Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

Characteristics of the 11th wave by SARS-CoV-2 KP.3 subvariant: Re-increase in pneumonia severity

OBJECTIVES

We investigated the incidence and risk factors for requiring intensive care unit (ICU) admission or invasive mechanical ventilation (IMV) in pneumonia patients with Omicron subvariants between the 9th and 11th waves.

METHODS

We analyzed 536 patients with pneumonia caused by SARS-CoV-2 Omicron subvariants (175 cases were XBB lineage, 169 cases were JN.1, and 192 cases were KP.3 subvariants).

RESULTS

Rates of ICU admission or requirement for IMV were significantly higher in patients with the KP.3 subvariant group than those with the XBB lineage and JN.1 subvariant groups. Patient age (odds ratio [OR]: 1.09, P < 0.001), immunodeficiency (OR: 2.82), 2 or more co-morbid illnesses (OR: 2.54), and more than 2 years since last vaccination (OR: 1.29) were significantly associated with increased severity.

CONCLUSIONS

Physicians should recommend SARS-CoV-2 vaccination and positive use anti-SARS-CoV-2 drugs when COVID-19 is found in patients who are ≥65 years old or who have multiple comorbidities.

Development of an automated plaque-counting program for the quantification of the Chikungunya virus

Chikungunya virus (CHIKV) induces a massive cytopathic effect (CPE) on various cell types. Therefore, the plaque assay, a CPE-based virus titration method, remains the gold standard for quantifying the infectious units of CHIKV. However, manual plaque counting is often a labor-intensive task, especially in experiments involving multiple samples. In this study, we developed plaQuest, a stand-alone plaque-counting software running on a Windows operating system, for rapid and reliable quantification of CHIKV plaques in a 24-well plate. Our evaluation experiments using the conventional CPE-based plaque assay showed that the CHIKV plaque counts provided by plaQuest strongly correlated with the plaque counts manually determined by four analysts. In addition, the CHIKV inhibition curve of mycophenolic acid (MPA) determined by plaQuest was identical to that determined by manual counting, resulting in a similar 50% inhibitory concentration of MPA. Furthermore, the automated plaque counting by plaQuest was applicable to the evaluation of inhibitors against other RNA viruses using the CPE-based and immunostain-based plaque assay, which is an alternative titration assay for non- (or less) cytopathic viruses. Thus, our study demonstrates that plaQuest is an effective option for quantifying infectious virus titers, reducing the workload of the plaque assay.

The immunopathogenesis of SARS-CoV-2 infection: Overview of lessons learned in the first 5 years

This review provides a broad overview of lessons learned in the five years since COVID-19 was identified. It is a bimodal disease, starting with an initially virus-driven phase, followed by resolution or ensuing inappropriate immune activation causing severe inflammation that is no longer strictly virus dependent. Humoral immunity is beneficial for preventing or attenuating the early stage, without benefit once the later stage begins. Neutralizing antibodies elicited by natural infection or vaccination are short-lived and highly vulnerable to viral sequence variation. By contrast, cellular immunity, particularly the CD8+ T cell arm, has a role in preventing or attenuating severe disease, is far less susceptible to viral variation, and is longer-lived than antibodies. Finally, an ill-defined phenomenon of prolonged symptoms after acute infection, termed "long COVID," is poorly understood but may involve various immunologic defects that are hyperactivating or immunosuppressive. Remaining issues include needing to better understand the immune dysregulation of severe disease to allow more tailored therapeutic interventions, developing antibody strategies that cope with the viral spike sequence variability, prolonging vaccine efficacy, and unraveling the mechanisms of long COVID to design therapeutic approaches.

Human Source Severe Acute Respiratory Syndrome Coronavirus 2 Aerosol Transmission to Remote Sentinel Hamsters

Background

Bioaerosol-mediated transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via building ventilation systems has yet to be convincingly demonstrated. We used the South African Airborne Infections Research (AIR) facility near Pretoria to study human-to-animal (H2A) transmission of SARS-CoV-2 in newly diagnosed patients. While the facility was built to study tuberculosis transmission, this was its first adaptation to study H2A virus transmission.

Methods

Patients with clinically confirmed coronavirus disease 2019 were housed for up to 4 days in in the AIR facility with continuously exhausting patient ward air to hamsters housed in animal exposure rooms. After a 3-week exposure period, animals were held for an additional week to allow for antibody development. Animal sera were analyzed for anti-spike and plaque reduction activities and lung samples for pathology.

Results

Seven patients provided ≥400 in-residence hours over a 17-day period. Pair-housed naive golden Syrian hamsters (n = 216) received continuous exposure to mixed patient ward exhaust. Serum analyses revealed anti-SARS-CoV-2 immunoglobulin G in 58% of animals tested. Plaque reduction assays on 7 high-titer serum samples revealed neutralizing activity.

Conclusions

These results support the concept that viral bioaerosols generated from patients remain infectious over long-distance transport through a building ventilation system. The seroconversion among sentinel animals supports the long-held belief that airborne infections manifest as a stochastic rather than deterministic event that is subject to a threshold dose effect. Further confirmatory studies are necessary to characterize the relationship between the bioaerosol delivered and the infections that result in this controlled H2A transmission model.

Long-Term Effects of the COVID-19 Open Strategy on the Mental Health of Chinese University Students: A Prospective Cohort Study

Background

In December 2022, the Chinese government shifted its COVID-19 prevention and control policy to full openness, leading to a widespread pandemic within a short period. This study aimed to examine the trajectories of stress, anxiety, and depressive symptoms among Chinese university students within 1 year after the implementation of the open policy. Additionally, it investigated the influence of sleep quality, psychological resilience, and medical specialization on these psychological trajectories.

Methods

A cohort study was conducted among Chinese university students using stratified sampling. Follow-up assessments were conducted at three time points: T1 (December 2022-January 2023), T2 (May-June 2023), and T3 (December 2023-January 2024). Generalized Estimating Equations were used to estimate mean differences in symptom levels over time and to examine the influence of sleep quality, psychological resilience, and medical specialization on these changes.

Results

At T1, a total of 2,062 university students were recruited. By T3, the follow-up rate was 63.43%, resulting in a final analytical cohort of 1,308 participants. Among them, 769 (58.8%) were female, and 539 (41.2%) were male. The majority (54.7%, n = 716) were between 19 and 22 years old. Stress, anxiety, and depression levels were highest among Chinese university students at the beginning of the open policy and gradually decreased over the following year. Students with poor sleep quality and poor psychological resilience exhibited worsening psychological trajectories, which showed more severe and persistent symptoms. Medical and Nonmedical students consistently exhibited similar psychological trajectories.

Conclusions

Collectively, the present study indicated that the change of COVID-19 prevention and control policy had more serious negative impacts on the mental health of Chinese university students than the epidemic itself. Thus, strengthening psychological treatments and psychosocial interventions for university students would be crucial in the context of a protracted infectious disease epidemic.

The Effect of COVID-19 Infection on Orofacial Pain: A Cross-sectional Study

BACKGROUND

COVID-19 infection shows variant symptoms apart from respiratory symptoms, including the orofacial pain. We aim to research the morbidity, characteristics and potential risk factors of orofacial pain associated with COVID-19 pandemic in China from December 2022 to early 2023.

METHODS

A cross-sectional survey was conducted in Fujian Province, China. The demographic and characteristic data of the subjects were collected and analysed.

RESULTS

A total of 1526 subjects responded to the survey. The morbidity of orofacial pain increased significantly before and after COVID-19 infection. (42.26% vs. 46.52%, P < .001) A total of 217 (14.22%) subjects with orofacial pain before COVID-19 infection reported the phenomenon of "COVID-19 infection with orofacial pain" (CIOP). Univariate and multivariate logistic regression showed that male (OR = 1.761, P < .001) and other symptoms of COVID-19 (OR = 1.494, P < .001) may be the risk factors for the aggravation of CIOP, while the time of first infection (OR = 0.580, P = .004) and preference for drinking tea or coffee (OR = 0.610, P = .003) may be the protective factors for the aggravation of CIOP. While, the subjects who did not concern about the spread of COVID-19 in oral treatment (OR = 0.639, P = .001), female (OR = 0.749, P = .03), education level (OR = 1.687, P < .001) and income level (OR = 1.796, P < .001), higher PSS-10 score (OR = 1.076, P < .001), and more drugs taken for infection (OR = 1.330, P < .001) were more willing to seek medical treatment.

CONCLUSION

The morbidity of orofacial pain appears to have increased significantly due to the COVID-19 epidemic; a number of factors can influence the CIOP including gender, infection period, and beverage preference' psychological factors, gender, education and income level can also influence the intent to seek a dentist.

Clinical manifestations of COVID-19 Omicron variants in medical healthcare workers: Focusing on the cough

INTRODUCTION

Important points in cough management are that it is necessary to be familiar with the characteristic medical history for each disease, such as infection and cough variant asthma. To clarify whether cough due to SARS-CoV-2 has any characteristics or not, we investigated the clinical manifestations of COVID-19 Omicron variant focused especially on infectious cough.

METHODS

We enrolled adult patients consecutively diagnosed with mild COVID-19 who were medical healthcare workers in our five hospitals. A total of 2449 patients were analyzed: 300 patients with BA.1 subvariant, 202 patients with BA.2 subvariant, 1030 patients with BA.5 subvariant, 413 patients with XBB lineage, 103 patients with BA.2.86, and 401 patients with JN.1 subvariant.

RESULTS

Among the clinical symptoms, cough was most frequent symptom in all Omicron subvariants groups and all age groups. The most frequent pattern of symptoms was cough appearing after pharyngeal symptoms in 38 % of patients, with cough appearing after fever observed in 25.1 % of patients. The pattern in which cough and pharyngeal symptoms were the initial symptoms was observed in 19.6 % of cases, and where cough and fever were the initial symptoms was observed in 14.9 % of cases.

CONCLUSIONS

Cough was the most frequent symptom in patients with COVID-19 Omicron variant and cough was the initial symptom in 1/3 of cases, and 2/3 of cases were preceded by symptoms other than cough. There were few cases of cough only or paroxysmal cough. However, it is considered difficult to differentiate between sources of infectious cough based on symptoms alone.

Comparison of the pathogenicity and neutrophil and monocyte response between SARS-CoV-2 prototype and Omicron BA.1 in a lethal mouse model

BACKGROUND

SARS-CoV-2, first identified in late 2019, has given rise to numerous variants of concern (VOCs), posing a significant threat to human health. The emergence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022. At present, the lethal mouse model for the study of SARS-CoV-2 needs supplementation, and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated.

METHODS

Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 prototype and Omicron BA.1, respectively. The pathogenicity of the two strains was evaluated by observing clinical symptoms, viral load and pathology. Complete blood count, immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains.

RESULTS

Our findings revealed that Omicron BA.1 exhibited significantly lower virulence compared to the SARS-CoV-2 prototype in the mouse model. Additionally, we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1. We found that the proportion of monocytes increased at first and then decreased. The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar.

CONCLUSION

Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1. SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.

The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19

Immunocompromised individuals are susceptible to severe coronavirus disease 2019 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in K18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered, and viral load and viral sequence diversity were assessed. Treatment of infected but immunocompromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion ratio, representative of G > A and C > U mutations, and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir. Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristics of variants of concern (VOCs). Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimized public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.

IMPORTANCE

The central aim of this study was to risk-assess the impact of administering a mutagenic antiviral compound, molnupiravir, to patients believed to already be at risk of generating increased viral diversity, which could have severe implications for antiviral resistance development. Combination therapy has a long history of mitigating antiviral resistance risk and was used in this study to demonstrate its potential usefulness in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) context. Animals treated with molnupiravir showed an increase in transition/transversion ratios over time, consistent with the drug's mechanism of action and a recent UK-wide phase II clinical trial assessing the efficacy of molnupiravir in humans. The addition of nirmatrelvir increased viral clearance, which in turn reduces the probability of viral persistence and rapid intra-host evolution of SARS-CoV-2.

Increased pathogenicity and transmissibility in hamsters of all age groups reveal an underestimated perniciousness of severe acute respiratory syndrome coronavirus 2 EG.1 variant

The evolution and mutation of SARS-CoV-2 is elusive. However, the diverse in vivo pathogenicity and transmissibility of different SARS-CoV-2 Omicron/XBB variants are not well understood. We compared virological attributes of two XBB variants, XBB.1.16 and XBB.1.9.2.1 (EG.1) in new-born, juvenile, adult, middle-aged and senescent Syrian hamsters. In particular, EG.1 has a specific Q613H mutation and causes fatal severe pneumonia in hamsters of all ages. In contrast, all hamsters infected with XBB.1.16 survived and showed milder symptoms. The XBB.1.16 infected hamsters lost significantly less body weight and exhibited lower respiratory viral loads, pro-inflammatory cytokines and lung injury than those with EG.1 infection. In addition, EG.1 is more transmissible than XBB.1.16 in close contact co-housing. Both EG.1 and XBB.1.16 are highly resistant to therapeutic antibodies and convalescent serum. Overall, the unpredictable evolution, global transmission and potential threat of emerging SARS-CoV-2 variants necessitate the updating of prophylactic and therapeutic countermeasures in all age groups.

Diagnostic Efficiency of Tongue-Coating Microbiome in Patients With SARS-CoV-2 Omicron Variant Infection and Recovery

SARS-CoV-2 variants still pose threats to human public health. However, there has been little research regarding alterations in the tongue-coating microbiome in patients infected with the Omicron variant (PIOVs). Herein, we collected 963 tongue-coating samples prospectively, including 349 samples from PIOVs, 242 samples from recovered PIOVs, 300 samples from healthy controls (HCs) and 72 samples from patients infected with the original strain (PIOSs). We randomly selected tongue-coating samples from PIOVs and HCs as the discovery cohort and validation cohort. Tongue-coating microbiota was analyzed using Miseq sequencing. Our results showed that the tongue-coating microbial diversity of PIOVs was increased. We found that in PIOVs, the abundance was increased in 20 genera, including Prevonella and Atopobium, while the abundance was decreased in 23 genera, including Neisseria and Haemophilus. The classifier based on six optimal microbial markers had high diagnostic efficiency in the discovery cohort (area under the curve of 97.73%) and the validation cohort (area under the curve of 93.06%) between the PIOV and HC groups. Importantly, compared with PIOSs, PIOVs showed an increase in Fusobacterium. Recovery of patients was associated with the restoration of the tongue-coating microbiota. In conclusion, this study is the first to characterize the tongue-coating microbiota in PIOVs and to construct noninvasive diagnostic models, providing new strategies for the prevention and control of coronavirus variants.

Evaluating Hospital Admission Data as Indicators of COVID-19 Severity: A National Assessment in Qatar

Background

Accurately assessing SARS-CoV-2 infection severity is essential for understanding the health impact of the infection and evaluating the effectiveness of interventions. This study investigated whether SARS-CoV-2-associated hospitalizations can reliably measure true COVID-19 severity.

Methods

The diagnostic accuracy of SARS-CoV-2-associated acute care and ICU hospitalizations as indicators of infection severity was assessed in Qatar from 6 September 2021 to 13 May 2024. WHO criteria for severe, critical, and fatal COVID-19 served as the reference standard. Two indicators were assessed: (1) any SARS-CoV-2-associated hospitalization in acute care or ICU beds and (2) ICU-only hospitalizations.

Results

A total of 644 176 SARS-CoV-2 infections were analyzed. The percent agreement between any SARS-CoV-2-associated hospitalization (acute care or ICU) and WHO criteria was 98.7% (95% confidence interval (CI), 98.6-98.7); however, Cohen's kappa was only 0.17 (95% CI, 0.16-0.18), indicating poor agreement. Sensitivity, specificity, PPV, and negative predictive value were 100% (95% CI, 99.6-100), 98.7% (95% CI, 98.6-98.7), 9.7% (95% CI, 9.1-10.3), and 100% (95% CI, 100-100), respectively. For SARS-CoV-2-associated ICU-only hospitalizations, the percent agreement was 99.8% (95% CI, 99.8-99.9), with a kappa of 0.47 (95% CI, 0.44-0.50), indicating fair-to-good agreement. Sensitivity, specificity, PPV, and negative predictive value were 46.6% (95% CI, 43.4-49.9), 99.9% (95% CI, 99.9-99.9), 47.9% (95% CI, 44.6-51.2), and 99.9% (95% CI, 99.9-99.9), respectively.

Conclusions

Generic hospital admissions are unreliable indicators of COVID-19 severity, whereas ICU admissions are somewhat more accurate. The findings demonstrate the importance of applying specific, robust criteria-such as WHO criteria-to reduce bias in epidemiological and vaccine effectiveness studies.

A comprehensive review of current insights into the virulence factors of SARS-CoV-2

The evolution of SARS-CoV-2 pathogenicity has been a major focus of attention. However, the determinants of pathogenicity are still unclear. Various hypotheses have attempted to elucidate the mechanisms underlying the evolution of viral pathogenicity, but a definitive conclusion has yet to be reached. Here, we review the potential impact of all proteins in SARS-CoV-2 on the viral pathogenic process and analyze the effects of their mutations on pathogenicity evolution. We aim to summarize which virus-encoded proteins are crucial in influencing viral pathogenicity, defined as disease severity following infection. Mutations in these key proteins, which are the virulence factors in SARS-CoV-2, may be the driving forces behind the evolution of viral pathogenicity. Mutations in the S protein can impact viral entry and fusogenicity. Mutations in proteins such as NSP2, NSP5, NSP14, and ORF7a can alter the virus's ability to suppress host protein synthesis and innate immunity. Mutations in NSP3, NSP4, NSP6, N protein, NSP5, and NSP12 may alter viral replication efficiency. The combined effects of mutations in the S protein and NSP6 can significantly reduce viral replication. In addition, various viral proteins, including ORF3a, ORF8, NSP4, Spike protein, N protein, and E protein, directly participate in the inflammatory process. Mutations in these proteins can modulate the levels of inflammation following infection. Collectively, these viral protein mutations can influence SARS-CoV-2 pathogenicity by impacting viral immune evasion, replication capacity, and the level of inflammation mediated by infection. In conclusion, the evolution of SARS-CoV-2 pathogenicity is likely determined by multiple virulence factors.

Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses an ongoing threat to the efficacy of vaccines and therapeutic antibodies. Mutations predominantly affect the receptor-binding domain (RBD) of the spike protein, which mediates viral entry. The RBD is also a major target of monoclonal antibodies that were authorised for use during the pandemic. In this study, an in silico approach was used to investigate the mutational landscape of SARS-CoV-2 RBD variants, including currently circulating Omicron subvariants. A total of 40 single-point mutations were assessed for their potential effect on protein stability and dynamics. Destabilising effects were predicted for mutations such as L455S and F456L, while stabilising effects were predicted for mutations such as R346T. Conformational B-cell epitope predictions were subsequently performed for wild-type (WT) and variant RBDs. Mutations from SARS-CoV-2 variants were located within the predicted epitope residues and the epitope regions were found to correspond to the sites targeted by therapeutic antibodies. Furthermore, homology models of the RBD of SARS-CoV-2 variants were generated and were utilised for protein-antibody docking. The binding characteristics of 10 monoclonal antibodies against WT and 14 SARS-CoV-2 variants were evaluated. Through evaluating the binding affinities, interactions, and energy contributions of RBD residues, mutations that were contributing to viral evasion were identified. The findings from this study provide insight into the structural and molecular mechanisms underlying neutralising antibody evasion. Future antibody development could focus on broadly neutralising antibodies, engineering antibodies with enhanced binding affinity, and targeting spike protein regions beyond the RBD.

Aerosol dynamics in dental clinics: Effects of ventilation mode on the mitigation of airborne diseases transmission

Dental operations inherently involve a high risk of airborne cross-infection among medical staff and patients due to the exposure of respiratory secretions, which contain pathogenic microorganisms and typically spread in the form of aerosols. In order to contribute to the understanding of aerosol dynamics during dental operation and efficiently mitigate their dispersion and deposition through appropriate ventilation, 3D numerical simulations and full-scale experimental measurements were performed in this study. The indoor airflow distribution and dynamic aerosol behaviors observed under three optimized ventilation schemes (Scenario I-III) were compared with those observed under the current ventilation system. Qualitative analysis was performed together with quantitative examination using the air age, air change efficiency, contaminant removal effectiveness, and deposition ratio. It is demonstrated that the ventilation currently in use is unable to effectively discharge aerosols, resulting in most of them depositing on surfaces routinely accessed by dental workers. The pronounced air mixing effect induced by the design of Scenario I facilitates the rapid dispersion of aerosols throughout the clinic, impeding the efficient removal via the outlet. Moreover, the effective elimination of indoor aerosols is only attainable by implementing high ventilation rates in Scenario II. The Scenario III exhibits better overall performance, as evidenced by the successful discharge of approximately 69.8% of injected aerosols with limited deposition on indoor surfaces under ACH = 6h-1, and further enhanced performance is observed at higher ACHs for contaminant removal. The prevailing ventilation design in dental clinics, which primarily focuses on maintaining a desirable temperature and relative humidity, often overlooks the necessity of proper ventilation for reducing the exposure risk of occupants. This study provides solid evidence for the upgrading or reconstruction of ventilation systems in dental clinics, aiming to promote a safe and healthy treatment environment.

Outcomes of COVID-19 in the Omicron-predominant wave: large-scale real-world data analysis with a comparison to influenza

PURPOSE

Studies on COVID-19 mortality during the Omicron-predominant wave have focused primarily on the inpatient/emergency room setting, and real-world data including both inpatients and outpatients are lacking.

METHODS

Patients diagnosed with COVID-19 (n = 27,440,148) or influenza (n = 8,179,641) from January 2020 to April 2023 were identified using nationwide claims data in Japan. Patients with COVID-19 in the Omicron-predominant wave were compared with their counterparts in earlier waves, and a subset of the former group (May 2022-April 2023) was compared with patients with influenza as controls.

RESULTS

The mortality rates (average number of deaths/cases per week) of COVID-19 decreased over time, being 2.7% (169/6312), 2.1% (397/18,754), 0.7% (195/28,273), and 0.4% (1613/378,848) in the wild-type-, Alpha-, Delta-, and Omicron-predominant waves, respectively. However, the number of deaths increased substantially in the Omicron-predominant wave, especially among the elderly (e.g., in the Delta- and Omicron-predominant waves, the average numbers of deaths/cases per week were < 1/5527 (< 0.01%) and 4/105,763 (< 0.01%) respectively, in patients aged 0-19, versus 101/925 (10.9%) and 1212/20,771 (5.8%), respectively, in patients aged ≥ 80). The mortality rate was lower for patients with COVID-19 than in those with influenza among those aged ≤ 39 years but higher among those aged ≥ 40 years.

CONCLUSIONS

In the Omicron-predominant wave, the mortality rate of COVID-19 decreased, but the number of patients increased, leading to a substantial increase in the number of deaths, especially among the elderly. The mortality rate of COVID-19 was higher than that of influenza in the elderly but not in the young, highlighting the need for age-specific interventions.

Antibody-dependent enhancement of coronaviruses

The COVID-19 pandemic presents a significant challenge to the global health and the world economy, with humanity engaged in an extended struggle against the virus. Notable advancements have been achieved in the development of vaccines and therapeutic interventions, including the application of neutralizing antibodies (NAbs) and convalescent plasma (CP). While antibody-dependent enhancement (ADE) has not been observed in human clinical studies related to SARS-CoV-2, the potential for ADE remains a critical concern and challenge in addressing SARS-CoV-2 infections. Moreover, the causal relationship between ADE and viral characteristics remains to be clearly elucidated. Viruses that present with severe clinical manifestations of ADE have demonstrated the capacity to replicate in macrophages or other immune cells, or to alter the immunological status of these cells, which induces abortive infections characterized by systemic inflammation. In this review, we summarize experimental observations and clinical evidence concerning the ADE effect associated with coronaviruses. We critically examine the potential mechanisms through which coronaviruses mediate ADE, and propose strategies to mitigate this phenomenon in the context of viral infection treatment. Our aim is to offer informed recommendations for the containment of the COVID-19 pandemic and to strengthen the response to SARS-CoV-2, as well as to prepare for potential future coronavirus threats.

Infection with SARS-CoV-2 during the first trimester did not adversely impact perinatal and obstetric outcomes subsequent to in vitro fertilization with frozen embryo transfer: a retrospective cohort study

PURPOSE

To investigate the impact of first-trimester COVID-19 infection on the perinatal and obstetric outcomes following in vitro fertilization-frozen embryo transfer.

METHODS

This retrospective study was conducted at a university-affiliated IVF center. The infection group included women who contracted SARS-CoV-2 during the first trimester following frozen embryo transfer in China's initial pandemic wave that occurred from 7 December 2022 to 7 January 2023. The control group consisted of pregnant women from the pre-pandemic period, considering the widespread incidence of the disease among the Chinese population during such a large outbreak. The primary outcome was perinatal and obstetric parameters.

RESULTS

A total of 346 pregnant women who tested positive for COVID-19 during the first trimester were included in the analysis, while the control group comprised 705 uninfected women (pre-COVID-19 controls). Perinatal outcomes, such as preterm birth, low birthweight, birthweight Z scores, macrosomia, small for gestational age, large for gestational age, and congenital malformations, showed no significant differences between the infected and control groups in both the unadjusted and confounder-adjusted logistic regression models. Additionally, there were no significant differences between the groups concerning obstetric complications, including gestational diabetes mellitus, hypertensive disorders of pregnancy, placenta previa, preterm premature rupture of the membrane, and mode of delivery.

CONCLUSION

The current study demonstrated that contracting COVID-19 during the first trimester did not adversely impact future obstetric and perinatal outcomes following in vitro fertilization-frozen embryo transfer. This data holds practical significance and offers essential insights for reproductive specialists and obstetricians advising expectant mothers.

Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2

Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2hi cell subsets, which was distinct from that of ancestral cases. Delta-infected samples had a marked increase in viral RNA, and a subset of PER2+EGR1+GDF15+ epithelial cells was enriched in SARS-CoV-2 RNA+ cells in all variants. Prior vaccination was associated with increased frequency and activation of nasal macrophages. Expression of interferon-stimulated genes negatively correlated with coronavirus disease 2019 (COVID-19) severity in patients with ancestral and Delta but not Omicron variants. Our study defines nasal cell responses and signatures of disease severity across SARS-CoV-2 variants and vaccination.

Pregnancy-Related and Neonatal Outcomes during Omicron Variant-Dominant COVID-19 Pandemic among the Black-Dominant Population

OBJECTIVE

 This study aimed to determine the effect of the Omicron variant on pregnancy-related and neonatal outcomes among the Black-dominant population.

STUDY DESIGN

 We performed a single-center, retrospective cohort study during the prepandemic period from December 1, 2019, to February 29, 2020, and the Omicron surging period from December 1, 2021, to February 28, 2022. A total of 518 pregnant women were admitted for delivery during the study period. Multiple gestations (n = 21) and deliveries at less than 20 weeks of gestation (n = 5) were excluded. We analyzed and compared the sociodemographic and clinical data from mothers and their neonates between the two cohorts as well as between severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) positive and negative mothers during the Omicron surge. Subgroup analyses were also conducted specifically among the Black-only population.

RESULTS

 The cohorts were predominantly Black (88.6%), with smaller proportions of Hispanic (8.9%), Asian (0.8%), White (0.8%), and other ethnicities (0.8%). Of 492 singleton deliveries, 275 live births, 8 (2.8%) stillbirths, and 31 (11.3%) preterm births (PTBs) occurred during the prepandemic period, and 207 live births, 2 (1%) stillbirths, and 33 (15.9%) PTBs occurred during the Omicron wave. There was no statistically significant difference in the rates of PTBs, stillbirths, medically indicated PTBs, and cesarean delivery between the two cohorts. SARS-CoV-2-positive mothers were not at an increased risk of adverse outcomes. However, neonatal intensive care unit (NICU) admission rate significantly increased among neonates born to SARS-CoV-2 positive mothers compared with negative mothers (32.3 vs. 16.5%, p = 0.038). In subgroup analyses among Black individuals, this difference was not observed.

CONCLUSION

 There was no significant difference in pregnancy-related or neonatal outcomes in the Black-dominant population between the two cohorts. SARS-CoV-2 infection did not alter these findings except for an increased NICU admission rate among neonates born to SARS-CoV-2-positive mothers.

KEY POINTS

· Most pregnant women infected with SARS-CoV-2 during the Omicron wave were asymptomatic.. · The Omicron wave did not increase the risk of pregnancy-related or neonatal adverse outcomes when compared with the prepandemic period.. · Maternal SARS-CoV-2 infection increased NICU admission rate.. · Among Black individuals, no significant increase in adverse outcomes was observed during the Omicron pandemic..

Symptoms of post COVID-19 condition and diseases/conditions diagnosed after COVID-19 in Japanese patients: A real-world study using a claims database

BACKGROUND

More than 200 symptoms of post coronavirus disease (COVID-19) condition (PCC) impacting patients' quality of life have been reported. This study describes the symptoms of well-known PCC and diseases/conditions diagnosed after COVID-19 and analyzes the trends in well-known PCC according to the epidemic waves in the Japanese population.

METHODS

Patients with a COVID-19 diagnosis in the JMDC claims database were matched 1:1 with individuals without COVID-19 diagnosis (controls) based on sex, year and month of birth, and risk factors for aggravation. The first month of COVID-19 diagnosis from January 2020-March 2022 was the index month, and the observation period was from July 2019 to 6 months from the index month (patients) and July 2019-September 2022 (controls).

RESULTS

Of 263,456 each of patients and controls after matching, 51.8 % were aged 18-49 years, 56.3 % were male, and 24.5 % had risk factors for aggravation. One in 18 patients experienced well-known PCC 2-3 months after severe acute respiratory syndrome cornonavirus 2 infection, with the highest odds ratio (OR) being for pulmonary thromboembolism (29.37), followed by smell/taste disorder (13.34) and respiratory failure (8.28). Some of the common diseases/conditions diagnosed after COVID-19 comprised those of the genitourinary system, eye and adnexa, and ear and mastoid process and certain infectious and parasitic diseases. Overall, the risk difference decreased from the first to the sixth wave, but the OR was >1.00 for most symptoms even during the sixth wave.

CONCLUSIONS

PCC symptoms showed a declining trend over time but persisted. Physicians and patients need to recognize PCC symptoms.

The respective roles of TMPRSS2 and cathepsins for SARS-CoV-2 infection in human respiratory organoids

A critical aspect of the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is the protease-mediated activation of the viral spike (S) protein. The type II transmembrane serine protease TMPRSS2 is crucial for SARS-CoV-2 infection in lung epithelial Calu-3 cells and murine airways. However, the importance of TMPRSS2 needs to be re-examined because the ability to utilize TMPRSS2 is significantly reduced in the Omicron variants that spread globally. For this purpose, replication profiles of SARS-CoV-2 were analyzed in human respiratory organoids. All tested viruses, including Omicron variants, replicated efficiently in these organoids. Notably, all SARS-CoV-2 strains retained replication ability in TMPRSS2-gene knockout (KO) respiratory organoids, suggesting that TMPRSS2 is not essential for SARS-CoV-2 infection in human respiratory tissues. However, TMPRSS2-gene knockout significantly reduces the inhibitory effect of nafamostat, indicating the advantage of TMPRSS2-utilizing ability for the SARS-CoV-2 infection in these organoids. Interestingly, Omicron variants regained the TMPRSS2-utilizing ability in recent subvariants. The basal infectivity would be supported mainly by cathepsins because the cathepsin inhibitor, EST, showed a significant inhibitory effect on infection with any SARS-CoV-2 strains, mainly when used with nafamostat. A supplementary contribution of other serine proteases was also suggested because the infection of the Delta variant was still inhibited partially by nafamostat in TMPRSS2 KO organoids. Thus, various proteases, including TMPRSS2, other serine proteases, and cathepsins, co-operatively contribute to SARS-CoV-2 infection significantly in the respiratory organoids. Thus, SARS-CoV-2 infection in the human respiratory tissues would be more complex than observed in cell lines or mice.

IMPORTANCE

We explored how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infects human respiratory organoids, which are a cultured cell model made to mimic the physiological conditions of the human airways. We focused on understanding the role of different proteases of host cells in activating the virus spike proteins. Specifically, we looked at TMPRSS2, a transmembrane serine protease, and cathepsin L, a lysosomal enzyme, which helps the virus enter cells by cutting the viral spike protein. We discovered that while TMPRSS2 is crucial for the virus in certain cells and animal models, other proteases, including cathepsins and various serine proteases, also play significant roles in the SARS-CoV-2 infection of human respiratory organoids. We suggest that SARS-CoV-2 uses a more complex mechanism involving multiple proteases to infect human airways, differing from what we see in conventional cell lines or animal models. This complexity might help explain how different variants can spread and infect people effectively.

Combined mutations in nonstructural protein 14, envelope, and membrane proteins mitigate the neuropathogenicity of SARS-CoV-2 Omicron BA.1 in K18-hACE2 mice

We previously reported that mutations outside the spike protein play a role in the attenuation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 variant in human ACE2 transgenic mice (K18-hACE2). Here, we assessed the pathogenicity of SARS-CoV-2 (WA1/2020) containing mutations from the Omicron BA.1 variant in K18-hACE2 mice. At an infection dose of 104 plaque-forming units (PFU), WA1 virus carrying Omicron BA.1 Nsp14(I42V), E(T9I), M(D3G/Q19E/A63T), but not Nsp6(Δ105-107, I189V), substitutions showed significant reduction in lethality. Interestingly, reduction of viral load is more pronounced in the brains than in the lungs. Subsequent analyses suggest that BA.1 E(T9I) and M(D3G/Q19E/A63T) substitutions result in less efficient packaging of virus-like particles. Given that Nsp14(I42V), E(T9I), M(Q19E/A63T) are well preserved in subsequent omicron subvariants, including currently circulating variants, our findings highlight the importance of understanding how non-spike mutations affect the pathogenicity of SARS-CoV-2 variants.

IMPORTANCE

Inoculation of transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) with SARS-CoV-2 often leads to a fatal brain infection. Omicron BA.1 variant, however, was found to be non-lethal in this model. Here, we systematically assessed the effect of individual mutations of Omicron BA.1 on the pathogenicity of the virus in hACE2 transgenic mice and found that combination of 5 mutations of Nsp14, E, and M of BA.1 variant significantly lowered brain viral load and reduced lethality. These results provide new insights into how SARS-CoV-2 Omicron BA.1 is attenuated.

Recombinant XBB.1.5 boosters induce robust neutralization against KP.2- and KP.3-included JN.1 sublineages

The newly emerged variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) demonstrate resistance to present therapeutic antibodies as well as the capability to evade vaccination-elicited antibodies. JN.1 sublineages were demonstrated as one of the most immune-evasive variants, showing higher neutralization resistance compared to XBB.1.5. In this study, serum samples were collected from adult participants including those who had gone through the BA.5/BF.7, EG.5/HK.3 and XBB/JN.1 infection waves, characterized by different infection and vaccination histories. We evaluated the neutralization in these serum samples against pseudoviruses of Omicron lineages. We further investigated humoral immune response of recombinant XBB vaccines against Omicron variants and estimated the neutralization resistance of JN.1 sublineages, including KP.2 and KP.3. Our results showed that sera from previous circulating Omicron subvariant breakthrough infections exhibited low neutralization against pseudoviruses of Omicron lineages. The GMTs of 50% neutralization against all tested pseudoviruses were significantly elevated in sera from individuals who received WSK-V102C or WSK-V102D boosters. Importantly, the GMTs of 50% neutralization in serum samples from individuals 4 months after a WSK-V102D booster against XBB.1.5, JN.1, JN.1.13, KP.2 and KP.3 pseudoviruses were 3479, 1684, 1397, 1247 and 1298, with 9.86-, 9.79-, 8.73-, 8.66- and 8.16-fold increase compared to those without booster, respectively, indicating that boosting with XBB.1.5 subunit vaccines still induced strong antibody responses against JN.1 sublineages. However, JN.1 sublineages, including KP.2 and KP.3, revealed more than 2-fold decreases in neutralizing antibody titers compared to XBB.1.5, suggesting significantly enhanced neutralization evasion and the necessity of boosters based on JN.1, KP.2 or KP.3.

Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology

The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion of pre-existing immunity and decreased disease severity. Continuous evolution within the Omicron lineage raised concerns of potential increased transmissibility and/or disease severity. To address this, we evaluate the fitness and pathogenesis of contemporary Omicron variants XBB.1.5, XBB.1.16, EG.5.1, and JN.1 in the upper (URT) and lower respiratory tract (LRT). We compare in vivo infection in Syrian hamsters with infection in primary human nasal and lung epithelium cells and assess differences in transmissibility, antigenicity, and innate immune activation. Omicron variants replicate efficiently in the URT but display limited pathology in the lungs compared to previous variants and fail to replicate in human lung organoids. JN.1 is attenuated in both URT and LRT compared to other Omicron variants and fails to transmit in the male hamster model. Our data demonstrate that Omicron lineage evolution has favored increased fitness in the URT.

Binding ability of Delta and Omicron towards the angiotensin-converting enzyme 2 receptor and antibodies: a computational study

The COVID-19 pandemic posed a threat to global society. Delta and Omicron are concerning variants due to the risk of increasing human-to-human transmissibility and immune evasion. This study aims to evaluate the binding ability of these variants toward the angiotensin-converting enzyme 2 receptor and antibodies using a computational approach. The receptor-binding domain (RBD) of the two variants was created by CHARMM-GUI and then docked to the hACE2 receptor and two antibodies (REGN10933 and REGN10987). These complexes were also subjected to molecular dynamics simulation within 100 ns. As a result, the two variants, Omicron and Delta, exhibited stronger interaction with the hACE2 receptor than the wild type. The mutations in the RBD region also facilitated the virus's escape from antibody neutralization.

Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic

SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform. Here we generated a panel of recombinant viruses carrying different spike proteins from 27 variants circulating between 2020 and 2024 in the same genomic background. We then assessed several of their phenotypic traits both in vitro and in vivo. We found distinct phenotypic trajectories of spike among and between variants circulating before and after the emergence of Omicron variants. Spike of post-Omicron variants maintained enhanced tropism for the nasal epithelium and large airways but displayed, over time, several phenotypic traits typical of the pre-Omicron variants. Hence, spike with phenotypic features of both pre- and post-Omicron variants may continue to emerge in the future.

Facility wastewater monitoring as an effective tool for pandemic infection control: An experience in COVID-19 pandemic with long-term monitoring

INTRODUCTION

Since the first report of a novel coronavirus infection caused by SARS-CoV-2 in late 2019, the infection has spread rapidly and had a significant impact on our lives. In the early stages of the COVID-19 pandemic, there was no adequate testing system in place, despite an urgent need for infection control measures in student dormitories.

METHODS

We have been monitoring SARS-CoV-2 in wastewater as part of our infection control efforts in the university facilities since fall 2020. In the four dormitories, absorbent cotton was placed in the drains that the facility wastewater passed through, and samples were collected twice a week and processed by RT-PCR for SARS-CoV-2. The dormitory residents were informed of the monitoring results the next morning.

RESULTS

The positivity of residents in the dormitories was highly consistent with the positivity of wastewater. Wastewater was positive in 89 % of cases before any residents were tested and found positive. Facility wastewater monitoring showed sensitivities of 80.4 % and specificities of 87.6 %. No traceable resident-to-resident transmission of infection within the facility was confirmed during the study period.

CONCLUSION

Sampling a single wastewater outlet in a building for SARS-CoV-2 PCR can effectively indicate the presence or absence of COVID-19 cases and be very useful for infection control of a facility. This simple and effective monitoring is applicable to future outbreaks of both emerging and re-emerging infectious diseases.

Comparison of viral load in the nasopharyngeal swabs of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in different epidemic seasons in Gunma prefecture, Japan

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has repeatedly undergone mutations since its emergence, based on which it has been assumed that there was a change in its characteristic, including virulence or antigenicity. In this study, we investigated the viral load in the nasopharyngeal samples of patients with SARS-CoV-2 in Gunma prefecture, Japan, from April 2, 2020, to April 1, 2023. The amount of virus in samples in the Omicron-variant-prevalent period was higher than that of strains detected in samples before week 50 of 2020, the B.1.1.284-prevalent period, the Alpha-variant-prevalent period, and the Delta-variant- prevalent period. Moreover, among Omicron variants, the sublineage BA.5-prevalent period showed higher amount of virus in the samples than BA.1-prevalent period and BA.2-prevalent period. Hence, the new variant may have been able to release more viruses into the nasopharyngeal samples during the process of repeated mutations, resulting in widespread infection. The amount of virus detected in the nasopharyngeal samples showed an increasing tendency with the evolution of the virus. Therefore, considering that the amount of virus in specimens is also vital factor contributing to the spread of infection, it is important to examine this factor in samples.

Berbamine prevents SARS-CoV-2 entry and transmission

Effective antiviral drugs are essential to combat COVID-19 and future pandemics. Although many compounds show antiviral in vitro activity, only a few retain effectiveness in vivo against SARS-CoV-2. Here, we show that berbamine (Berb) is effective against SARS-CoV, MER-CoV, SARS-CoV-2 and its variants, including the XBB.1.16 variant. In hACE2.Tg mice, Berb suppresses SARS-CoV-2 replication through two distinct mechanisms: inhibiting spike-mediated viral entry and enhancing antiviral gene expression during infection. The administration of Berb, in combination with remdesivir (RDV), clofazimine (Clof) and fangchinoline (Fcn), nearly eliminated viral load and promoted recovery from acute SARS-CoV-2 infection and its variants. Co-housed mice in direct contact with either pre-treated or untreated infected mice exhibited negligible viral loads, reduced lung pathology, and decreased viral shedding, suggesting that Berb may effectively hinder virus transmission. This broad-spectrum activity positions Berb as a promising preventive or therapeutic option against betacoronaviruses.

The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19

Objectives

Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection.

Methods

Mice were immunosuppressed using cyclophosphamide and infected with a B daughter lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed.

Results

Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of G>A and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs).

Conclusions

Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.

Detrimental Effects of Anti-Nucleocapsid Antibodies in SARS-CoV-2 Infection, Reinfection, and the Post-Acute Sequelae of COVID-19

Antibody-dependent enhancement (ADE) is a phenomenon in which antibodies enhance subsequent viral infections rather than preventing them. Sub-optimal levels of neutralizing antibodies in individuals infected with dengue virus are known to be associated with severe disease upon reinfection with a different dengue virus serotype. For Severe Acute Respiratory Syndrome Coronavirus type-2 infection, three types of ADE have been proposed: (1) Fc receptor-dependent ADE of infection in cells expressing Fc receptors, such as macrophages by anti-spike antibodies, (2) Fc receptor-independent ADE of infection in epithelial cells by anti-spike antibodies, and (3) Fc receptor-dependent ADE of cytokine production in cells expressing Fc receptors, such as macrophages by anti-nucleocapsid antibodies. This review focuses on the Fc receptor-dependent ADE of cytokine production induced by anti-nucleocapsid antibodies, examining its potential role in severe COVID-19 during reinfection and its contribution to the post-acute sequelae of COVID-19, i.e., prolonged symptoms lasting at least three months after the acute phase of the disease. We also discuss the protective effects of recently identified anti-spike antibodies that neutralize Omicron variants.

The Clinical Anatomy of SARS-CoV-2 Variants of Concern in Central Greece During October 2020-July 2022

The emergence of SARS-CoV-2 variants of concern (VOCs) during the COVID-19 pandemic necessitates investigation into their clinical differentiation and outcomes. This study aimed to examine these differences among VOCs, considering multiple related factors. An observational cohort study was conducted on patients diagnosed with SARS-CoV-2 infection via nasopharyngeal/oropharyngeal swab who visited the emergency department of a public Greek hospital between October 2020 and July 2022 during different VOC circulation in the region. Data on clinical manifestations, outcomes, and medical history (comorbidities, prior SARS-CoV-2 infection, vaccination status against COVID-19) were collected through a questionnaire and medical records for those hospitalized. A total of 913 patients were included in this study (813 adults ≥18 years old, 100 children <18 years old). Significant differences were observed across VOCs for both adults and children. A lower proportion of children developed symptoms during the non-Omicron variants, 73.5%, compared to Omicron variants, 86.4%. Fever, dyspnea, and taste and smell disorders were observed more frequently among non-Omicron adult cases, in contrast to upper respiratory symptoms, which were more common symptoms among Omicron infections. The non-Omicron variants were associated with higher rates of hospitalization at 30.6%, pneumonia at 23.0%, and death at 6.1% compared to Omicron variants at 8.0%, 5.0%, and 1.8%, respectively. Vaccination against COVID-19 was shown to be a protective factor for severe outcomes. Our findings suggest distinct clinical presentations and outcomes associated with different VOCs. Despite the fact that current VOCs circulating are less severe, the COVID-19 vaccine continues to play a protective role for severe cases.

Unraveling the impact of SARS-CoV-2 mutations on immunity: insights from innate immune recognition to antibody and T cell responses

Throughout the COVID-19 pandemic, the emergence of new viral variants has challenged public health efforts, often evading antibody responses generated by infections and vaccinations. This immune escape has led to waves of breakthrough infections, raising questions about the efficacy and durability of immune protection. Here we focus on the impact of SARS-CoV-2 Delta and Omicron spike mutations on ACE-2 receptor binding, protein stability, and immune response evasion. Delta and Omicron variants had 3-5 times higher binding affinities to ACE-2 than the ancestral strain (KDwt = 23.4 nM, KDDelta = 8.08 nM, KDBA.1 = 4.77 nM, KDBA.2 = 4.47 nM). The pattern recognition molecule mannose-binding lectin (MBL) has been shown to recognize the spike protein. Here we found that MBL binding remained largely unchanged across the variants, even after introducing mutations at single glycan sites. Although MBL binding decreased post-vaccination, it increased by 2.6-fold upon IgG depletion, suggesting a compensatory or redundant role in immune recognition. Notably, we identified two glycan sites (N717 and N801) as potentially essential for the structural integrity of the spike protein. We also evaluated the antibody and T cell responses. Neutralization by serum immunoglobulins was predominantly mediated by IgG rather than IgA and was markedly impaired against the Delta (5.8-fold decrease) and Omicron variants BA.1 (17.4-fold) and BA.2 (14.2-fold). T cell responses, initially conserved, waned rapidly within 3 months post-Omicron infection. Our data suggests that immune imprinting may have hindered antibody and T cell responses toward the variants. Overall, despite decreased antibody neutralization, MBL recognition and T cell responses were generally unaffected by the variants. These findings extend our understanding of the complex interplay between viral adaptation and immune response, underscoring the importance of considering MBL interactions, immune imprinting, and viral evolution dynamics in developing new vaccine and treatment strategies.

SARS-CoV-2 Nsp6-Omicron causes less damage to the Drosophila heart and mouse cardiomyocytes than ancestral Nsp6

A few years into the COVID-19 pandemic, the SARS-CoV-2 Omicron strain rapidly becomes and has remained the predominant strain. To date, Omicron and its subvariants, while more transmittable, appear to cause less severe disease than prior strains. To study the cause of this reduced pathogenicity we compare SARS-CoV-2 ancestral Nsp6 with Nsp6-Omicron, which we have previously identified as one of the most pathogenic viral proteins. Here, through ubiquitous expression in Drosophila, we show that ancestral Nsp6 causes both structural and functional damage to cardiac, muscular, and tracheal (lung) tissue, whereas Nsp6-Omicron has minimal effects. Moreover, we show that ancestral Nsp6 dysregulates the glycolysis pathway and disrupts mitochondrial function, whereas Nsp6-Omicron does not. Through validation in mouse primary cardiomyocytes, we find that Nsp6-induced dysregulated glycolysis underlies the cardiac dysfunction. Together, the results indicate that the amino acid changes in Omicron might hinder its interaction with host proteins thereby minimizing its pathogenicity.

Pathogenesis and virulence of coronavirus disease: Comparative pathology of animal models for COVID-19

Animal models that can replicate clinical and pathologic features of severe human coronavirus infections have been instrumental in the development of novel vaccines and therapeutics. The goal of this review is to summarize our current understanding of the pathogenesis of coronavirus disease 2019 (COVID-19) and the pathologic features that can be observed in several currently available animal models. Knowledge gained from studying these animal models of SARS-CoV-2 infection can help inform appropriate model selection for disease modelling as well as for vaccine and therapeutic developments.

A MULTICENTER, RANDOMIZED, OPEN-LABEL, PLACEBO-CONTROLLED CLINICAL TRIAL OF THE EFFECT OF CETYLPYRIDINIUM CHLORIDE (CPC) MOUTHWASH AND ON-DEMAND AQUEOUS CHLORINE DIOXIDE MOUTHWASH ON SARS-COV-2 VIRAL TITER IN PATIENTS WITH MILD COVID-19

OBJECTIVES

The established effect of cetylpyridinium chloride (CPC) mouthwash on SARS-CoV-2 viral titers is unclear. No clinical trial has examined the impact of on-demand aqueous chlorine dioxide mouthwash on SARS-CoV-2 viral titer.

METHODS

In this multicenter, 3-armed, randomized, open-label, placebo-controlled clinical trial involving mildly symptomatic COVID-19 patients, we randomly assigned them to receive 20 mL of 0.05% CPC, 10 mL of 0.01% on-demand aqueous chlorine dioxide, or 20 mL of purified water as a placebo mouthwash in a 1:1:1 ratio. The primary measurement was the SARS-CoV-2 viral titer in saliva, evaluated by a mixed-effects linear regression model.

RESULTS

49 patients received CPC mouthwash (n=16), on-demand aqueous chlorine dioxide mouthwash (n=16), and placebo (n=17) between January 14, 2024, and February 20, 2024. 0.05% CPC mouthwash significantly reduced salivary viral titer at 10 minutes postuse (-0.97 log10 PFU/mL; 95% CI, -1.64 to -0.30; P = .004), while no such effect was observed at 30 minutes (difference vs placebo, -0.26 log10 PFU/mL; 95% CI, -0.92 to 0.40; P = .435) or 60 minutes (difference vs. placebo, -0.05 log10 PFU/mL; 95% CI, -0.68 to 0.58; P = .877). 0.01% on-demand chlorine dioxide mouthwash did not reduce salivary viral titer at 10 minutes, 30 minutes, or 60 minutes compared to placebo.

CONCLUSIONS

10 minutes after using a 0.05% CPC mouthwash, the salivary viral titer of SARS-CoV-2 decreased compared to placebo. 0.01% on-demand aqueous chlorine dioxide mouthwash and placebo had no significant difference in SARS-CoV-2 viral titers.

TRIAL REGISTRATION

Japan Registry of Clinical Trials (jRCT): jRCTs031230566.

Assessment of Single-Cycle M-Protein Mutated Vesicular Stomatitis Virus as a Safe and Immunogenic Mucosal Vaccine Platform for SARS-CoV-2 Immunogen Delivery

The goal of the next-generation COVID-19 vaccine is to provide rapid respiratory tract protection with a single dose. Circulating antibodies do not protect the olfactory mucosa from viral infection, necessitating localized mucosal immunization. Live attenuated vesicular stomatitis virus (VSVMT)-based COVID-19 vaccines effectively stimulate mucosal immunity in animals, though safety concerns remain, particularly in immunocompromised populations. A viral vector capable of single-cycle replication may face less stringent regulatory requirements. A replication-defective VSVMT is developed with its G protein replaced by a SARS-CoV-2 spike protein (S) mutant, where residues K986 and V987 are substituted by prolines (S2P). This studies show that single-cycle VSVMT encoding Omicron subvariant S2P (VSVMT-S2P) is safe in both healthy and immunocompromised animals treated with cyclophosphamide (CP). Significant antibody and T-cell responses against the spike protein are observed in VSVMT-S2P vaccinated healthy animals. Intramuscular VSVMT-S2P administration induces neutralizing antibody responses comparable to those from replication-competent VSVMT-S. In immunocompromised animals, lower and delayed immune responses are observed. Thus, single-cycle M-protein mutated VSV offers a safe and effective platform for SARS-CoV-2 immunogen delivery. Remarkably, replication-competent VSVMT-S caused no pathogenicity and elicited potent mucosal immunity via intranasal administration, highlighting its potential as a mucosal COVID-19 vaccine.

Efficacy and safety of early administration of remdesivir in hemodialysis patients with COVID-19: A case report and literature review

RATIONALE

Although the mortality of severe coronavirus disease 2019 (COVID-19) has decreased after the emergence of the Omicron variant, it remains high in patients on hemodialysis (HD). Remdesivir (RDV) is considered as the first line drug for hospitalized COVID-19 patients, however the evidence regarding the usage in HD patients is lacking because clinical trials of RDV have excluded HD patients for safety reasons. Thus, accumulation of knowledge on the regimen, efficacy, and tolerability of RDV in HD patients is important.

PATIENT CONCERNS

A nosocomial COVID-19 cluster was occurred from August 31 to October 12 in 2021 when the Delta variant was predominant. During the cluster, 11 health-care workers and 20 inpatients including 7 HD patients were infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

DIAGNOSES

The diagnosis of COVID-19 was confirmed by the real-time polymerase chain reaction (PCR) for SARS-CoV-2.

INTERVENTIONS

RDV was initiated within 16 hours after the onset of fever (≥ 37.4°C) or positive PCR result in all HD patients, and continued at 100 mg/day intravenously once daily for either consecutive 5 or 10 days.

OUTCOMES

All patients fully recovered within 2 weeks and did not develop severe COVID-19. Two patients experienced mild liver dysfunction, but it was temporary and remitted spontaneously even continuing RDV treatment. Discontinuation of RDV therapy due to adverse events was not required in any patients.

LESSONS

Present cases indicated early intervention with RDV may contribute the favorable outcome and daily administration of RDV for up to 10 days was well tolerated even in HD patients. Literature review showed no previous article reported the efficacy and safety of such earlier and longer administration of remdesivir as in the present cases, therefore this report is informative for clinicians to consider the usage of RDV in HD patients.

Genomic Diversity and Evolution of Identified SARS-CoV-2 Variants in Iraq

The COVID-19 pandemic caused by the SARS-CoV-2 virus continues to circulate worldwide, causing the deaths of millions of people. The continuous circulation of the virus, its genetic diversity, the emergence of new variants with increased transmissibility, and/or the capacity of the virus to escape from the immune system constitute a major public health concern. In our study, we aimed to characterize SARS-CoV-2 strains in Iraq from the first introduction until the end of 2023, and to identify their variants, lineages, clades, and mutation patterns. All published Iraqi full genome sequences (2020-2023) were obtained from Global Initiative on Sharing All Influenza Data (GISAID) and subjected to molecular characterization along with 19 samples of full genome sequences that were collected during the fifth and sixth waves of the SARS-CoV-2 pandemic in this study. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences. Three established global platforms, GISAID, Nextstrain, and PANGO, were used for the classification of isolates into distinct clades, variants, and lineages. Six wave peaks of COVID-19 cases have been identified in Iraq, resulting in approximately 2,400,000 cumulative confirmed cases and more than 25,000 deaths. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the pandemic waves in the country.

A Comparative Study of Clinical Characteristics and COVID-19 Vaccine Effectiveness Against SARS-CoV-2 Variants: Wild-Type, Alpha, Delta, and Omicron in Beijing, China

Background

To compare the clinical characteristics of symptoms and laboratory findings across SARS-CoV-2 variants (Wild-type, Alpha, Delta, Omicron) and assess the effectiveness of COVID-19 vaccines in preventing symptoms and laboratory abnormalities.

Methods

We conducted a retrospective cohort study of individuals with SARS-CoV-2 infection at Beijing Ditan Hospital, Capital Medical University. Patients were grouped by the SARS-CoV-2 variant (Wild-type, Alpha, Delta, Omicron) based on whole-genome sequencing. Thirteen symptoms and 22 laboratory indices were compared across variants, and Omicron patients were further analyzed by vaccination status with generalized estimating equations (GEE) model.

Results

One thousand four hundred and thirteen participants were included for the analysis as following: Wild-type group (N=322), Alpha group (N=67), Delta group (N=98), and Omicron group (N=926). Omicron patients showed the highest proportion (30.1%) of respiratory symptoms across groups. Patients displayed normal laboratory manifestation, except for inflammatory markers, coagulation function index and glucose. Meanwhile, the Omicron variant was featured by higher inflammatory biomarkers (serum amyloid A protein [SAA] and C-reactive protein [CRP]). In addition, Omicron patients with three or more vaccine doses had fewer symptoms and higher values of SAA and CRP compared to those with fewer than three doses. Results of GEE showed, when compared with ≤ 1 vaccine dose, red blood cell count, white blood cell count, neutrophil count, platelet count, haemoglobin, and C-reactive protein in patients with ≥ 3 doses of vaccine significantly increased; while aspartic transaminase, creatine kinase, blood urea nitrogen, activated partial thromboplastin time, prothrombin time and thrombin time dramatically decreased, respectively.

Conclusion

Omicron variant resulted in abnormal inflammatory response. Individuals with three or more vaccine doses are more likely to experience fewer symptoms and have stronger protection against the virus. This study highlights key differences in symptom onset and laboratory profiles across SARS-CoV-2 variants, reinforcing the importance of three vaccine doses in providing strong protection against the Omicron variant.

Animal models of Long Covid: A hit-and-run disease

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2) pandemic has caused more than 7 million deaths globally. Despite the presence of infection- and vaccine-induced immunity, SARS-CoV-2 infections remain a major global health concern because of the emergence of SARS-CoV-2 variants that can cause severe acute coronavirus disease 2019 (COVID-19) or enhance Long Covid disease phenotypes. About 5 to 10% of SARS-CoV-2-infected individuals develop Long Covid, which, similar to acute COVID 19, often affects the lung. However, Long Covid can also affect other peripheral organs, especially the brain. The causal relationships between acute disease phenotypes, long-term symptoms, and involvement of multiple organ systems remain elusive, and animal model systems mimicking both acute and post-acute phases are imperative. Here, we review the current state of Long Covid animal models, including current and possible future applications.

COVID-19 Outcomes Among Hematopoietic Cell Transplant and Chimeric Antigen Receptor T-Cell Recipients in the Era of SARS-CoV-2 Omicron Variants and COVID-19 Therapeutics

Recipients of cellular therapies, including hematopoietic cell transplant (HCT) and chimeric antigen receptor T-cell (CART) therapy, are at risk for poor outcomes from coronavirus disease 2019 (COVID-19). There are limited data describing outcomes among patients in the pre- and early post-cellular therapy period during the Omicron era when multiple antiviral therapeutics were widely available. The objective of this study is to describe COVID-19 treatment and outcomes in patients diagnosed with COVID-19 during the pre- or early post-cellular therapy period. This is a single-center retrospective cohort study of adult HCT and CART recipients diagnosed with COVID-19 in the pre- and early post-cellular therapy period who tested positive for COVID-19 at our cancer center between January 1, 2022 and March 1, 2023. Primary outcomes were 30-day COVID-19-related hospitalization and death. A secondary outcome was development of persistent COVID-19, defined by a positive SARS-CoV-2 polymerase chain reaction (PCR) 31 to 90 days after COVID-19 diagnosis. Among 65 patients included, 52 (80%) received at least one COVID-19 therapeutic. The most common treatment after initial COVID-19 diagnosis was nirmatrelvir/ritonavir (29%), followed by monoclonal antibody therapy (26%) and remdesivir (11%). Of the 64 patients with at least 30 days of follow-up, 8 (12%) had at least one COVID-19-related hospitalization and one patient died, though cause of death was not due to COVID-19. Of the 8 patients hospitalized for COVID-19, one had severe disease and 7 had mild or moderate infection. Persistent COVID-19 was observed in 13/65 (20%) patients, with 4 patients requiring additional antiviral therapy. Three pre-cellular therapy patients had delays in receiving cellular therapy due to persistent COVID-19. During the Omicron era, rates of 30-day COVID-19-related hospitalization and death were relatively low in this cohort of pre- and early post-HCT and CART recipients, the majority of whom received treatment with at least one antiviral agent. Persistent COVID-19 occurred in 1 in 5 patients in the peri-cellular therapy period and led to cellular therapy treatment delays in several patients, highlighting the need for new COVID-19 treatment strategies.

Clinical characteristics and prognosis of SARS-CoV-2 infection in children with hematological malignancies: A multicenter, retrospective study in China

BACKGROUND

Data on SARSCoV-2 infection in children with hematological malignancies (HM) are limited. Here, we describe the clinical features of children with HM after SARS-CoV-2 infection and investigate the potential risk factors for disease severity.

METHODS

Children with HM and SARS-CoV-2 infection from five hospitals in five cities in Henan, China from October 2022 to January 2023 were retrospectively included. Clinical information and Coronavirus disease 2019 (COVID-19) vaccination status were collected for further analyses.

RESULTS

A total of 285 children with HM and SARS-CoV-2 infections were included. COVID-19 was asymptomatic in 3.2% of the patients (n = 9), mild in 89.1% (n = 254), moderate in 5.3% (n = 15), severe in 1.8% (n = 5), and critical in 0.7% (n = 2). Fever (92.4%) and cough (56.9%) were the most common symptoms. Most (249, 88.3%) children were managed at home during their COVID-19 illness. Of the 36 children admitted to the hospital, two required intensive care unit care, 11 required supplementary oxygen, and two non-invasive ventilation. A total of 283 (99.3%) children fully recovered and two (0.7%) died due to COVID-19. Significant risk factors for increased severity of infection in multivariable analyses were the presence of comorbidity (OR, 10.4; 95%CI, 2.8-38.7; p < 0.0001), neutropenia (OR, 10.4; 95%CI, 2.6-41.8; p = 0.001), and lymphopenia (OR, 4.2; 95%CI, 1.2-15.4; p = 0.029). A total of 30.9% (88/285) of the children received at least one dose of the inactivated COVID-19 vaccine at COVID-19 diagnosis. Compared with children who received at least one dose of the COVID-19 vaccine, fever was significantly more common in unvaccinated children (79.3% vs. 93.8%, p < 0.001).

CONCLUSIONS

Children with HM are not at an increased risk of severe COVID-19 compared to the general pediatric population. However, comorbidities such as lymphopenia and neutropenia may increase the risk of developing moderate or severe/critical disease. Our data may help in management decisions for this vulnerable population.

Comparative Analysis of Host Cell Entry Efficiency and Neutralization Sensitivity of Emerging SARS-CoV-2 Lineages KP.2, KP.2.3, KP.3, and LB.1

New SARS-CoV-2 lineages continue to evolve and may exhibit new characteristics regarding host cell entry efficiency and potential for antibody evasion. Here, employing pseudotyped particles, we compared the host cell entry efficiency, ACE2 receptor usage, and sensitivity to antibody-mediated neutralization of four emerging SARS-CoV-2 lineages, KP.2, KP.2.3, KP.3, and LB.1. The XBB.1.5 and JN.1 lineages served as controls. Our findings reveal that KP.2, KP.2.3, KP.3, and LB.1 lineages enter host cells efficiently and in an ACE2-dependent manner, and that KP.3 is more adept at entering Calu-3 lung cells than JN.1. However, the variants differed in their capacity to employ ACE2 orthologues from animal species for entry, suggesting differences in ACE2 interactions. Moreover, we demonstrate that only two out of seven therapeutic monoclonal antibody (mAbs) in preclinical development retain robust neutralizing activity against the emerging JN.1 sublineages tested, while three mAbs displayed strongly reduced neutralizing activity and two mAbs lacked neutralizing activity against any of the lineages tested. Furthermore, our results show that KP.2, KP.2.3, KP.3, and LB.1 lineages evade neutralization by antibodies induced by infection or vaccination with greater efficiency than JN.1, particularly in individuals without hybrid immunity. This study indicates that KP.2, KP.2.3, KP.3, and LB.1 differ in ACE2 interactions and the efficiency of lung cell entry and suggest that evasion of neutralizing antibodies drove the emergence of these variants.

Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants

Due to the incessant emergence of various SARS-CoV-2 variants with enhanced fitness in the human population, controlling the COVID-19 pandemic has been challenging. Understanding how the virus enhances its fitness during a pandemic could offer valuable insights for more effective control of viral epidemics. In this manuscript, we review the evolution of SARS-CoV-2 from early 2022 to the end of 2023-from Omicron BA.2 to XBB descendants. Focusing on viral evolution during this period, we provide concrete examples that SARS-CoV-2 has increased its fitness by enhancing several functions of the spike (S) protein, including its binding affinity to the ACE2 receptor and its ability to evade humoral immunity. Furthermore, we explore how specific mutations modify these functions of the S protein through structural alterations. This review provides evolutionary, molecular, and structural insights into how SARS-CoV-2 has increased its fitness and repeatedly caused epidemic surges during the pandemic.

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1

Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization.

Virological characteristics of SARS-CoV-2 Omicron BA.5.2.48

With the prevalence of sequentially-emerged sublineages including BA.1, BA.2 and BA.5, SARS-CoV-2 Omicron infection has transformed into a regional epidemic disease. As a sublineage of BA.5, the BA.5.2.48 outbroke and evolved into multi-subvariants in China without clearly established virological characteristics. Here, we evaluated the virological characteristics of two isolates of the prevalent BA.5.2.48 subvariant, DY.2 and DY.1.1 (a subvariant of DY.1). Compared to the normal BA.5 spike, the double-mutated DY.1.1 spike demonstrates efficient cleavage, reduced fusogenicity and higher hACE2 binding affinity. BA.5.2.48 demonstrated enhanced airborne transmission capacity than BA.2 in hamsters. The pathogenicity of BA.5.2.48 is greater than BA.2, as revealed in Omicron-lethal H11-K18-hACE2 rodents. In both naïve and convalescent hamsters, DY.1.1 shows stronger fitness than DY.2 in hamster turbinates. Thus regional outbreaking of BA.5.2.48 promotes the multidirectional evolution of its subvariants, gaining either enhanced pathogenicity or a fitness in upper airways which is associated with higher transmission.

Developing a Coccidioides posadasii and SARS-CoV-2 Co-infection Model in the K18-hACE2 Transgenic Mouse

BACKGROUND

Early reports showed that patients with COVID-19 had recrudescence of previously resolved coccidioidomycosis (Valley fever, VF), and there were indications that coinfection had more severe outcomes. We therefore investigated serial infection of Coccidioides posadasii and SARS-CoV-2 in a K18-hACE2 mouse model to assess disease outcomes.

METHODS

In our model, we challenged K18-hACE2 mice sequentially with a sub-lethal dose of SARS-CoV-2 and 24 hours later with low virulence strain of Coccidioides posadasii, and vice versa, compared to mice that only received a single infection challenge. We performed survival and pathogenesis mouse studies as well as looked at the systemic immune response differences between treatment groups.

RESULTS

Here we show that co-infected groups have a more severe disease progression as well as a decrease in survival. Importantly, results differ depending on the SARS-CoV-2 variant (WA-1, Delta, or Omicron) and infection timing (SARS-CoV-2 first, C. posadasii second or vice versa). We find that groups that are infected with the virus first had a decrease in survival, increased morbidity and weight loss, increased fungal and viral burdens, differences in immune responses, and the amount and size of fungal spherules. We also find that groups coinfected with C. posadasii first have a decrease fungal burden and inflammatory responses.

CONCLUSIONS

This is the first in vivo model investigation of a coinfection of SARS-CoV-2 and Coccidioides. Because of the potential for increased severity of disease in a coinfection, we suggest populations that live in areas of high coccidioidomycosis endemicity may experience higher incidence of complicated disease progression with COVID-19.