control among type 2 diabetic patients with employment. METHODS: This is a sequential mixed-methods study. The exploratory qualitative study involved focus group interviews with 31 type 2 diabetic patients with employment, which guided the design of a subsequent cross-sectional investigation involving 185 patients with employment. Thematic analysis was conducted on the qualitative data to identify workplace eating patterns most relevant to glycaemic control. Hierarchical multiple linear regression was performed to examine association between workplace eating pattern and glycaemic control, proxied by HbA1c. RESULTS: The focus group interviews identified frequency in the consumption of home-prepared meals (HPM) and meal hours as the major workplace eating patterns that affected glycaemic control. The cross-sectional study confirmed that regular consumption of HPM at workplace could explain variance of HbA1c, independent of socio-demographic factors, lifestyle factors and disease condition, with R2 = 0.146, F(14, 170) = 2.075, p = 0.015; adjusted R2 = 0.076. Patients who were female, in non-skilled occupation, on shift, with fixed work location and had break during work were more likely to consume HPM. CONCLUSIONS: Consumption of HPM at workplace should be promoted to facilitate better glycaemic control by type 2 diabetic patients with employment, possibly through more practical dietary advice, and workplace accommodation in terms of space and facilities. In the context of COVID-19 pandemic, consumption of HPM also meant additional protection for diabetic patients through reducing close contact exposures in restaurants.

Challenges of Data Availability and Use in Conducting Health-EDRM Research in a Post-COVID-19 World

Disasters disrupt communication channels, infrastructure, and overburden health systems. This creates unique challenges to the functionality of surveillance tools, data collection systems, and information sharing platforms. The WHO Health Emergency and Disaster Risk Management (Health-EDRM) framework highlights the need for appropriate data collection, data interpretation, and data use from individual, community, and global levels. The COVID-19 crisis has evolved the way hazards and risks are viewed. No longer as a linear event but as a protracted hazard, with cascading and compound risks that affect communities facing complex risks such as climate-related disasters or urban growth. The large-scale disruptions of COVID-19 show that disaster data must evolve beyond mortality and frequency of events, in order to encompass the impact on the livelihood of communities, differentiated between population groups. This includes relative economic losses and psychosocial damage. COVID-19 has created a global opportunity to review how the scientific community classifies data, and how comparable indicators are selected to inform evidence-based resilience building and emergency preparedness. A shift into microlevel data, and regional-level information sharing is necessary to tailor community-level interventions for risk mitigation and disaster preparedness. Real-time data sharing, open governance, cross-organisational, and inter-platform collaboration are necessary not just in Health-EDRM and control of biological hazards, but for all natural hazards and man-made disasters.

Alveolar regeneration following viral infection is independent of tuft cells (preprint)

Severe injuries following viral infection cause lung epithelial destruction with the presence of ectopic basal progenitor cells (EBCs), although the exact function of EBCs remains controversial. We and others previously showed the presence of ectopic tuft cells in the disrupted alveolar region following severe influenza infection. Here, we further revealed that the ectopic tuft cells are derived from EBCs. This process is amplified by Wnt signaling inhibition but suppressed by Notch inhibition. Further analysis revealed that p63-CreER labeled population de novo arising during regeneration includes alveolar epithelial cells when Tamoxifen was administrated after viral infection. The generation of the p63-CreER labeled alveolar cells is independent of tuft cells, demonstrating segregated differentiation paths of EBCs in lung repair. EBCs and ectopic tuft cells can also be found in the lung parenchyma post SARS-CoV-2 infection, suggesting a similar response to severe injuries in humans.

Efficacy and practice of facemask use in general population: a systematic review and meta-analysis.

In recent decades, respiratory infections, including SARS, HINI and the currently spreading COVID-19, caused by various viruses such as influenza and coronavirus have seriously threatened human health. It has generated inconsistent recommendations on the mandatory use of facemasks across countries on a population level due to insufficient evidence on the efficacy of facemask use among the general population. This meta-analysis aimed to explore (1) the efficacy of facemask use on preventing respiratory infections, and (2) the perceptions, intentions, and practice about facemask use among the general population worldwide. We searched PubMed, MEDLINE, Web of Science, Cochrane, bioRxiv, and medRxiv databases since inception to August 17, 2020. From 21,341 records identified, eight RCTs on facemask in preventing infections and 78 studies on perception, intention, and practice of facemask use among the general population were included in the analysis. The meta-analysis of RCTs found a significant protective effect of facemask intervention (OR = 0.84; 95% CI = 0.71-0.99; I2 = 0%). This protective effect was even more pronounced when the intervention duration was more than two weeks (OR = 0.76; 95% CI = 0.66-0.88; I2 = 0%). The meta-analysis of observational studies on perception, intention, and practice on facemask use showed that 71% of respondents perceived facemasks to be effective for infection prevention, 68% of respondents would wear facemasks, and 54% of respondents wore facemasks for preventing respiratory infections. Differences in perception, intention, and practice behavior of facemask use in different regions may be related to the impact of respiratory infections, regional culture, and policies. The governments and relevant organizations should make effort to reduce the barriers in the use of facemasks.

Population Adherence to Infection Control Behaviors during Hong Kong's First and Third COVID-19 Waves: A Serial Cross-Sectional Study.

BACKGROUND: Although COVID-19 has affected over 220 countries by October 2021, there is limited research examining the patterns and determinants of adherence to infection control measures over time. AIMS: Our study examines the sociodemographic factors associated with changes in the frequency of adherence to personal hygiene and social distancing behaviors in Hong Kong. METHODS: A serial cross-sectional telephone survey in the general population was conducted during the first (March 2020) (n = 765) and third wave (December 2020) (n = 651) of the local outbreak of the COVID-19 pandemic. Respondents were asked about their level of compliance with various personal hygiene and social distancing recommendations. RESULTS: By the third wave, mask use increased to 100%, and throughout the study periods, >90% practiced frequent hand hygiene. However, adherence to social distancing measures significantly waned over time: avoidance of social gatherings (80.5% to 72.0%), avoidance of public places/public transport (53.3% to 26.0%), avoidance of international travel (85.8% to 76.6%) (p < 0.05). The practice of ordering food takeout/home delivery, however, increased, particularly among high-income respondents. Higher education, female gender and employment status were the most consistently associated factors with adherence to COVID-19 preventive practices in the multivariable models. CONCLUSIONS: In urban areas of this region, interventions to improve personal hygiene in a prolonged pandemic should target males and those with low education. In addition to these groups, the working population needs to be targeted in order to improve adherence to social distancing guidelines.

Unequal availability of workplace policy for prevention of coronavirus disease 2019 across occupations and its relationship with personal protection behaviours: a cross-sectional survey.

BACKGROUND: The evolving pandemic of coronavirus disease 2019 (COVID-19) has become a severe threat to public health, and the workplace presents high risks in terms of spreading the disease. Few studies have focused on the relationship between workplace policy and individual behaviours. This study aimed to identify inequalities of workplace policy across occupation groups, examine the relationship of workplace guidelines and measures with employees' behaviours regarding COVID-19 prevention. METHODS: A cross-sectional online survey using a structured questionnaire was conducted to gather employees' access to workplace guidelines and measures as well as their personal protection behaviours. Statistical associations between these two factors in different occupations were examined using multiple ordinal logistic regressions. RESULTS: A total of 1048 valid responses across five occupational groups were analysed. Manual labourers reported lower availability of workplace guidelines and measures (76.9% vs. 89.9% for all, P = 0.003). Employees with available workplace guidelines and measures had higher compliance of hand hygiene, wearing masks, and social distancing, and this association was more significant among managers/administrators and manual labourers. CONCLUSIONS: Protection of the quantity and quality of employment is important. Awareness about the disease and its prevention among employers and administrators should be promoted, and resources should be allocated to publish guidelines and implement measures in the workplace during the pandemic. Both work-from-home arrangement and other policies and responses for those who cannot work from home including guidelines encouraging the health behaviours, information transparency, and provision of infection control materials by employers should be established to reduce inequality. Manual labourers may require specific attention regarding accessibility of relevant information and availability of medical benefits and compensation for income loss due to the sickness, given their poorer experience of workplace policy and the nature of their work. Further studies are needed to test the effectiveness of specific workplace policies on COVID-19 prevention.

Psychobehavioral Responses and Likelihood of Receiving COVID-19 Vaccines during the Pandemic, Hong Kong.

To access temporal changes in psychobehavioral responses to the coronavirus disease (COVID-19) pandemic, we conducted a 5-round (R1-R5) longitudinal population-based online survey in Hong Kong during January-September 2020. Most respondents reported wearing masks (R1 99.0% to R5 99.8%) and performing hand hygiene (R1 95.8% to R5 97.7%). Perceived COVID-19 severity decreased significantly, from 97.4% (R1) to 77.2% (R5), but perceived self-susceptibility remained high (87.2%-92.8%). Female sex and anxiety were associated with greater adoption of social distancing. Intention to receive COVID-19 vaccines decreased significantly (R4 48.7% to R5 37.6%). Greater anxiety, confidence in vaccine, and collective responsibility and weaker complacency were associated with higher tendency to receive COVID-19 vaccines. Although its generalizability should be assumed with caution, this study helps to formulate health communication strategies and foretells the initial low uptake rate of COVID-19 vaccines, suggesting that social distancing should be maintained in the medium term.

Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome (preprint)

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

The Evolution in Anxiety and Depression with the Progression of the Pandemic in Adult Populations from Eight Countries and Four Continents.

Nearly a year after the classification of the COVID-19 outbreak as a global pandemic, it is clear that different factors have contributed to an increase in psychological disorders, including public health measures that infringe on personal freedoms, growing financial losses, and conflicting messages. This study examined the evolution of psychosocial impacts with the progression of the pandemic in adult populations from different countries and continents, and identified, among a wide range of individual and country-level factors, which ones are contributing to this evolving psychological response. An online survey was conducted in May/June 2020 and in November 2020, among a sample of 17,833 adults (Phase 1: 8806; Phase 2: 9027) from eight countries/regions (Canada, the United States, England, Switzerland, Belgium, Hong Kong, the Philippines, New Zealand). Probable generalized anxiety disorder (GAD) and major depressive episode (MDE) were assessed. The independent role of potential factors was examined using multilevel logistic regression. Probable GAD or MDE was indicated by 30.1% and 32.5% of the respondents during phases 1 and 2, respectively (a 7.9% increase over time), with an important variation according to countries/regions (range from 22.3% in Switzerland to 38.8% in the Philippines). This proportion exceeded 50% among young adults (18-24 years old) in all countries except for Switzerland. Beyond young age, several factors negatively influenced mental health in times of pandemic; important factors were found, including weak sense of coherence (adjusted odds ratio aOR = 3.89), false beliefs (aOR = 2.33), and self-isolation/quarantine (aOR = 2.01). The world has entered a new era dominated by psychological suffering and rising demand for mental health interventions, along a continuum from health promotion to specialized healthcare. More than ever, we need to innovate and build interventions aimed at strengthening key protective factors, such as sense of coherence, in the fight against the adversity caused by the concurrent pandemic and infodemic.

Evolving Epidemiological Characteristics of COVID-19 in Hong Kong From January to August 2020: Retrospective Study.

BACKGROUND: COVID-19 has plagued the globe, with multiple SARS-CoV-2 clusters hinting at its evolving epidemiology. Since the disease course is governed by important epidemiological parameters, including containment delays (time between symptom onset and mandatory isolation) and serial intervals (time between symptom onsets of infector-infectee pairs), understanding their temporal changes helps to guide interventions. OBJECTIVE: This study aims to characterize the epidemiology of the first two epidemic waves of COVID-19 in Hong Kong by doing the following: (1) estimating the containment delays, serial intervals, effective reproductive number (Rt), and proportion of asymptomatic cases; (2) identifying factors associated with the temporal changes of the containment delays and serial intervals; and (3) depicting COVID-19 transmission by age assortativity and types of social settings. METHODS: We retrieved the official case series and the Apple mobility data of Hong Kong from January-August 2020. The empirical containment delays and serial intervals were fitted to theoretical distributions, and factors associated with their temporal changes were quantified in terms of percentage contribution (the percentage change in the predicted outcome from multivariable regression models relative to a predefined comparator). Rt was estimated with the best fitted distribution for serial intervals. RESULTS: The two epidemic waves were characterized by imported cases and clusters of local cases, respectively. Rt peaked at 2.39 (wave 1) and 3.04 (wave 2). The proportion of asymptomatic cases decreased from 34.9% (0-9 years) to 12.9% (≥80 years). Log-normal distribution best fitted the 1574 containment delays (mean 5.18 [SD 3.04] days) and the 558 serial intervals (17 negative; mean 4.74 [SD 4.24] days). Containment delays decreased with involvement in a cluster (percentage contribution: 10.08%-20.73%) and case detection in the public health care sector (percentage contribution: 27.56%, 95% CI 22.52%-32.33%). Serial intervals decreased over time (6.70 days in wave 1 versus 4.35 days in wave 2) and with tertiary transmission or beyond (percentage contribution: -50.75% to -17.31%), but were lengthened by mobility (percentage contribution: 0.83%). Transmission within the same age band was high (18.1%). Households (69.9%) and social settings (20.3%) were where transmission commonly occurred. CONCLUSIONS: First, the factors associated with reduced containment delays suggested government-enacted interventions were useful for achieving outbreak control and should be further encouraged. Second, the shorter serial intervals associated with the composite mobility index calls for empirical surveys to disentangle the role of different contact dimensions in disease transmission. Third, the presymptomatic transmission and asymptomatic cases underscore the importance of remaining vigilant about COVID-19. Fourth, the time-varying epidemiological parameters suggest the need to incorporate their temporal variations when depicting the epidemic trajectory. Fifth, the high proportion of transmission events occurring within the same age group supports the ban on gatherings outside of households, and underscores the need for residence-centered preventive measures.

Differential transcriptomic landscapes of multiple organs from SARS-CoV-2 early infected rhesus macaques (preprint)

SARS-CoV-2 infection causes complicated clinic manifestations with variable multi-organ injuries, however, the underlying mechanism, in particular immune responses in different organs, remains elusive. In this study, comprehensive transcriptomic alterations of 14 tissues from rhesus macaque infected with SARS-CoV-2 were analyzed. Compared to normal controls, SARS-CoV-2 infection resulted in dysregulation of genes involving diverse functions in various tissues/organs examined, with drastic transcriptomic changes in cerebral cortex and right ventricle. Intriguingly, cerebral cortex exhibited a hyperinflammatory state evidenced by significant upregulation of inflammation response-related genes. Meanwhile, expressions of coagulation, angiogenesis and fibrosis factors were also up-regulated in cerebral cortex. Neuronal receptor NRP1 expression showed a significant induction by SARS-CoV-2 in cerebral cortex, which might be responsible for a higher infectivity and consequent inflammatory response. Overall, our study depicts a multi-tissue/organ transcriptomic landscapes of rhesus macaque with early infection of SARS-CoV-2, and provides important insights into the mechanistic basis for COVID-19-associated clinical complications.