Two Years into the COVID-19 Pandemic: Lessons Learned

Cost-effective 3D lung tissue spheroid as a model for SARS-CoV-2 infection and drug screening

BACKGROUND

The SARS-CoV-2 pandemic has spurred an unparalleled scientific endeavor to elucidate the virus' structure, infection mechanisms, and pathogenesis. Two-dimensional culture systems have been instrumental in shedding light on numerous aspects of COVID-19. However, these in vitro systems lack the physiological complexity to comprehend the infection process and explore treatment options. Three-dimensional (3D) models have been proposed to fill the gap between 2D cultures and in vivo studies. Specifically, spheroids, composed of lung cell types, have been suggested for studying SARS-CoV-2 infection and serving as a drug screening platform.

METHODS

3D lung spheroids were prepared by coculturing human alveolar or bronchial epithelial cells with human lung stromal cells. The morphology, size, and ultrastructure of spheroids before and after SARS-CoV-2 infection were analyzed using optical and electron microscopy. Immunohistochemistry was used to detect spike protein and, thus, the virus presence in the spheroids. Multiplex analysis elucidated the cytokine release after virus infection.

RESULTS

The spheroids were stable and kept their size and morphology after SARS-CoV-2 infection despite the presence of multivesicular bodies, endoplasmic reticulum rearrangement, tubular compartment-enclosed vesicles, and the accumulation of viral particles. The spheroid responded to the infection releasing IL-6 and IL-8 cytokines.

CONCLUSION

This study demonstrates that coculture spheroids of epithelial and stromal cells can serve as a cost-effective infection model for the SARS-CoV-2 virus. We suggest using this 3D spheroid as a drug screening platform to explore new treatments related to the cytokines released during virus infection, especially for long COVID treatment.

Development and field validation of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for the rapid detection of chikungunya virus in patient and mosquito samples

OBJECTIVES

We aimed to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) platform for the rapid detection of chikungunya virus (CHIKV) in both patient and mosquito samples from Brazil.

METHODS

We optimized an RT-LAMP assay and then evaluated the specificity and sensitivity using visual detection. In comparison with the RT-qPCR reference method, we validated the utility of this assay as a molecular diagnostic test in a reference laboratory for arbovirus diagnostics using 100 serum samples collected from suspected CHIKV cases.

RESULTS

Our RT-LAMP assay specifically detected CHIKV without cross-reactivity against other arboviruses. The limit of detection of our RT-LAMP was estimated in -1.18 PFU (confidence interval [CI] ranging from -2.08 to 0.45), resulting in a similar analytical sensitivity when directly compared with the reference standard RT-qPCR assay. Then, we demonstrate the ability of our RT-LAMP assay to detect the virus in different human specimens (serum, urine, and saliva), and crude lysate of Aedes aegypti mosquitoes in as little as 20-30 minutes and without a separate RNA isolation step. Lastly, we showed that our RT-LAMP assay could be lyophilized and reactivated by adding water, indicating potential for room-temperature storage. Our RT-LAMP had a clinical sensitivity of 100% (95% CI, 90.97-100.00%), clinical specificity of 96.72% (95% CI, 88.65-99.60%), and overall accuracy of 98.00% (95% CI, 92.96-99.76%).

DISCUSSION

Taken together, these findings indicate that the RT-LAMP assay reported here solves important practical drawbacks to the deployment of molecular diagnostics in the field and can be used to improve testing capacity, particularly in low- and middle-income countries.

Clinical and laboratory diagnosis of Mayaro virus (MAYV): Current status and opportunities for further development

The recent outbreaks related to Mayaro virus (MAYV) infection in the Americas have brought this neglected virus as a potential threat to global public health. Given the range of symptoms that can be associated with MAYV infection, it can be challenging to diagnose individuals based on clinical signs, especially in countries with simultaneous circulation of other mosquito-borne viruses, such as dengue virus (DENV) and chikungunya virus (CHIKV). With this challenge in mind, laboratory-based diagnosis assumes a critical role in the introduction of measures to help prevent virus dissemination and to adequately treat patients. In this review, we provide an overview of the clinical features reported in infected patients and currently available laboratory tools that are used for MAYV diagnosis, discussing their advances, advantages, and limitations to apply in the field. Moreover, we explore novel point-of-care (PoC) diagnostic platforms that can provide de-centralised diagnostics for use in areas with limited laboratory infrastructure.

Structure determination needs to go viral

Viral diseases are expected to cause new epidemics in the future, therefore, it is essential to assess how viral diversity is represented in terms of deposited protein structures. Here, data were collected from the Protein Data Bank to screen the available structures of viruses of interest to WHO. Excluding SARS-CoV-2 and HIV-1, less than 50 structures were found per year, indicating a lack of diversity. Efforts to determine viral structures are needed to increase preparedness for future public health challenges.

ELMO CPAP: an innovative type of ventilatory support for COVID-19-related acute respiratory distress syndrome

OBJECTIVE

To assess whether the use of ELMO, a helmet for noninvasive ventilation created in Brazil, had a positive impact on the prognosis of patients with hypoxemic respiratory failure caused by severe COVID-19.

METHODS

This is a retrospective study of 50 critically ill COVID-19 patients. Epidemiological, clinical, and laboratory data were collected on ICU admission, as well as before, during, and after ELMO use. Patients were divided into two groups (success and failure) according to the outcome.

RESULTS

ELMO use improved oxygenation parameters such as Pao2, Fio2, and the Pao2/Fio2 ratio, and this contributed to a gradual reduction in Fio2, without an increase in CO2, as determined by arterial blood gas analysis. Patients in the success group had significantly longer survival (p < 0.001), as determined by the Kaplan-Meier analysis, less need for intubation (p < 0.001), fewer days of hospitalization, and a lower incidence of acute kidney injury in comparison with those in the failure group.

CONCLUSIONS

The significant improvement in oxygenation parameters, the longer survival, as reflected by the reduced need for intubation and by the mortality rate, and the absence of acute kidney injury suggest that the ELMO CPAP system is a promising tool for treating ARDS and similar clinical conditions.

Relationship of right ventricular functions with in-hospital and 1 year later mortality in patients hospitalized for COVID-19 pneumonia

BACKGROUND

The aim of this study was to determine the association of right ventricular function with in-hospital mortality and mortality 1 year after discharge in patients hospitalized for COVID-19 pneumonia.

METHODS

The study was conducted in Van Yuzuncu Yil University Faculty of Medicine hospital between February 10, 2021 and August 10, 2022. A total of 156 patients hospitalized in intensive care and wards due to COVID-19 pneumonia were included in this study. Echocardiography was performed in all patients.

RESULTS

Among the demographic findings of the patients included in the study, male gender, patients hospitalized in the intensive care unit (ICU), patients receiving O2 support, and smokers were found to have higher mortality rates during hospitalization. At the end of 1 year, the mortality rate was higher in patients who were hospitalized in the ICU received O2 support and had diabetes mellitus. Among echocardiographic findings, those with a low left ventricular ejection fraction had higher early and 1-year mortality rates. Of the right ventricular functions, low fractional area change, high systolic pulmonary artery pressure (SPAP), shortened pulmonary acceleration time, low right ventricle systolic wave S' velocity, increased right atrium area, and inferior vena cava diameter were found to be associated with high mortality. Increased right atrial area and inferior vena cava diameter, increased SPAP, and shortened pulmonary acceleration time were found to be significant in 1-year mortality. The presence of pericardial effusion was associated with mortality during hospitalization but not with 1-year mortality. B-type natriuretic peptide, D-dimer, and hemoglobin levels were significantly correlated with both hospital mortality and 1-year mortality.

CONCLUSIONS

In the follow-up of COVID-19 pneumonia, right ventricular function is considered to be an important factor in early and late mortality. It could be helpful to establish a follow-up program for discharged patients from the parameters involved in mortality.

After action review of the COVID-19 pandemic response in North West province, South Africa

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused coronavirus disease 2019 (COVID-19) pandemic with major disruptions globally. Northwest Province Department of Health (NWDoH) in South Africa set up comprehensive epidemiological emergency response plans for preventing, finding, containing and stopping the spread of COVID-19 in accordance with the National Disaster Management Act.

Objectives

This After-Action Report (AAR) describes the provincial response to the pandemic from September 2020 to October 2022.

Method

The AAR was conducted using the World Health Organization AAR methodology. Focus groups discussed five items: coordination, leadership and governance; epidemiology, surveillance and laboratory; case management and continuity of essential services; risk communication and community engagement and COVID-19 vaccination.

Results

The timely establishment and activation of provincial intergovernmental and intersectoral coordinating structures led to effective coordination, resource mobilisation, leadership, decision-making and intervention. The effective communication in the department and other stakeholders resulted in improved surveillance data quality, timelier response and increased ownership of data. Dissemination, training and implementation of case management protocols ensured standardised case management. The multi-channel information dissemination targeting different audiences empowered people with real-time knowledge on the infection and encouraged health-seeking behaviours.

Conclusion

The AAR demonstrated the importance of coordinated epidemiological, laboratory and communication response that requires significant public health reserve capacity in peacetime for rapid expansion in an emergency.

Contribution

This review contributes to the body of knowledge emerging from the COVID-19 pandemic and provides guidance on enhanced public health response to future emergencies.

LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens

PURPOSE AND METHODS

The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation.

RESULTS

LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database.

CONCLUSION

LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.

An Agentic Familiarity: The Context of HIV/AIDS and Sexual Orientation for Older Canadians during the COVID-19 Pandemic

This paper examines how experiences with a previous pandemic, particularly HIV/AIDS, may have informed approaches to COVID-19, with a focus on sexual orientation.

METHOD

The sample was drawn from an online survey of Canadians 55+ conducted in 2020, comprising 1143 persons (mean age = 67; 88 gay or bisexual (GB) men, 65 lesbian or bisexual (LB) women, 818 heterosexual women, and 172 heterosexual men). Respondents reported if they, or someone close to them, "had been affected by" one or more pandemics and whether COVID-19 led them to "think more about their prior epidemic/pandemic experiences" and/or feel they "couldn't handle it again". Correlated items reflecting feeling "they have been here before"; "prepared for what is happening"; and "like they needed to act or do something" formed a scale named "agentic familiarity".

RESULTS

About half of respondents reported thinking about their previous pandemic experience; about 5% reporting feeling like "they couldn't handle it again" with no gender or sexual orientation differences. Higher agentic familiarity scores were found for GB men and for those with experience with HIV/AIDS vs. other pandemics.

DISCUSSION

These outcomes speak to resilience and growth experienced by LGBT (and especially GB) persons through shared stigma and trauma-with implications for current pandemic experiences and future actions, like advance care planning.

Evaluating the Use of a Robot in a Hematological Intensive Care Unit: A Pilot Study

The aim of the SYRIACA project was to test the capability of a social robot to perform specific tasks in healthcare settings, reducing infection risks for patients and caregivers. The robot was piloted in an Intensive Hematological Unit, where the patients' and healthcare operators' acceptability of the robot was evaluated. The robot's functions, including logistics, surveillance, entertainment, and remote visits, were well accepted. Patients expressed interest in having multiple interactions with the robot, which testifies to its engaging potential and that it provides useful services. During remote visits, the robot reduced perceived stress among patients, alleviating feelings of isolation. The successful implementation of the robot suggests its potential to enhance safety and well-being in healthcare settings.

Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose lineages were either 'not classified' or were 'unclassifiable' indicated the virus could still be evolving.

COVID-19 lockdown effect on healthcare utilization and in-hospital mortality in children under 5 years in Cape Town, South Africa: a cross-sectional study

BACKGROUND

COVID-19 pandemic measures resulted in the de-escalation of non-COVID-19 healthcare provision.

METHODS

A retrospective cross-sectional study of routinely collected data was done to investigate the effect of COVID-19 policies on the healthcare utilization and mortality of children younger than 5 years in Eastern Cape Town, South Africa. We compared visits to primary and urgent care facilities, hospitalization, in-hospital deaths, and vaccine uptake from 1 January to 31 December 2020 to similar periods in 2018 and 2019.

RESULTS

During April and May 2020, the most restricted period, visits to primary care facilities declined from 126 049 in 2019 to 77 000 (1.8-fold; p < 0.05). This corresponded with a 1.2-fold reduction in the provision of the first dose of measles vaccine at 6 months compared to 2019. Throughout 2020 there was a 4-fold decline in the number of fully immunized children at 1 year of age (p = 0.84). Emergency room visits fell by 35.7% in 2020 (16 368) compared to 2019 (25 446). Hospital admissions decreased significantly (p < 0.01) in 2020 (9810) compared to 2018 (11 698) and 2019 (10 247). The in-hospital mortality rate increased from 2.3% (96/4163) in 2019 to 3.8% (95/2498) (p < 0.01) in Tygerberg Hospital, where 80% (95/119) of deaths were recorded. Twelve of the 119 (10%) deaths occurred in HIV-positive children (p = <0.01).

CONCLUSION

Measures instituted during the COVID-19 pandemic disrupted access to healthcare services for children. This resulted in an immediate, and potential future, indirect effect on child morbidity and mortality in Cape Town.

Coronavirus and co-infections: A Saudi Arabian perspective

Mortality due to infectious diseases continues to rise globally, despite advances in antimicrobial therapy and supportive care. This is evident with the occurrence of coronavirus disease 2019 (COVID-19) pandemic, instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Saudi Arabia, an eminent country within the Arab region, has had significant impact during global pandemics, concomitant with the fact that millions of Muslims travel to Saudi Arabia for pilgrimages every year. Herein, we discuss the significance of SARS-CoV-1, SARS-CoV-2, as well as the Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia with particular reference to global transmission and/or emergence of new variants due to genetic mixing of different strains. Furthermore, we also discuss the role of Saudi Arabia with reference to novel emerging infectious diseases and re-emerging infections, such as Ebola, zika, and monkeypox, as well as in the context on coinfections. Future strategies to limit the spread of viral infections and the pivotal role of Saudi Arabia, are deliberated upon.

Readmission rates and outcomes in adults with and without COVID-19 following inpatient chemotherapy admission: A nationwide analysis

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has received considerable attention in the scientific community due to its impact on healthcare systems and various diseases. However, little focus has been given to its effect on cancer treatment.

AIM

To determine the effect of COVID-19 pandemic on cancer patients' care.

METHODS

A retrospective review of a Nationwide Readmission Database (NRD) was conducted to analyze hospitalization patterns of patients receiving inpatient chemotherapy (IPCT) during the COVID-19 pandemic in 2020. Two cohorts were defined based on readmission within 30 d and 90 d. Demographic information, readmission rates, hospital-specific variables, length of hospital stay (LOS), and treatment costs were analyzed. Comorbidities were assessed using the Elixhauser comorbidity index. Multivariate Cox regression analysis was performed to identify independent predictors of readmission. Statistical analysis was conducted using Stata® Version 16 software. As the NRD data is anonymous and cannot be used to identify patients, institutional review board approval was not required for this study.

RESULTS

A total of 87755 hospitalizations for IPCT were identified during the pandemic. Among the 30-day index admission cohort, 55005 patients were included, with 32903 readmissions observed, resulting in a readmission rate of 59.8%. For the 90-day index admission cohort, 33142 patients were included, with 24503 readmissions observed, leading to a readmission rate of 73.93%. The most common causes of readmission included encounters with chemotherapy (66.7%), neutropenia (4.36%), and sepsis (3.3%). Comorbidities were significantly higher among readmitted hospitalizations compared to index hospitalizations in both readmission cohorts. The total cost of readmission for both cohorts amounted to 1193000000.00 dollars. Major predictors of 30-day readmission included peripheral vascular disorders [Hazard ratio (HR) = 1.09, P < 0.05], paralysis (HR = 1.26, P < 0.001), and human immunodeficiency virus/acquired immuno-deficiency syndrome (HR = 1.14, P = 0.03). Predictors of 90-day readmission included lymphoma (HR = 1.14, P < 0.01), paralysis (HR = 1.21, P = 0.02), and peripheral vascular disorders (HR = 1.15, P < 0.01).

CONCLUSION

The COVID-19 pandemic has significantly impacted the management of patients undergoing IPCT. These findings highlight the urgent need for a more strategic approach to the care of patients receiving IPCT during pandemics.

Rescinding evidence-based care and practices during the initial COVID-19 outbreak in the United States: a qualitative study of the experiences of lactation support providers

Background

The COVID-19 pandemic disrupted healthcare systems and services including along the childbearing continuum. The aim of this study was to explore the experiences and perceptions of professional lactation support providers who cared for breastfeeding families during the early months of the pandemic (March 2020 - August 2020) in the United States.

Design/methods

We conducted a qualitative survey among active lactation support providers in the United States. Eligible participants spoke English, were Certified Lactation Counselors who maintained an active certification and who provided lactation care and services prior to and after the onset of the COVID-19 pandemic. Participants were recruited via email from the national database of Certified Lactation Counselors obtained from the national certification body. All ten Health and Human Service regions of the United States were included. Demographic data was collected on each respondent. Qualitative survey responses were analyzed thematically following the framework method.

Findings

Six-hundred and seventy-four (674) Certified Lactation Counselors responded to the survey from June to July of 2022. Their responses fell within the overarching theme of rescinding evidence-based care and practices that had been in place prior to the pandemic. Affected care practices included the insertion of limits on access to care and insinuating stigma and bias based on COVID-19 status. Irregular appointment schedules and staffing shortages also affected care. Participants reported that separation of the mother and their infant became the norm. Decisions made by management seemed to be grounded in fear and uncertainty, rather than on the evidence-based principles that had been in place prior to the pandemic.

Conclusion

A lack of coordination, consistency and support, along with fear of the unknown, troubled lactation support providers and impacted their ability to provide evidence-based care and to maintain access to care for all families. The findings of the survey and analysis underscore the importance of adequately preparing for future public health crises by determining how evidence-based care and practices can be preserved in emergent situations.

Epidemiology of COVID-19 and the Utility of Cycle Threshold (Ct) Values in Predicting the Severity of Disease

OBJECTIVES

Advanced molecular diagnostic methods like real-time polymerase chain reaction (PCR) play a vital role in the early recognition of viral infections, including the coronavirus disease 2019 (COVID-19). Therefore, in the context of the recent COVID-19 pandemic, this study aimed to determine the correlation of cycle threshold (Ct) values with symptoms in COVID-19-positive patients.

MATERIALS AND METHODS

A retrospective study was conducted in a virus research diagnostic laboratory (VRDL) at a COVID-19-dedicated tertiary care hospital in South India. A total of 5563 COVID-19-positive patients were analyzed for symptom spectrum and duration of illness with Ct values of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

Around 80% (n= 4401) of the patients were symptomatic and the rest were asymptomatic. Among the symptomatic patients, fever (66%) was the most common symptom. About 44% of symptomatic patients had a low Ct value (Ct ≤ 24). There was a significant difference in symptoms among patients with low, medium, and high Ct values. In the subpopulation of symptomatic patients analyzed for the association of Ct value and duration of illness, the mean duration of illness was three days and almost 88% of the patients were tested within five days of onset of symptoms. It has been observed that a shorter duration of illness lowers the Ct values. A significant association was seen between the mean Ct value and days since symptom onset (p-value = 0.016).

CONCLUSION

Most of the symptomatic patients had lower Ct values in comparison to the asymptomatic patients. A significant association between low Ct values and the duration of symptoms observed in our study explains the viral dynamics, i.e., higher viral shedding at the onset of symptoms and declines thereafter.

Clinical and laboratory diagnosis of monkeypox (mpox): Current status and future directions

The emergence and rapid spread of the monkeypox virus (MPXV) to non-endemic countries has brought this once obscure pathogen to the forefront of global public health. Given the range of conditions that cause similar skin lesions, and because the clinical manifestation may often be atypical in the current mpox outbreak, it can be challenging to diagnose patients based on clinical signs and symptoms. With this perspective in mind, laboratory-based diagnosis assumes a critical role for the clinical management, along with the implementation of countermeasures. Here, we review the clinical features reported in mpox patients, the available laboratory tests for mpox diagnosis, and discuss the principles, advances, advantages, and drawbacks of each assay. We also highlight the diagnostic platforms with the potential to guide ongoing clinical response, particularly those that increase diagnostic capacity in low- and middle-income countries. With the outlook of this evolving research area, we hope to provide a resource to the community and inspire more research and the development of diagnostic alternatives with applications to this and future public health crises.

Mother-to-child transmission of SARS-CoV-2 infection in high-income countries: a systematic review and meta-analysis of prospective observational studies

Mother-to-child transmission of SARS-CoV-2 has been reported since the onset of the COVID-19 pandemic. We conducted a study to summarize evidence on the risk of mother-to-child transmission in the first 30 days after birth in high-income countries and to evaluate the association between preventive measures and the risk of infection for the neonate. A systematic review and meta-analysis were undertaken following PRISMA guidelines. The National Library of Medicine, Web of Science, and Excerpta Medica databases were screened on February 26, 2022. All prospective observational studies addressing the frequency of infection in infants born to mothers SARS-CoV-2 positive were included. Twenty-six studies were included, reporting data of 2653 mothers with SARS-CoV-2 and 2677 neonates. The proportion meta-analysis pointed out an overall estimate of SARS-CoV-2 infection among infants of 2.3% (95% CI: 1.4-3.2%). Data from studies with (1.4%, 95% CI: 0.8-2) and without (1.3%, 95% CI: 0.0-2.7%) rooming-in provided similar risk of infection. Adopting at least two prevention measures during rooming-in resulted in a rate of mother-to-child infection of 1.0% (95%CI: 0.3-1.7%). The results of this study show a low rate of perinatal infection, support the rooming-in and confirm the effectiveness of preventive measures in reducing the risk of mother-to-child viral transmission.

Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2

SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS-CoV-2 S. We identify that S813T mutation is sufficient in S2 interfering with the cleavage of SARS-CoV-2 S by TMPRSS2, reducing spike fusogenicity and pseudoparticle entry. Conversely, the mutation of T813S in SARS-CoV S increased fusion ability and viral replication. Our data suggested that residue 813 in the S was critical for the proteolytic activation, and the change from threonine to Serine at 813 position might be an evolutionary feature adopted by SARS-2-related viruses. This finding deepened the understanding of Spike fusogenicity and could provide a new perspective for exploring Sarbecovirus' evolution.

Influence of polymorphic variations of IFNL, HLA, and IL-6 genes in severe cases of COVID-19

The administration of vaccination doses to the global population has led to a decrease in the incidence of COVID-19. However, the clinical picture developed by infected individuals remains extremely concerning due to the great variability in the severity of cases even in vaccinated individuals. The clinical progression of the pathology is characterized by various influential factors such as sex, age group, comorbidities, and the genetics of the individual. The immune response to viral infections can be strongly influenced by the genetics of individuals; nucleotide variations called single-nucleotide polymorphisms (SNPs) in structures involved in the innate and adaptive immune response such as interferon (IFN)-λ, human leukocyte antigen (HLA), and interleukin (IL)-6 are frequently associated with pathological progression. In this study, we conducted a review of the main SNPs of these structures that are associated with severity in COVID-19. Searches were conducted on some platforms of the National Center for Biotechnology and Information (NCBI), and 102 studies were selected for full reading according to the inclusion criteria. IFNs showed a strong association with antiviral function, specifically, IFN-λ3 (IL-28B) demonstrated genetic variants commonly related to clinical progression in various pathologies. For COVID-19, rs12979860 and rs1298275 presented frequently described unfavorable genotypes for pathological conditions of hepatitis C and hepatocellular carcinoma. The high genetic variability of HLA was reported in the studies as a crucial factor relevant to the late immune response, mainly due to its ability to recognize antigens, with the HLA-B*46:01 SNP being associated with susceptibility to COVID-19. For IL-6, rs1554606 showed a strong relationship with the clinical progression of COVID-19. In addition, rs2069837 was identified with possible host protection relationships when linked to this infection.

A Comprehensive Sampling Study on SARS-CoV-2 Contamination of Air and Surfaces in a Large Meat Processing Plant Experiencing COVID-19 Clusters in June 2020

OBJECTIVE

We aimed to assess SARS-CoV-2 contamination of air and surfaces to gain insight into potential occupational exposure in a large meat processing plant experiencing COVID-19 clusters. Methods: Oro-nasopharyngeal SARS-CoV-2 screening was performed in 76 workers. Environmental samples ( n = 275) including air, ventilation systems, sewage, and swabs of high-touch surfaces and workers' hands were tested for SARS-CoV-2 RNA by real-time quantitative polymerase chain reaction. Results: Twenty-seven (35.5%) of the (predominantly asymptomatic) workers tested positive with modest to low viral loads (cycle threshold ≥ 29.7). Six of 203 surface swabs, 1 of 12 personal air samples, and one of four sewage samples tested positive; other samples tested negative. Conclusions: Although one third of workers tested positive, environmental contamination was limited. Widespread SARS-CoV-2 transmission via air and surfaces was considered unlikely within this plant at the time of investigation while strict COVID-19 control measures were already implemented.

Effect of surfactants on SARS-CoV-2: Molecular dynamics simulations

Surfactants are commonly used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. Here, we employ coarse grain (CG) and all-atom (AA) molecular dynamics simulations to investigate the interaction between general families of surfactants and the SARS-CoV-2 virus. To this end, we considered a CG model of a full virion. Overall, we found that surfactants have only a small impact on the virus envelope, being inserted into the envelope without dissolving it or generating pores, at the conditions considered here. However, we found that surfactants may induce a deep impact on the spike protein of the virus (responsible for its infectivity), easily covering it and inducing its collapse over the envelope surface of the virus. AA simulations confirmed that both negatively and positively charged surfactants are able to extensively adsorb over the spike protein and get inserted into the virus envelope. Our results suggest that the best strategy for the design of surfactants as virucidal agents will be to focus on those strongly interacting with the spike protein.

SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic

We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During the pandemic, we experienced several things, such as the virus and its pathogenesis, clinical manifestations, and treatments; emerging variants; different vaccines; and the vaccine development processes. This review describes how each vaccine has been developed and approved with the help of modern technology. We also discuss critical milestones during the vaccine development process. Several lessons were learned from different countries during the two years of vaccine research, development, clinical trials, and vaccination. The lessons learned during the vaccine development process will help to fight the next pandemic.

Food Plant Secondary Metabolites Antiviral Activity and Their Possible Roles in SARS-CoV-2 Treatment: An Overview

Natural products and plant extracts exhibit many biological activities, including that related to the defense mechanisms against parasites. Many studies have investigated the biological functions of secondary metabolites and reported evidence of antiviral activities. The pandemic emergencies have further increased the interest in finding antiviral agents, and efforts are oriented to investigate possible activities of secondary plant metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection. In this review, we performed a comprehensive analysis of studies through in silico and in vitro investigations, also including in vivo applications and clinical trials, to evaluate the state of knowledge on the antiviral activities of secondary metabolites against human viruses and their potential application in treating or preventing SARS-CoV-2 infection, with a particular focus on natural compounds present in food plants. Although some of the food plant secondary metabolites seem to be useful in the prevention and as a possible therapeutic management against SARS-CoV-2, up to now, no molecules can be used as a potential treatment for COVID-19; however, more research is needed.

Infliximab as a potential treatment for COVID-19

INTRODUCTION

As the third year of the SARS-CoV-2 pandemic approaches, COVID-19 continues to cause substantial morbidity and mortality due to waning vaccine efficacy and the emergence of new, highly contagious subvariants and better therapies are urgently needed.

AREAS COVERED

Hospitalized patients who develop hypoxia due to SARS-CoV-2 infection are typically treated with an antiviral agent, remdesivir, as well as an immunomodulator, dexamethasone, but mortality rates for severe COVID-19 remain unacceptably high. Mounting evidence suggests a second immunomodulator added to the standard of care may benefit some hospitalized patients; however, the optimal treatment remains controversial.

EXPERT OPINION

On 2 June 2022, the United States National Institutes of Health reported results from a large, randomized placebo-controlled clinical trial known as ACTIV-1. The study found a mortality benefit and substantially improved clinical status for adults hospitalized with COVID-19 who were treated with infliximab, a chimeric monoclonal antibody that binds to and inhibits TNF-α, and is widely used to treat a variety of autoimmune conditions, including rheumatoid arthritis, Crohn's disease, and ulcerative colitis. This manuscript reviews what is known about infliximab as an immunomodulator for patients with COVID-19 and explores how this agent may be used in the future to address the SARS-CoV-2 pandemic.

Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro

In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl₂•8H₂O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (M^Pro) and papain-like protease (PL^Pro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent M^Pro protein that surprisingly contains zinc^II (Zn^II) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 M^Pro inhibitors, is performed for the first time in this paper, to the best of our knowledge.

Maternal and infant outcomes in women with and without gestational diabetes mellitus in the COVID-19 era in China: Lessons learned

Aims

The global COVID-19 pandemic has required a drastic transformation of prenatal care services. Whether the reformulation of the antenatal care systems affects maternal and infant outcomes remains unknown. Particularly, women with gestational diabetes mellitus (GDM) are among those who bear the greatest brunt. Thus, this study aimed to evaluate the impact of COVID-19 lockdown during late pregnancy on maternal and infant outcomes in women stratified by the GDM status in China.

Study design

The participants were women who experienced the COVID-19 lockdown during late pregnancy (3185 in the 2020 cohort) or not (2540 in the 2019 cohort) that were derived from the Beijing Birth Cohort Study. Maternal metabolic indicators, neonatal outcomes, and infant anthropometrics at 12 months of age were compared between the two cohorts, stratified by the GDM status.

Results

Participants who experienced COVID-19 lockdown in late pregnancy showed lower gestational weight gain than those in the control cohort. Nevertheless, they displayed a worse metabolic profile. COVID-19 lockdown during pregnancy was associated with higher glycosylated hemoglobin (HbA1c) (β= 0.11, 95% CI = 0.05-0.16, q-value = 0.002) and lower high density lipoprotein cholesterol level (HDL-C) level (β=-0.09, 95% CI = -0.14 to -0.04, q-value = 0.004) in women with GDM, adjusted for potential confounders. In normoglycemic women, COVID-19 lockdown in late pregnancy was associated with higher fasting glucose level (β= 0.10, 95% CI = 0.08-0.12, q-value <0.0001), lower HDL-C level (β=-0.07, 95% CI = -0.08 to -0.04, q-value <0.0001), and increased risk of pregnancy-induced hypertension (adjusted OR=1.80, 95%CI=1.30-2.50, q-value=0.001). The fasting glucose level decreased less from early to late pregnancy in women who experienced COVID-19 lockdown than in the controls, regardless of the GDM status. The HDL-C has risen less with COVID-19 lockdown in the normoglycemic subgroup. In contrast, no significant differences regarding neonatal outcomes or infant weight were found between the two cohorts.

Conclusion

Experiencing the COVID-19 lockdown in pregnancy was associated with worse maternal metabolic status but similar neonatal outcomes and infant weight.

Use of traditional and complementary medicine for COVID 19 prophylaxis among healthcare professionals and students in Jordan: A cross-sectional study

INTRODUCTION

There is inadequate evidence to recommend the use of any traditional and complementary medicine (T&CM) methods such as vitamin, mineral, herbal or other dietary supplements to prevent or treat COVID 19. Members of the medical team are particularly at risk of exposure to high viral load of coronavirus. They have also the best access to professional information regarding disease treatment and prophylaxis and disseminate such knowledge. The aim of the study was to assess the prevalence of use of T&CM for the prophylaxis of COVID 19 among the healthcare professionals and students in Jordan, along with the most common types and the factors associated with T&CM use.

METHODOLOGY

A cross-sectional study of T&CM use was conducted in Jordan using a snowball sampling method to distribute Google Forms and to enrol participants during coronavirus outbreak between June 10, 2021, and August 28, 2021. The study included healthcare professionals or students who consented to participate in the survey. The survey excluded those participants who had filled the questionnaire at least once or were pregnant/breast-feeding at the time of the study. The questionnaire consisted of 29 items, including screening, checkbox, dichotomous, matrix and open-ended questions.

RESULTS

The response rate was 97.1%. Out of 560 study respondents, 359 (64.1%) reported using T&CM for COVID 19 prevention. Vitamins and nutrients were consumed by almost half (48.4%) of study participants, while nonpharmacological methods and herbal remedies were consumed by 35.2% and 25.2%, respectively. The most common source of information regarding T&CM use for COVID 19 prophylaxis included scientific publications (59.5%), followed by disease treatment guidelines (38.0%) and social media (32.3%). Adverse effects were reported by 8.5% and possible adverse effects were reported by another 8.5% of participants. The T&CM use was associated with working in contact with COVID 19 patients (OR: 1.625 (95% CI 1.047-2.523) (P = 0.03) and having a colleague as a source of information (OR: 1.720 (95% CI 1.026-2.883) (P = 0.04).

CONCLUSIONS

The prevalence of T&CM use for COVID 19 prevention among healthcare professionals and students in Jordan is high, with a significant proportion of participants reporting adverse effects. There is an urgent need for further research toward efficacy and safety of T&CM in COVID 19 prophylaxis as well as development of appropriate public health policy on this issue specific to each country.

Toward a Home Test for COVID 19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples

Nucleic acid-based detection of RNA viruses requires annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structure of folded viral RNA. In this study, we designed a protein enzymes-free nano-construction, names four-armed DNA machine (4DNM), that requires neither amplification stage nor high temperature annealing step for SARS-CoV-2 detection. It uses binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with total of four RNA-binding arms. Additional arms improved limit of detection at least 10 times. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.