On the road to ending the COVID-19 pandemic: Are we there yet?

Perspective vaccines for emerging viral diseases in farm animals

The world has watched the emergence of numerous animal viruses that may threaten animal health which were added to the perpetual growing list of animal pathogens. This emergence drew the attention of the experts and animal health groups to the fact that it has become necessary to work on vaccine development. The current review aims to explore the perspective vaccines for emerging viral diseases in farm animals. This aim was fulfilled by focusing on modern technologies as well as next generation vaccines that have been introduced in the field of vaccines, either in clinical developments pending approval, or have already come to light and have been applied to animals with acceptable results such as viral-vectored vaccines, virus-like particles, and messenger RNA-based platforms. Besides, it shed the light on the importance of differentiation of infected from vaccinated animals technology in eradication programs of emerging viral diseases. The new science of nanomaterials was explored to elucidate its role in vaccinology. Finally, the role of Bioinformatics or Vaccinomics and its assist in vaccine designing and developments were discussed. The reviewing of the published manuscripts concluded that the use of conventional vaccines is considered an out-of-date approach in eliminating emerging diseases. However, these types of vaccines are considered the suitable plan especially in countries with few resources and capabilities. Piloted vaccines that rely on genetic-based technologies with continuous analyses of current viruses should be the aim of future vaccinology. Smart genomics of emerging viruses will be the gateway to choosing appropriate vaccines, regardless of the evolutionary rates of viruses.

Prime-Pull Immunization of Mice with a BcfA-Adjuvanted Vaccine Elicits Sustained Mucosal Immunity That Prevents SARS-CoV-2 Infection and Pathology

Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. In this study, we demonstrate the efficacy of Bordetella colonization factor A (BcfA), a novel bacteria-derived protein adjuvant, in SARS-CoV-2 spike-based prime-pull immunizations. We show that i.m. priming of mice with an aluminum hydroxide- and BcfA-adjuvanted spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17-polarized CD4+ tissue-resident memory T cells and neutralizing Abs. Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 (MA10) and reduced viral replication in the respiratory tract. Histopathology showed a strong leukocyte and polymorphonuclear cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. Importantly, neutralizing Abs and tissue-resident memory T cells were maintained until 3 mo postbooster. Viral load in the nose of mice challenged with the MA10 virus at this time point was significantly reduced compared with naive challenged mice and mice immunized with an aluminum hydroxide-adjuvanted vaccine. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, provide sustained protection against SARS-CoV-2 infection.

Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2

The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.

The impact of the COVID-19 pandemic on a surgical PICU in China that did not admit COVID-19 patients

Background

The unprecedented COVID-19 pandemic has been spreading for a long time. However, it is unclear whether the pandemic influenced admission in a surgical pediatric intensive care unit (PICU) that never received COVID-19 patients during the early outbreak in China.

Methods

A retrospective study was conducted in a surgical PICU in a tertiary hospital in Chengdu, China. We sought to describe the trend in admission numbers from January 2018 to April 2021. We explored the impact of the COVID-19 outbreak on PICU admission characteristics by including all patients younger than 18 years admitted to the PICU between January 23 and April 8 in 2020 and those admitted in the same time periods in prepandemic years (2018 and 2019) and in 2021.

Results

The percentage of patients admitted to the PICU from the Chengdu region increased from 34.2 percent in 2019 to 40.4 percent in 2020, whereas that from other provinces decreased from 11.7 percent in 2019 to 5.8 percent in 2020 (P = 0.012). The median length of stay (LOS) in the PICU was significantly longer in the 2020 cohort (4.0 days) than in the 2019 cohort (2.0 days) (P < 0.001); the median hospital LOS was also significantly longer in the former (12.0 days) than in the latter (8.0 days) (P < 0.001). Hospital outcomes (P = 0.005) and primary diagnosis distributions (P = 0.025) between the 2020 and 2019 cohorts were both statistically significant.

Conclusions

In a surgical PICU that never received COVID-19 patients, the onset of the 2020 major outbreak was accompanied by changes in the composition of the regional sources of patients, longer PICU and hospital stays, increased proportions of unauthorized discharges, and changes in the distribution of primary diseases for admission. These findings have yet to be strengthened by additional studies involving similar healthcare backgrounds.

The Global Impact of COVID-19 on Craniomaxillofacial Surgeons: A Follow-Up Survey After One Year

Study Design

Comparative cross-sectional.

Objective

To measure the impact that COrona VIrus Disease-19 (COVID-19) has had on craniomaxillofacial (CMF) surgeons after 1 year and compare it with 2020 data by (1) measuring access to adequate personal protective equipment (PPE), (2) performance of elective surgery, and (3) the vaccination status. This should be investigated because most CMF surgeons felt that hospitals did not provide them with adequate PPE.

Methods

The investigators surveyed the international AO CMF membership using a 30-item online questionnaire and compared it to a previous study. The primary predictor variable was year of survey administration. Primary outcome variables were availability of adequate personal protective equipment (adequate/inadequate), performance of elective surgery (yes/no), and vaccination status (fully vaccinated/partly vaccinated/not vaccinated). Descriptive and analytic statistics were computed. Binary logistic regression models were created to measure the association between year and PPE availability. Statistical significance level was set at P < .05.

Results

The sample was composed of 523 surgeons (2% response rate). Most surgeons reported access to adequate PPE (74.6%). The most adequate PPE was offered in Europe (87.8%) with the least offered in Africa (45.5%). Surgeons in 2021 were more likely to report adequate PPE compared to 2020 (OR 3.74, 95% CI [2.59-4.39]). Most of the respondents resumed elective surgery (79.5% vs 13.3% in 2020) and were fully vaccinated (59.1%).

Conclusions

Most CMF surgeons now have access to adequate PPE, resumed elective surgery, and are either fully or partly vaccinated. Future studies should investigate the long-term impact of the fast-evolving COVID-19 pandemic on CMF surgeons.

Multimeric ACE2-IgM fusions as broadly active antivirals that potently neutralize SARS-CoV-2 variants

Coronavirus infections are a world-wide threat to human health. A promising strategy to develop a broadly active antiviral is the use of fusion proteins consisting of an antibody IgG Fc region and a human ACE2 domain to which the viral spike proteins bind. Here we create antiviral fusion proteins based on IgM scaffolds. The hexameric ACE2-IgM-Fc fusions can be efficiently produced in mammalian cells and they neutralize the infectious virus with picomolar affinity thus surpassing monomeric ACE2-IgM-Fc by up to 96-fold in potency. In addition, the ACE2-IgM fusion shows increased neutralization efficiency for the highly infectious SARS-CoV-2 omicron variant in comparison to prototypic SARS-CoV-2. Taken together, these multimeric IgM fusions proteins are a powerful weapon to fight coronavirus infections.

Body fat percentage is independently and inversely associated with serum antibody responses to SARS-CoV-2 mRNA vaccines

Vaccination is widely considered the most effective preventative strategy to protect against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. An individual's exercise habits, and physical fitness have been shown to impact the immune response following vaccination using traditional vaccine platforms, but their effects are not well characterized following administration of newer vaccination technology (mRNA vaccines). We investigated these effects on the magnitude of antibody responses following SARS-CoV-2 mRNA vaccination while accounting for known covariates (age, sex, time since vaccination, and the type of vaccine administered). Adults of varying fitness levels (18-65 years; N = 50) who had received either the Moderna or Pfizer SARS-CoV-2 mRNA vaccine between 2 weeks and 6 months prior, completed health history and physical activity questionnaires, had their blood drawn, body composition, cardiorespiratory fitness, and strength assessed. Multiple linear regressions assessed the effect of percent body fat, hand grip strength, cardiorespiratory fitness, and physical activity levels on the magnitude of receptor binding domain protein (RBD) and spike protein subunit 1 (S1) and 2 (S2) while accounting for known covariates. Body fat percentage was inversely associated with the magnitude of S1 (p = 0.006, β = - 366.56), RBD (p = 0.003, β = - 249.30), and S2 (p = 0.106, β = - 190.08) antibodies present in the serum following SARS-CoV-2 mRNA vaccination. Given the increasing number of infections, variants, and the known waning effects of vaccination, future mRNA vaccinations such as boosters are encouraged to sustain immunity; reducing excess body fat may improve the efficacy of these vaccinations.

The explanatory ability of COVID-19 life changes on quality of life: A comparison of those who have had and not had COVID-19

The COVID-19 pandemic has undoubtedly negatively affected individuals' quality of life through multiple means such as social isolation, exacerbated mental health conditions, and financial instability. Multiple studies have demonstrated that one of the negative correlates of quality of life is the perceived danger of COVID-19 (i.e., fear of and anxiety about COVID-19). The current study addresses limitations in the literature by testing how life changes from COVID-19 explain the direct effect of the perceived danger of COVID-19 on quality of life using a United States sample between those who have had COVID-19 compared to those who have not had COVID-19. Undergraduate students (n = 196) from a Midwestern University in the United States participated in this study for course credit (White: n = 109; 55.61%; Male: n = 94; 48.0%). Participants completed this study online and at home where they responded to a demographic form and several measures of the effects of COVID-19 and quality of life. The results suggest that COVID-19 life changes fully explain the negative relationship between the perceived danger of COVID-19 and quality of life, but only in those who have had COVID-19. In the group that has never had COVID-19, the only significant relationship was the positive relationship between the perceived danger of COVID-19 on COVID-19 life changes. The results suggest that researchers may consider steering research away from the perceived danger of COVID-19 and onto remedying life changes from COVID-19 to improve individuals' quality of life. I further discuss the theoretical findings, implications, limitations, and future directions.

A robust high-throughput fluorescence polarization assay for rapid screening of SARS-CoV-2 papain-like protease inhibitors

The global scourge of COVID-19 is a serious threat to public health, but effective therapies remain very limited for this disease. Therefore, the discovery of novel antiviral agents is urgently needed to fight against COVID-19. In the lifecycle of SARS-CoV-2, the causing pathogen of COVID-19, papain-like protease (PLpro) is responsible for the cleavage of polyprotein into functional units as well as immune evasion of vaccines. Hence, PLpro has been regarded as an attractive target to develop antiviral agents. Herein, we first developed a robust and simple sandwich-like fluorescence polarization (FP) screening assay for the discovery of PLpro inhibitors, and identified anacardic acid as a novel competitive inhibitor against PLpro in vitro with an IC₅₀ value of 24.26 ± 0.4 μM. This reliable FP screening assay could provide a prospective avenue for rapid discovery of antiviral agents targeting PLpro in a large-scale screening.

Pay attention to the speech: COVID-19 diagnosis using machine learning and crowdsourced respiratory and speech recordings

Since the outbreak of COVID-19, many efforts have been made to utilize the respiratory sounds and coughs collected by smartphones for training Machine Learning models to classify and distinguish COVID-19 sounds from healthy ones. Embedding those models into mobile applications or Internet of things devices can make effective COVID-19 pre-screening tools afforded by anyone anywhere. Most of the previous researchers trained their classifiers with respiratory sounds such as breathing or coughs, and they achieved promising results. We claim that using special voice patterns besides other respiratory sounds can achieve better performance. In this study, we used the Coswara dataset where each user has recorded 9 different types of sounds as cough, breathing, and speech labeled with COVID-19 status. A combination of models trained on different sounds can diagnose COVID-19 more accurately than a single model trained on cough or breathing only. Our results show that using simple binary classifiers can achieve an AUC of 96.4% and an accuracy of 96% by averaging the predictions of multiple models trained and evaluated separately on different sound types. Finally, this study aims to draw attention to the importance of the human voice alongside other respiratory sounds for the sound-based COVID-19 diagnosis.

Viral Etiological Agent(s) of Respiratory Tract Infections in Symptomatic Individuals during the Second Wave of COVID-19 Pandemic: A Single Drive-Thru Mobile Collection Site Study

One of the tools to contain the SARS-CoV-2 pandemic was to increase the number of performed tests and to improve the access to diagnostics. To this effect, mobile collection sites (MCSs) were established. This study was performed on samples collected at the MCS between November 2020 and March 2021. We aimed to confirm/exclude SARS-CoV-2, differentiate SARS-CoV-2 variants, and detect other respiratory pathogens. SARS-CoV-2 and other respiratory viruses were identified by RT-qPCRs. A total of 876 (46.35%) SARS-CoV-2 positive specimens in the diagnostic tests were identified. The wild-type variant was determined in 667 (76.14%) samples; the remaining 209 (23.86%) samples specimens were identified as Alpha variant. A total of 51 (5.6%) non-SARS-CoV-2 cases were detected in retrospective studies. These accounted for 33 cases of mono-infection including rhinovirus (RV), human adenovirus (HAdV), human metapneumovirus (HMPV), enterovirus (EV), and influenza virus, and 18 cases of co-infection (SARS-CoV-2 with RV or HAdV or HMPV, and RV with EV). Our research shows that the results obtained from the MCS have value in epidemiological studies, reflecting national trends on a micro scale. Although the spread of COVID-19 is a major public health concern, SARS-CoV-2 is not the only pathogen responsible for respiratory infections.

Physiological Network Is Disrupted in Severe COVID-19

The human body is a complex system maintained in homeostasis thanks to the interactions between multiple physiological regulation systems. When faced with physical or biological perturbations, this system must react by keeping a balance between adaptability and robustness. The SARS-COV-2 virus infection poses an immune system challenge that tests the organism's homeostatic response. Notably, the elderly and men are particularly vulnerable to severe disease, poor outcomes, and death. Mexico seems to have more infected young men than anywhere else. The goal of this study is to determine the differences in the relationships that link physiological variables that characterize the elderly and men, and those that characterize fatal outcomes in young men. To accomplish this, we examined a database of patients with moderate to severe COVID-19 (471 men and 277 women) registered at the "Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán" in March 2020. The sample was stratified by outcome, age, and sex. Physiological networks were built using 67 physiological variables (vital signs, anthropometric, hematic, biochemical, and tomographic variables) recorded upon hospital admission. Individual variables and system behavior were examined by descriptive statistics, differences between groups, principal component analysis, and network analysis. We show how topological network properties, particularly clustering coefficient, become disrupted in disease. Finally, anthropometric, metabolic, inflammatory, and pulmonary cluster interaction characterize the deceased young male group.

Molecular Techniques as Alternatives of Diagnostic Tools in China as Schistosomiasis Moving towards Elimination

Schistosomiasis japonica caused by the trematode flukes of Schistosoma japonicum was one of the most grievous infectious diseases in China in the mid-20th century, while its elimination has been placed on the agenda of the national strategic plan of healthy China 2030 after 70 years of continuous control campaigns. Diagnostic tools play a pivotal role in warfare against schistosomiasis but must adapt to the endemic status and objectives of activities. With the decrease of prevalence and infection intensity of schistosomiasis in human beings and livestock, optimal methodologies with high sensitivity and absolute specificity are needed for the detection of asymptomatic cases or light infections, as well as disease surveillance to verify elimination. In comparison with the parasitological methods with relatively low sensitivity and serological techniques lacking specificity, which both had been widely used in previous control stages, the molecular detection methods based on the amplification of promising genes of the schistosome genome may pick up the baton to assist the eventual aim of elimination. In this article, we reviewed the developed molecular methods for detecting S. japonicum infection and their application in schistosomiasis japonica diagnosis. Concurrently, we also analyzed the chances and challenges of molecular tools to the field application process in China.

Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey

To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).

Traveler Precautions Relating to Covid-19 Countries

Over the past two years, the issue of the rapid spread of coronavirus infection has been actively discussed. In this regard, special attention is paid to measures related to restrictions on international movement. Need to know what measures exist in different countries, what documents are required for unhindered entry into the territory of a foreign country. This article analyzes and compares passenger traffic before and during the outbreak of coronavirus infection. The analysis and comparison of air transportation was also carried out and the economic losses of companies that carried passengers to various countries of the world were indicated.

Reduced antibody activity against SARS-CoV-2 B.1.617.2 delta virus in serum of mRNA-vaccinated individuals receiving tumor necrosis factor-α inhibitors

BACKGROUND

Although vaccines effectively prevent coronavirus disease 2019 (COVID-19) in healthy individuals, they appear to be less immunogenic in individuals with chronic inflammatory disease (CID) or receiving chronic immunosuppression therapy.

METHODS

Here we assessed a cohort of 77 individuals with CID treated as monotherapy with chronic immunosuppressive drugs for antibody responses in serum against historical and variant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses after immunization with the BNT162b2 mRNA vaccine.

FINDINGS

Longitudinal analysis showed the greatest reductions in neutralizing antibodies and Fc effector function capacity in individuals treated with tumor necrosis factor alpha (TNF-α) inhibitors (TNFi), and this pattern appeared to be worse against the B.1.617.2 delta virus. Within 5 months of vaccination, serum neutralizing titers of all TNFi-treated individuals tested fell below the presumed threshold correlate for antibody-mediated protection. However, TNFi-treated individuals receiving a third mRNA vaccine dose boosted their serum neutralizing antibody titers by more than 16-fold.

CONCLUSIONS

Vaccine boosting or administration of long-acting prophylaxis (e.g., monoclonal antibodies) will likely be required to prevent SARS-CoV-2 infection in this susceptible population.

FUNDING

This study was supported by grants and contracts from the NIH (R01 AI157155, R01AI151178, and HHSN75N93019C00074; NIAID Centers of Excellence for Influenza Research and Response (CEIRR) contracts HHSN272201400008C and 75N93021C00014; and Collaborative Influenza Vaccine Innovation Centers [CIVIC] contract 75N93019C00051).

Impact of COVID-19 on Liver Transplantation in Hong Kong and Singapore: A Modelling Study

BACKGROUND

Liver transplantation (LT) activities during the COVID-19 pandemic have been curtailed in many countries. The impact of various policies restricting LT on outcomes of potential LT candidates is unclear.

METHODS

We studied all patients on the nationwide LT waitlists in Hong Kong and Singapore between January 2016 and May 2020. We used continuous time Markov chains to model the effects of different scenarios and varying durations of disruption on LT candidates.

FINDINGS

With complete cessation of LT, the projected 1-year overall survival (OS) decreased by 3•6%, 10•51% and 19•21% for a 1-, 3- and 6-month disruption respectively versus no limitation to LT, while 2-year OS decreased by 4•1%, 12•55%, and 23•43% respectively. When only urgent (acute-on-chronic liver failure [ACLF] or acute liver failure) LT was allowed, the projected 1-year OS decreased by a similar proportion: 3•1%, 8•41% and 15•20% respectively. When deceased donor LT (DDLT) and urgent living donor LT (LDLT) were allowed, 1-year projected OS decreased by 1•2%, 5•1% and 8•85% for a 1-, 3- and 6-month disruption respectively. OS was similar when only DDLT was allowed. Complete cessation of LT activities for 3-months resulted in an increased projected incidence of ACLF and hepatocellular carcinoma (HCC) dropout at 1-year by 49•1% and 107•96% respectively. When only urgent LT was allowed, HCC dropout and ACLF incidence were comparable to the rates seen in the scenario of complete LT cessation.

INTERPRETATION

A short and wide-ranging disruption to LT results in better outcomes compared with a longer duration of partial restrictions.

FUNDING

None to disclose.

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants and not with other major known variants. The assay's specificity was tested against a panel of respiratory pathogens (n = 16), showing high specificity toward SC-2 RNA. The assay's sensitivity was assessed using both in vitro transcribed RNA and clinical samples and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole-genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide-circulating SC-2 variants. IMPORTANCE This study describes the design and utilization of a multiplex reverse transcriptase quantitative PCR (RT-qPCR) to identify SARS-COV-2 (SC2) RNA in general and, specifically, to detect whether it is of lineage B.1.1.7 or B.1.351. Implementation of this method in diagnostic and research laboratories worldwide may help the efforts to contain the COVID-19 pandemic. The method can be easily scaled up and be used in high-throughput laboratories, as well as small ones. In addition to immediate help in diagnostic efforts, this method may also help in epidemiological studies focused on the spread of emerging SC-2 lineages.

COVID-19 lockdown and the forestry sector: Insight from Gandaki province of Nepal

Almost all countries have imposed large-scale mobility restrictions (or lockdown) to stop the spreading of the novel coronavirus (COVID-19). The mobility restriction has disrupted all types of business; causing a devastating impact on countries' economies; and pushing millions of people into extreme poverty. Scientists have been assessing the impact of COVID-19 lockdown on various fronts but there is limited scholarship in the forestry sector. We navigated the impact of COVID-19 lockdown on the forestry sector by taking Gandaki Province (21,974 km2) of Nepal as a case. Employing semi-structured interviews (n = 62) with all ten stakeholder groups, literature review and media analysis, our study revealed that the COVID-19 lockdown suspended all types of forestry and ecotourism businesses; obstructed research and monitoring activities; halted capacity development and extension services; impacted forest development work; and increased incidences of illegal logging and poaching and trafficking of wildlife. Because of the complete shutdown of businesses, the forestry sector of Gandaki province lost 9.6 million USD and 3.2 million man-days of employment during the lockdown period. The economic cost of the lockdown was 1.73 million USD for NTFPs traders, 1.26 million USD for ecotourism entrepreneurs, 0.55 million USD for the community forest user groups and 0.24 million USD for the smallholder or private forest owner. We suggested four post-COVID recovery pathways, including sustainable forest management, nature-based tourism, improvement of forest products value chain and community-based natural resource management to bounce back from the loss. As the current pandemic is most likely to derail the Sustainable Development Pathways of several countries, including Nepal and necessitates the need for an immediate response, the finding and recommendation of our study may inform decision-makers to reimage post-pandemic recovery and leverage sustainable development.

Case Report of COVID-19 after Full Vaccination: Viral Loads and Anti-SARS-CoV-2 Antibodies

The introduction of effective vaccines against SARS-CoV-2 is expected to prevent COVID-19. However, sporadic cases of infection in vaccinated persons have been reported. We describe a case of a double-dose vaccinated woman with COVID-19. All stages of infection were observed, from no identification of virus, then the start of the infection, a high viral load, coming out of viraemia, and finally no detection of the virus. Despite the high viral load, the woman demonstrated mild COVID-19 symptoms, manifested only by a sore throat. The antibody results showed that she produced both post-infectious and post-vaccination immune responses. Phylogenetic analysis of the obtained viral genome sequence indicated that the virus belonged to the UK SARS-CoV-2 lineage B.1.1.7 (GR 501Y.V1; 20I/S:501Y.V1; Alpha variant).

Know your enemy and know yourself - the case of SARS-CoV-2 host factors

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent that causes Coronavirus Disease 2019 (COVID-19) pandemic, is a newly emerging respiratory RNA virus with exceptional transmissibility and pathogenicity. Numerous COVID-19 related studies have been fast-tracked, with the ultimate goal to end the pandemic. Here we review the major stages of SARS-CoV-2 infection cycle in cells, with specific emphasis on essential host factors. Insights into the cell biology of SARS-CoV-2 infection have accelerated the development of host-directed therapeutics, as shown by dozens of clinical trials evaluating COVID-19 treatments using host-targeting compounds.

Assessment of Severe COVID-19 Outcomes Using Measures of Smoking Status and Smoking Intensity

Objective: Smoking status does not indicate the amount or length of tobacco use, and thus, it is an imperfect measure to assess the association between cigarette smoking and severe coronavirus disease 2019 (COVID-19) outcomes. This investigation assessed whether cigarette smoking status, intensity of smoking (i.e., average daily packs of cigarettes smoked), duration of smoking, and pack-years of smoking are associated with severe outcomes among adults diagnosed with COVID-19. Methods: We conducted a retrospective, cross-sectional study in which we identified consecutive patients diagnosed with COVID-19 at the University of Cincinnati healthcare system between 13 March 2020 and 30 September 2020 who had complete information on smoking status, severe COVID-19 outcomes, and covariates (i.e., demographics and comorbidities). We used logistic regression to evaluate the associations of smoking status and intensity of smoking with COVID-19 severity, defined as hospitalization, admission to intensive care unit (ICU), or death, adjusting for sociodemographics and comorbidities. Results: Among the 4611 COVID-19 patients included in the analysis, 18.2% were current smokers and 20.7% were former smokers. The prevalence of COVID-19 outcomes was 28.9% for hospitalization, 9.8% for ICU admission, and 1.4% for death. In the adjusted analysis, current smoking (AOR: 1.23, 95% CI: 1.02–1.49), former smoking (AOR: 1.28, 95% CI: 1.07–1.54), and pack-years of smoking (AOR: 1.09, 95% CI: 1.02–1.17) were associated with a higher prevalence of hospitalization. Average daily packs of cigarettes smoked was associated with a higher prevalence of hospitalization (AOR: 1.30, 95% CI: 1.10–1.53) and ICU admission (AOR: 1.23, 95% CI: 1.04–1.44). Conclusions: Smoking status, pack-years, and intensity of smoking were associated with hospitalizations in patients with COVID-19 and intensity of smoking was associated with ICU admission. The findings underscore the need for detailed information beyond smoking status when evaluating smokers with COVID-19 so that the potential for adverse sequelae may be optimally managed in at-risk patients.

Keep out! SARS-CoV-2 entry inhibitors: their role and utility as COVID-19 therapeutics

The COVID-19 pandemic has put healthcare infrastructures and our social and economic lives under unprecedented strain. Effective solutions are needed to end the pandemic while significantly lessening its further impact on mortality and social and economic life. Effective and widely-available vaccines have appropriately long been seen as the best way to end the pandemic. Indeed, the current availability of several effective vaccines are already making a significant progress towards achieving that goal. Nevertheless, concerns have risen due to new SARS-CoV-2 variants that harbor mutations against which current vaccines are less effective. Furthermore, some individuals are unwilling or unable to take the vaccine. As health officials across the globe scramble to vaccinate their populations to reach herd immunity, the challenges noted above indicate that COVID-19 therapeutics are still needed to work alongside the vaccines. Here we describe the impact that neutralizing antibodies have had on those with early or mild COVID-19, and what their approval for early management of COVID-19 means for other viral entry inhibitors that have a similar mechanism of action. Importantly, we also highlight studies that show that therapeutic strategies involving various viral entry inhibitors such as multivalent antibodies, recombinant ACE2 and miniproteins can be effective not only for pre-exposure prophylaxis, but also in protecting against SARS-CoV-2 antigenic drift and future zoonotic sarbecoviruses.

Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides

The catalytic subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) Nsp12 has a unique nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain that transfers nucleoside monophosphates to the Nsp9 protein and the nascent RNA. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites, and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation in bacterial cells) Nsp12 exists in an inactive state in which NiRAN-RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or nucleoside triphosphates (NTPs) partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote the synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN-RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and the design of its inhibitors.

Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides

The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), Nsp12, has a unique NiRAN domain that transfers nucleoside monophosphates to the Nsp9 protein. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation) Nsp12 exists in inactive state in which NiRAN/RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or NTPs partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN/RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically-linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and design of its inhibitors.

HIGHLIGHTS

Codon-optimization of Nsp12 triggers misfolding and activity lossSlow translation, accessory Nsp7 and Nsp8 subunits, and NTPs rescue Nsp12Non-substrate nucleotides activate RNA chain synthesis, likely via NiRAN domainCrosstalk between two Nsp12 active sites that bind the same ligands.