Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner.

Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.

A bivalent subunit vaccine efficiently produced in Pichia pastoris against SARS-CoV-2 and emerging variants.

The emergence of severe acute respiratory syndrome coronavirus type II (SARS-CoV-2) variants have led to a decline in the protection of existing vaccines and antibodies, and there is an urgent need for a broad-spectrum vaccination strategy to reduce the pressure on the prevention and control of the pandemic. In this study, the receptor binding domain (RBD) of the SARS-CoV-2 Beta variant was successfully expressed through a glycoengineered yeast platform. To pursue a more broad-spectrum vaccination strategy, RBD-Beta and RBD-wild type were mixed at the ratio of 1:1 with Al(OH)3 and CpG double adjuvants for the immunization of BALB/c mice. This bivalent vaccine stimulated robust conjugated antibody titers and a broader spectrum of neutralizing antibody titers. These results suggested that a bivalent vaccine of RBD-Beta and RBD-wild type could be a possible broad-spectrum vaccination strategy.

Willingness to receive the COVID-19 vaccine among HIV positive men who have sex with men in China: a cross-sectional study.

BACKGROUND: People living with HIV(PLWH) are deemed more vulnerable to the SARS-CoV-2 infection than the uninfected population. Vaccination is an effective measure for COVID-19 control, yet, little knowledge exists about the willingness of men who have sex with men (MSM) living with HIV in China to be vaccinated. METHODS: This cross-sectional study evaluated the willingness of MSM living with HIV to receive COVID-19 vaccination in six cities of Guangdong, China, from July to September 2020. Factors associated with willingness to receive COVID-19 vaccination using multivariable logistic regression. RESULTS: In total, we recruited 944 HIV-positive MSM with a mean age of 29.2 ± 7.7 years. Of all participants, 92.4% of them were willing to receive the COVID-19 vaccine. Participants who were separated, divorced, or widowed (adjusted OR: 5.29, 95%CI: 1.02-27.48), had an annual income higher than 9,000 USD (adjusted OR: 1.70, 95%CI: 1.01-2.86), had ever taken an HIV self-test (adjusted OR: 1.78, 95%CI: 1.07-2.95), had ever disclosed sexual orientation to a doctor/nurse (adjusted OR: 3.16, 95%CI: 1.33-7.50), had ever disclosed sexual orientation to others besides their male partners (adjusted OR: 2.18, 95%CI: 1.29-3.69) were more willing to receive the vaccine. Sex with a female partner in the past six months decreased the likelihood of willingness to receive the vaccine (adjusted OR: 0.40, 95%CI: 0.17-0.95). Economic burden, worry that my health condition could not bear the risk of receiving COVID-19 vaccines, and concern that the vaccination would affect the immune status and antiretroviral therapy were the main reasons for unwillingness to receive vaccination. CONCLUSION: Our study showed that HIV-positive MSM had a high willingness to receive the COVID-19 vaccination. Targeted interventions such as health education should be conducted among MSM with HIV infection to enhance COVID-19 vaccine uptake.

A Vaccine with Multiple Receptor-Binding Domain Subunit Mutations Induces Broad-Spectrum Immune Response against SARS-CoV-2 Variants of Concern.

With the emergence of more variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the immune evasion of these variants from existing vaccines, the development of broad-spectrum vaccines is urgently needed. In this study, we designed a novel SARS-CoV-2 receptor-binding domain (RBD) subunit (RBD5m) by integrating five important mutations from SARS-CoV-2 variants of concern (VOCs). The neutralization activities of antibodies induced by the RBD5m candidate vaccine are more balanced and effective for neutralizing different SARS-CoV-2 VOCs in comparison with those induced by the SARS-CoV-2 prototype strain RBD. Our results suggest that the RBD5m vaccine is a good broad-spectrum vaccine candidate able to prevent disease from several different SARS-CoV-2 VOCs.

A Multi-Center Study on the Negative Psychological Impact and Associated Factors in Chinese Healthcare Workers 1 Year After the COVID-19 Initial Outbreak.

Objectives: The study aimed at analyzing the prevalence of five psychological outcomes (depression, anxiety, stress, post-traumatic stress disorder (PTSD), and suicidal ideation) among Chinese healthcare workers (HCWs), and measured the total possible negative psychological impact 1 year after the COVID-19 initial outbreak. Methods: A cross-sectional nationwide multi-center study was performed between November 2020 and March 2021 in China. A self-report questionnaire was applied, and three psychological scales were used. Binary logistic regression was performed to analyze the risk factors associated with each psychological outcome. Results: The findings demonstrated that the COVID-19 pandemic had a negative psychological impact on HCWs, which was still evident 1 year after the initial outbreak. Nurses showed higher depression and anxiety than other HCWs. Female gender, passive coping, long working hours, having a chronic disease, and experiencing violence, among other factors, were all risk factors for psychological impairment. Conclusion: Developing and promoting programs to improve mental health among HCWs, and identifying those who might need psychological support is still relevant 1 year after the initial outbreak.

Non-glycosylated SARS-CoV-2 RBD elicited a robust neutralizing antibody response in mice.

The glycosylated receptor-binding domain (glycoRBD) of SARS-CoV-2 can induce protective neutralizing antibodies to function as a vaccine. However, it is unclear whether vaccines using non-glycosylated RBD (non-glycoRBD) can induce protective immunity. Here, we report the efficacy of a SARS-CoV-2 non-glycoRBD vaccine produced by prokaryotic system in mice. The recombinant non-glycoRBD protein was overexpressed in Escherichia coli in the form of inclusion bodies, and was obtained after renaturation and three-step purification. From HPLC analysis, the purity of the RBD was 99%. Additionally, angiotensin converting enzyme 2 (ACE2)-binding assays revealed that E.coli-derived non-glycoRBD had binding activity consistent with glycoRBD. The RBD was formulated with CpG ODN and Al(OH)3 adjuvants and the obtained RBD candidate vaccine elicited potent antibody responses and neutralized SARS-CoV-2 wild-type, Delta, and Omicron pseudoviruses. In summary, our data showed that a non-glycoRBD candidate vaccine produced by E.coli provided a robust immune response and had pseudovirus neutralizing activity, making it a solid candidate vaccine for protection against SARS-CoV-2.

Kappa-RBD produced by glycoengineered Pichia pastoris elicited high neutralizing antibody titers against pseudoviruses of SARS-CoV-2 variants.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kappa (B.1.617.1) variant represented the main variant of concern (VOC) for the epidemic in India in May 2021. We have previously established a technology platform for rapidly preparing SARS-CoV-2 receptor-binding domain (RBD) candidate vaccines based on glycoengineered Pichia pastoris. Our previous study revealed that the wild-type RBD (WT-RBD) formulated with aluminum hydroxide and CpG 2006 adjuvant effectively induces neutralizing antibodies in BALB/c mice. In the present study, a glycoengineered P. pastoris expression system was used to prepare recombinant kappa-RBD candidate vaccine. Kappa-RBD formulated with CpG and alum induced BALB/c mice to produce a potent antigen-specific antibody response and neutralizing antibody titers against pseudoviruses of SARS-CoV-2 kappa, delta, lambda, beta, and omicron variants and WT. Therefore, the recombinant kappa-RBD vaccine has sufficient potency to be a promising COVID-19 vaccine candidate.

Knowledge, Awareness, and Attitudes Relating to the COVID-19 Pandemic Among Different Populations in Central China: Cross-Sectional Survey.

BACKGROUND: The COVID-19 pandemic has threatened the health systems of many countries worldwide. Several studies have suggested that the pandemic affects not only physical health but also all aspects of society. A lot of information has been reported about the disease since the beginning of the outbreak. For that reason, it is essential to investigate the attitudes and level of knowledge and awareness that different populations had regarding COVID-19 during the critical period of the outbreak. OBJECTIVE: This study aimed to assess the knowledge and awareness of and attitudes toward the COVID-19 pandemic among different populations in Central China during the critical period of the outbreak. METHODS: A cross-sectional web-based survey was conducted in Central China from February to March 2020. The study participants included three different populations: medical workers, students, and those with other occupations. In this study, a questionnaire was designed to collect information on the following four aspects: sociodemographic information, knowledge related to COVID-19, awareness of COVID-19, and attitude toward COVID-19. The chi-square test and Fisher test were used for comparison among groups. The level of significance was set at P<.05. RESULTS: This study enrolled a total of 508 participants. Among them, there were 380 students (74.8%), 39 medical workers (7.7%), and 89 people with other occupations (17.5%). Most of the participants were female (n=272, 53.5%), lived in rural areas (n=258, 50.8%), and were single (n=423, 86.9%). The majority of the respondents had attended college (n=454, 89.4%). Most of the participants said they had heard about COVID-19 by January, and most of them looked for information on social media (Sina Weibo, 84.7%), and WeChat and QQ groups (74.2%). The participants showed an adequate level of knowledge about COVID-19 with no significant differences among the groups. However, medical workers demonstrated a slightly advanced knowledge in their responses to professional questions such as the potential susceptible population, possible host, treatment of COVID-19, and disease category. A higher proportion of medical workers (71.8%) and those in the other occupations group (52.8%) were highly concerned about the COVID-19 pandemic. More than 43% of the participants stated that the lockdown of their village/city had a significant impact on their lives. Nevertheless, the majority of respondents had an overall optimistic attitude toward the control of the disease (92.1% of students [n=350], 94.9% of medical workers [n=37], and 92.3% of those in other occupations [n=83]). CONCLUSIONS: All three groups reported an adequate background knowledge about COVID-19 but medical workers showed a slightly advanced knowledge in their responses to professional questions. Most of the participants were highly concerned about COVID-19 during the critical period of the outbreak. The majority of respondents declared that the village/city lockdown policy had a significant impact on their daily life but most of them held an optimistic attitude toward the control of COVID-19.