Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

Comment on Shah et al. Genetic Characteristics and Phylogeographic Dynamics of Lagoviruses, 1988-2021. Viruses 2023, 15, 815

Shah and colleagues [...].

Impact of plasma Epstein-Barr virus DNA in posttreatment nasopharyngeal carcinoma patients after SARS-CoV-2 infection

BACKGROUND

Nasopharyngeal carcinoma (NPC) is prevalent in southern China. EBV DNA is the most useful biomarker in NPC. However, the value of EBV DNA in posttreatment NPC patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear.

METHODS

Sixty-four eligible NPC patients were enrolled between December 2022 and February 2023. Patients who met the following criteria were included: had non-metastatic NPC, completed radical treatment, were first firstly infected with SARS-CoV-2 and their EBV DNA changed from undetectable to detectable.

RESULTS

At the end of follow-up, 81.25% (52/64) of patients were confirmed not to relapse with undetectable EBV DNA (no-relapse). In addition, 18.75% (12/64) of patients experienced relapse with consistent detection of EBV DNA (yes-relapse). For all 64 patients, the average time from diagnosis of coronavirus disease 2019 (COVID-19) to detection of detectable EBV DNA was 35.41 days (2 to 139 days). For 52 no-relapse patients, the average time from EBV DNA changing from detectable to undetectable was 63.12 days (6 to 147 days). The levels of EBV DNA were greater in yes-relapse patients than that in no-relapse patients, and the average of EBV DNA levels were 1216 copies/ml and 53.18 copies/ml, respectively. Using 62.3 copies/mL as the threshold, the area under the curve for EBV DNA was 0.88 for distinguishing yes-relapse patients from no-relapse patients. The sensitivity and specificity were 81.97% (95% CI 0.71-0.95) and 86.67% (95% CI 0.70-0.95), respectively.

CONCLUSION

For NPC patients infected with SARS-CoV-2, EBV DNA alone is insufficient for monitoring relapse after radical therapy. Long-term follow-up and underlying mechanistic investigations of EBV DNA changes are urgently needed.

COVID-19 on the spectrum: a scoping review of hygienic standards

The emergence of COVID-19 in Wuhan, China, rapidly escalated into a worldwide public health crisis. Despite numerous clinical treatment endeavors, initial defenses against the virus primarily relied on hygiene practices like mask-wearing, meticulous hand hygiene (using soap or antiseptic solutions), and maintaining social distancing. Even with the subsequent advent of vaccines and the commencement of mass vaccination campaigns, these hygiene measures persistently remain in effect, aiming to curb virus transmission until the achievement of herd immunity. In this scoping review, we delve into the effectiveness of these measures and the diverse transmission pathways, focusing on the intricate interplay within the food network. Furthermore, we explore the virus's pathophysiology, considering its survival on droplets of varying sizes, each endowed with distinct aerodynamic attributes that influence disease dispersion dynamics. While respiratory transmission remains the predominant route, the potential for oral-fecal transmission should not be disregarded, given the protracted presence of viral RNA in patients' feces after the infection period. Addressing concerns about food as a potential viral vector, uncertainties shroud the virus's survivability and potential to contaminate consumers indirectly. Hence, a meticulous and comprehensive hygienic strategy remains paramount in our collective efforts to combat this pandemic.

Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.

The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is regarded as a threat because it spreads quickly across the world without requiring a passport or establishing an identity. This tiny virus has wreaked havoc on people's lives, killed people, and created psychological problems all over the world. The viral spike protein (S) significantly contributes to host cell entry, and mutations associated with it, particularly in the receptor-binding protein (RBD), either facilitate the escape of virus from neutralizing antibodies or enhance its transmission by increasing the affinity for cell entry receptor, angiotensin-converting enzyme 2 (ACE2). The initial variants identified in Brazil, South Africa, and the UK have spread to various countries. On the other hand, new variants are being detected in India and the USA. The viral genome and proteome were applied for molecular detection techniques, and nanotechnology particles and materials were utilized in protection and prevention strategies. Consequently, the SARS-CoV-2 pandemic has resulted in extraordinary scientific community efforts to develop detection methods, diagnosis tools, and effective antiviral drugs and vaccines, where prevailing academic, governmental, and industrial institutions and organizations continue to engage themselves in large-scale screening of existing drugs, both in vitro and in vivo. In addition, COVID-19 pointed on the possible solutions for the environmental pollution globe problem. Therefore, this review aims to address SARS-CoV-2, its transmission, where it can be found, why it is severe in some people, how it can be stopped, its diagnosis and detection techniques, and its relationship with the environment.

COVID-19 Affects Serum Brain-Derived Neurotrophic Factor and Neurofilament Light Chain in Aged Men: Implications for Morbidity and Mortality

BACKGROUND AND METHODS

Severe COVID-19 is known to induce neurological damage (NeuroCOVID), mostly in aged individuals, by affecting brain-derived neurotrophic factor (BDNF), matrix metalloproteinases (MMP) 2 and 9 and the neurofilament light chain (NFL) pathways. Thus, the aim of this pilot study was to investigate BDNF, MMP-2, MMP-9, and NFL in the serum of aged men affected by COVID-19 at the beginning of the hospitalization period and characterized by different outcomes, i.e., attending a hospital ward or an intensive care unit (ICU) or with a fatal outcome. As a control group, we used a novelty of the study, unexposed age-matched men. We also correlated these findings with the routine blood parameters of the recruited individuals.

RESULTS

We found in COVID-19 individuals with severe or lethal outcomes disrupted serum BDNF, NFL, and MMP-2 presence and gross changes in ALT, GGT, LDH, IL-6, ferritin, and CRP. We also confirmed and extended previous data, using ROC analyses, showing that the ratio MMPs (2 and 9) versus BDNF and NFL might be a useful tool to predict a fatal COVID-19 outcome.

CONCLUSIONS

Serum BDNF and NFL and/or their ratios with MMP-2 and MMP-9 could represent early predictors of NeuroCOVID in aged men.

An updated review of the scientific literature on the origin of SARS-CoV-2

More than two and a half years have already passed since the first case of COVID-19 was officially reported (December 2019), as well as more than two years since the WHO declared the current pandemic (March 2020). During these months, the advances on the knowledge of the COVID-19 and SARS-CoV-2, the coronavirus responsible of the infection, have been very significant. However, there are still some weak points on that knowledge, being the origin of SARS-CoV-2 one of the most notorious. One year ago, I published a review focused on what we knew and what we need to know about the origin of that coronavirus, a key point for the prevention of potential future pandemics of a similar nature. The analysis of the available publications until July 2021 did not allow drawing definitive conclusions on the origin of SARS-CoV-2. Given the great importance of that issue, the present review was aimed at updating the scientific information on that origin. Unfortunately, there have not been significant advances on that topic, remaining basically the same two hypotheses on it. One of them is the zoonotic origin of SARS-CoV-2, while the second one is the possible leak of this coronavirus from a laboratory. Most recent papers do not include observational or experimental studies, being discussions and positions on these two main hypotheses. Based on the information here reviewed, there is not yet a definitive and well demonstrated conclusion on the origin of SARS-CoV-2.

Tracing the origin of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A systematic review and narrative synthesis

The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through various available literatures and accessible databases. Although the world enters the third year of the coronavirus disease 2019 pandemic, health and socioeconomic impacts continue to mount, the origin and mechanisms of spill-over of the SARS-CoV-2 into humans remain elusive. Therefore, a systematic review of the literature was performed that showcased the integrated information obtained through manual searches, digital databases (PubMed, CINAHL, and MEDLINE) searches, and searches from legitimate publications (1966-2022), followed by meta-analysis. Our systematic analysis data proposed three postulated hypotheses concerning the origin of the SARS-CoV-2, which include zoonotic origin (Z), laboratory origin (L), and obscure origin (O). Despite the fact that the zoonotic origin for SARS-CoV-2 has not been conclusively identified to date, our data suggest a zoonotic origin, in contrast to some alternative concepts, including the probability of a laboratory incident or leak. Our data exhibit that zoonotic origin (Z) has higher evidence-based support as compared to laboratory origin (L). Importantly, based on all the studies included, we generated the forest plot with 95% confidence intervals (CIs) of the risk ratio estimates. Our meta-analysis further supports the zoonotic origin of SARS/SARS-CoV-2 in the included studies.

SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors

The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.

Coagulopathy during COVID-19 infection: a brief review

The COVID-19 pandemic caused by SARS-CoV-2 continues to spread rapidly due to its virulence and ability to be transmitted by asymptomatic infected persons. If they are present, the symptoms of COVID-19 may include rhinorrhea (runny nose), headache, cough, and fever. Up to 5% of affected persons may experience more severe COVID-19 illness, including severe coagulopathy, acute respiratory distress syndrome (ARDS) characterized by respiratory failure that requires supplementary oxygen and mechanical ventilation, and multi-organ failure. Interestingly, clinical evidence has highlighted the distinction between COVID-19-associated coagulopathy (CAC) and disseminated intravascular coagulation (DIC). Patients with CAC exhibit different laboratory values than DIC patients for activated partial thromboplastin time (aPTT) and prothrombin time (PT) which may be normal or shortened, varying platelet counts, altered red blood cell morphology, unique bleeding complications, a lack of schistocytes in the peripheral blood, and no decrease in fibrinogen levels. In this review, we consider the search for 1) laboratory results that can diagnose or predict development of CAC, including serum levels of D-dimers, fibrinogen, interleukin-6 (IL-6) and the growth factor angiopoietin-2 (Ang-2), 2) mechanisms of CAC induction, and 3) novel therapeutic regimens that will successfully treat COVID-19 before development of CAC.

Design and Analysis of Highly Sensitive LSPR-Based Metal–Insulator–Metal Nano-Discs as a Biosensor for Fast Detection of SARS-CoV-2

For over 2 years, the coronavirus has been the most urgent challenge to humanity, and the development of rapid and accurate detection methods is crucial to control these viruses. Here, a 3D FDTD simulation of Au/SiO2/Au metal–insulator–metal (MIM) nanostructures as a biosensor was performed. The strong coupling between the two plasmonic interfaces in the Au/SiO2/Au cavity helped us to obtain relatively higher sensitivity. The attachment of SARS-CoV-2 changed the refractive index, which was used to detect SARS-CoV-2. Due to the higher overlapping of plasmonic mode with the environment of nano-discs, a higher sensitivity of 312.8 nm/RIU was obtained. The peak wavelength of the proposed structure shifted by approximately 47 nm when the surrounding medium refractive index changed from 1.35 (no binding) to 1.5 (full binding). Consequently, the SPR peak intensity variation can be used as another sensing mechanism to detect SARS-CoV-2. Finally, the previously reported refractive index changes for various concentrations of the SARS-CoV-2 S-glycoprotein solution were used to evaluate the performance of the designed biosensor.

Evidence for yeast artificial synthesis in SARS-CoV-2 and SARS-CoV-1 genomic sequences

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should also be considered.    Results: Here we show that the genomes of SARS-CoV-2 and SARS-CoV-1 significantly diverge from other SARS-like coronaviruses through short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for host cell invasion, virus replication, and host immune response. For SARS-CoV-1, we identify two sites: one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain; for SARS-CoV-2, one at the start of the viral replicase domain, and the other toward the end of the spike gene past its domain junction. At this junction, we detect a highly specific stretch of yeast origin covering the critical furin cleavage site insert PRRA, which has not been seen in other lineage b betacoronaviruses. As yeast is not a natural host for this virus family, we propose an artificial synthesis model for viral constructs in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential yeast sequence patterns congruent with chromosomes harboring specific auxotrophic markers further support yeast artificial synthesis. Conclusions: These results provide evidence that the genomes of SARS-CoV-1 and SARS-CoV-2 contain sequence information that points to their artificial synthesis in genetically modified yeast cells. Our data specifically allow the identification of the yeast S. cerevisiae as a potential recombination donor for the critical furin cleavage site in SARS-CoV-2.

Are We Sure We Fully Understand What an Infodemic Is? A Global Perspective on Infodemiological Problems

Infodemic is defined as an information epidemic that can lead to engaging in dangerous behavior. Although the most striking manifestations of the latter occurred on social media, some studies show that dismisinformation is significantly influenced by numerous additional factors, both web-based and offline. These include social context, age, education, personal knowledge and beliefs, mood, psychological defense mechanisms, media resonance, and how news and information are presented to the public. Moreover, various incorrect scientific practices related to disclosure, publication, and training can also fuel such a phenomenon. Therefore, in this opinion article, we seek to provide a comprehensive overview of the issues that need to be addressed to bridge the gap between science and the public and build resilience to the infodemic. In particular, we stress that the infodemic cannot be curbed by simply disproving every single false or misleading information since the belief system and the cultural or educational background are chief factors regarding the success of fake news. For this reason, we believe that the process of forming a critical sense should begin with children in schools (ie, when the mind is more receptive to new ways of learning). Furthermore, we also believe that themes such as scientific method and evidence should be at the heart of the university education of a future scientist. Indeed, both the public and scientists must be educated on the concepts of evidence and validity of sources, as well as learning how to dialogue appropriately with each other. Finally, we believe that the scientific publishing process could be greatly improved by paying reviewers for their work and by ceasing to pursue academic success at all costs.

Serum NGF and BDNF in Long-COVID-19 Adolescents: A Pilot Study

COVID-19 (COronaVIrus Disease 19) is an infectious disease also known as an acute respiratory syndrome caused by the SARS-CoV-2. Although in children and adolescents SARS-CoV-2 infection produces mostly mild or moderate symptoms, in a certain percentage of recovered young people a condition of malaise, defined as long-COVID-19, remains. To date, the risk factors for the development of long-COVID-19 are not completely elucidated. Neurotrophins such as NGF (Nerve Growth Factor) and BDNF (Brain-Derived Neurotrophic Factor) are known to regulate not only neuronal growth, survival and plasticity, but also to influence cardiovascular, immune, and endocrine systems in physiological and/or pathological conditions; to date only a few papers have discussed their potential role in COVID-19. In the present pilot study, we aimed to identify NGF and BDNF changes in the serum of a small cohort of male and female adolescents that contracted the infection during the second wave of the pandemic (between September and October 2020), notably in the absence of available vaccines. Blood withdrawal was carried out when the recruited adolescents tested negative for the SARS-CoV-2 ("post-infected COVID-19"), 30 to 35 days after the last molecular test. According to their COVID-19 related outcomes, the recruited individuals were divided into three groups: asymptomatics, acute symptomatics and symptomatics that over time developed long-COVID-19 symptoms ("future long-COVID-19"). As a control group, we analyzed the serum of age-matched healthy controls that did not contract the infection. Inflammatory biomarkers (TNF-α, TGF-β), MCP-1, IL-1α, IL-2, IL-6, IL-10, IL-12) were also analyzed with the free oxygen radicals' presence as an oxidative stress index. We showed that NGF serum content was lower in post-infected-COVID-19 individuals when compared to healthy controls; BDNF levels were found to be higher compared to healthy individuals only in post-infected-COVID-19 symptomatic and future long-COVID-19 girls, leaving the BDNF levels unchanged in asymptomatic individuals if compared to controls. Oxidative stress and inflammatory biomarkers were unchanged in male and female adolescents, except for TGF-β that, similarly to BDNF, was higher in post-infected-COVID-19 symptomatic and future long-COVID-19 girls. We predicted that NGF and/or BDNF could be used as early biomarkers of COVID-19 morbidity in adolescents.

SARS-CoV-2: An Overview of the Genetic Profile and Vaccine Effectiveness of the Five Variants of Concern

With the onset of the COVID-19 pandemic, enormous efforts have been made to understand the genus SARS-CoV-2. Due to the high rate of global transmission, mutations in the viral genome were inevitable. A full understanding of the viral genome and its possible changes represents one of the crucial aspects of pandemic management. Structural protein S plays an important role in the pathogenicity of SARS-CoV-2, mutations occurring at this level leading to viral forms with increased affinity for ACE2 receptors, higher transmissibility and infectivity, resistance to neutralizing antibodies and immune escape, increasing the risk of infection and disease severity. Thus, five variants of concern are currently being discussed, Alpha, Beta, Gamma, Delta and Omicron. In the present review, a comprehensive summary of the following critical aspects regarding SARS-CoV-2 has been made: (i) the genomic characteristics of SARS-CoV-2; (ii) the pathological mechanism of transmission, penetration into the cell and action on specific receptors; (iii) mutations in the SARS-CoV-2 genome; and (iv) possible implications of mutations in diagnosis, treatment, and vaccination.

Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews

SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses – one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.

SARS-CoV-2 and human retroelements: a case for molecular mimicry?

Background

The factors driving the late phase of COVID-19 are still poorly understood. However, autoimmunity is an evolving theme in COVID-19’s pathogenesis. Additionally, deregulation of human retroelements (RE) is found in many viral infections, and has also been reported in COVID-19.

Results

Unexpectedly, coronaviruses (CoV) – including SARS-CoV-2 – harbour many RE-identical sequences (up to 35 base pairs), and some of these sequences are part of SARS-CoV-2 epitopes associated to COVID-19 severity. Furthermore, RE are expressed in healthy controls and human cells and become deregulated after SARS-CoV-2 infection, showing mainly changes in long interspersed nuclear element (LINE1) expression, but also in endogenous retroviruses.

Conclusion

CoV and human RE share coding sequences, which are targeted by antibodies in COVID-19 and thus could induce an autoimmune loop by molecular mimicry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01040-2.

Replicating Viral Vector-Based Vaccines for COVID-19: Potential Avenue in Vaccination Arena

The "severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)" is the third member of human coronavirus (CoV) that is held accountable for the current "coronavirus disease 2019 (COVID-19)" pandemic. In the past two decades, the world has witnessed the emergence of two other similar CoVs, namely SARS-CoV in 2002 and MERS-CoV in 2013. The extent of spread of these earlier versions was relatively low in comparison to SARS-CoV-2. Despite having numerous reports inclined towards the zoonotic origin of the virus, one cannot simply sideline the fact that no animal originated CoV is thus far identified that is considered similar to the initial edition of SARS-CoV-2; however, under-sampling of the diverse variety of coronaviruses remains a concern. Vaccines are proved to be an effective tool for bringing the end to such a devastating pandemic. Many vaccine platforms are explored for the same but in this review paper, we will discuss the potential of replicating viral vectors as vaccine carriers for SARS-CoV-2.

Evidence for yeast artificial synthesis in SARS-CoV-2 and SARS-CoV-1 genomic sequences

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be considered.    Results: Here we show that the genomes from SARS-CoV-2 and from SARS-CoV-1 are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for host cell invasion, virus replication, and host immune response. For SARS-CoV-1, we identify two sites: one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain; for SARS-CoV-2, one at the start of the viral replicase domain, and the other toward the end of the spike gene past its domain junction. At this junction, we detect a highly specific stretch of yeast DNA origin covering the critical furin cleavage site insert PRRA, which has not been seen in other lineage b betacoronaviruses. As yeast is not a natural host for this virus family, we propose a passage model for viral constructs in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Conclusions: These results provide evidence that among SARS-like coronaviruses only the genomes of SARS-CoV-1 and SARS-CoV-2 contain information that points to a synthetic passage in genetically modified yeast cells. Our data specifically allow the identification of the yeast S. cerevisiae as a potential recombination donor for the critical furin cleavage site in SARS-CoV-2.

SARS-CoV-2 origin, myths and diagnostic technology developments

Background

After the first case of COVID-19 being announced in China in December 2019, various diagnostic technologies have been developed at unprecedented pace with the aim of providing a basis for accurate clinical intervention. However, some assays including CRISPR-based diagnostics and loop-mediated isothermal amplification (LAMP) have been less explored. As new COVID-19 technologies emerge, there is need for them to be assessed, validated and improved upon. Moreover, there is paucity of data on the essential factors governing the selection of an appropriate diagnostic approach within the correct timeframe. Myths and origin of SARS-CoV-2 remain to be controversial. Consequently, this review aims at exploring the current COVID-19 diagnostic technologies, performance evaluation, principles, suitability, specificity, sensitivity, successes and challenges of the technologies for laboratory and bedside testing.

Main Body

To date, there exist more publications on COVID-19 diagnostics as compared to the Zika virus. The SARS-CoV-2 virus genome profiles were readily available by 31st of December 2019. This was attributed to the fast-paced sharing of the epidemiological and diagnostics data of COVID-19. Timely profiling of the virus genome accelerated the development of diagnostic technologies. Furthermore, the rapid publication of studies that evaluated several diagnostic methods available provided baseline information on how the various technologies work and paved way for development of novel technologies.

Conclusion

Up to date, RT-PCR is the most preferred as compared to the other assays. This is despite the repeated false negatives reported in many of the study findings. Considering that COVID-19 has caused devastating effects on the economy, healthcare systems, agriculture and culture, timely and accurate detection of the virus is paramount in the provision of targeted therapy hence reducing chances of drug resistance, increased treatment costs and morbidity. However, information on the origin of SARS-CoV-2 still remains elusive. Furthermore, knowledge and perception of the patients toward management of SARS-CoV-2 are also paramount to proper diagnosis and management of the pandemic. Future implications of the misperceptions are that they may lead to increased non-compliance to SARS-CoV-2-related World Health Organization (WHO) policies and guidelines.

Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution

Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least 500 in each SARS-CoV-2 protein, we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frame (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in the ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2.

Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic.

Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study

BACKGROUND

COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India.

OBJECTIVE

Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2.

METHODS

High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference.

RESULTS

Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241).

CONCLUSION

Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.

Immunological challenges of the “new” infections: corona viruses

The arrival of the most recent coronavirus in 2019, SARS-CoV-2, caught the entire world by surprise, and as a result has caused more anguish due to its rapid spread and serious health consequences for the elderly and those with underlying health conditions, and its ability to generate variants of ever increasing contagiousness. But this was not the first coronavirus to infect humans. This chapter explores the history of this virus family, the emergence of the first serious infection in 2003–04 (SARS-CoV), and the related virus MERS in 2012, and the possible origins of SARS-CoV-2. The lessons of those two outbreaks that never developed into pandemics may not all have been learnt by the world health leaders of today. Nevertheless, the rapidity of vaccine development and the conventional health measure introduced during 2020, not always in good time, has almost certainly led to lower morbidities and mortalities that would otherwise have been the case. This chapter will inevitably be out of date by time this book goes to press. Nevertheless, it is to be hoped that the origin of SARS-CoV-2 will eventually be established, but sadly not without the cooperation of the major countries having the resources to carry out such complex investigations. If such a cooperation did happen, maybe future pandemics of this will be more controllable, and even never progress beyond local outbreaks.

Consumption of Phenolic-Rich Food and Dietary Supplements as a Key Tool in SARS-CoV-19 Infection

The first cases of COVID-19, which is caused by the SARS-CoV-2, were reported in December 2019. The vertiginous worldwide expansion of SARS-CoV-2 caused the collapse of health systems in several countries due to the high severity of the COVID-19. In addition to the vaccines, the search for active compounds capable of preventing and/or fighting the infection has been the main direction of research. Since the beginning of this pandemic, some evidence has highlighted the importance of a phenolic-rich diet as a strategy to reduce the progression of this disease, including the severity of the symptoms. Some of these compounds (e.g., curcumin, gallic acid or quercetin) already showed capacity to limit the infection of viruses by inhibiting entry into the cell through its binding to protein Spike, regulating the expression of angiotensin-converting enzyme 2, disrupting the replication in cells by inhibition of viral proteases, and/or suppressing and modulating the host's immune response. Therefore, this review intends to discuss the most recent findings on the potential of phenolics to prevent SARS-CoV-2.

Can Science Help Resolve the Controversy on the Origins of the SARS-CoV-2 Pandemic?

The origins of the calamitous SARS-CoV-2 pandemic are now the subject of vigorous discussion and debate between two competing hypotheses for how it entered the human population: (i) direct infection from a feral source, likely a bat and possibly with an intermediate mammalian host, and (ii) a lab accident whereby bat isolates infected a researcher, who then passed it to others. Here, we ask whether the tools of science can help resolve the origins question and conclude that while such studies can provide important information, these are unlikely to provide a definitive answer. Currently available data combined with historical precedent from other outbreaks and viewed through the prism of Occam's razor favor the feral source hypothesis, but science can provide only probabilities, not certainty.

Biofilms and Coronavirus Reservoirs: a Perspective Review

Bats are a key reservoir of coronaviruses (CoVs), including the agent of the severe acute respiratory syndrome, SARS-CoV-2, responsible for the recent deadly viral pneumonia pandemic. However, understanding how bats can harbor several microorganisms without developing illnesses is still a matter under discussion. Viruses and other pathogens are often studied as stand-alone entities, despite that, in nature, they mostly live in multispecies associations called biofilms-both externally and within the host. Microorganisms in biofilms are enclosed by an extracellular matrix that confers protection and improves survival. Previous studies have shown that viruses can secondarily colonize preexisting biofilms, and viral biofilms have also been described. In this review, we raise the perspective that CoVs can persistently infect bats due to their association with biofilm structures. This phenomenon potentially provides an optimal environment for nonpathogenic and well-adapted viruses to interact with the host, as well as for viral recombination. Biofilms can also enhance virion viability in extracellular environments, such as on fomites and in aquatic sediments, allowing viral persistence and dissemination. Moreover, understanding the biofilm lifestyle of CoVs in reservoirs might contribute to explaining several burning questions as to persistence and transmissibility of highly pathogenic emerging CoVs.

Corona and polio viruses are sensitive to short pulses of W-band gyrotron radiation

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has raised the need of versatile means for virus decontamination. Millimeter waves are used in biochemical research in dynamic nuclear polarization enhanced nuclear magnetic resonance (DNP/NMR) spectroscopy. However, their efficiency in object decontamination for viruses has not been tested yet. Here we report the high efficiency of 95 GHz waves in killing both coronavirus 229E and poliovirus. An exposure of 2 s to 95 GHz waves reduced the titer of these viruses by 99.98% and 99.375%, respectively, and formed holes in the envelope of 229E virions as detected by scanning electron microscopy (SEM) analysis. The ability of 95 GHz waves to reduce the coronavirus titer to a range of limited infective dose of SARS-CoV-2 for humans and animal models along with precise focusing capabilities for these waves suggest 95 GHz waves as an effective way to decontaminate objects.

A two diffusion stochastic model for the spread of the new corona virus SARS-CoV-2

We propose a refined version of the stochastic SEIR model for epidemic of the new corona virus SARS-Cov-2, causing the COVID-19 disease, taking into account the spread of the virus due to the regular infected individuals (transmission coefficient β ), hospitalized individuals (transmission coefficient l β , l > 0 ) and superspreaders (transmission coefficient β ' ). The model is constructed from the corresponding ordinary differential model by introducing two independent environmental white noises in transmission coefficients for above mentioned classes - one noise for infected and hospitalized individuals and the other for superspreaders. Therefore, the model is defined as a system of stochastic differential equations driven by two independent standard Brownian motions. Existence and uniqueness of the global positive solution is proven, and conditions under which extinction and persistence in mean hold are given. The theoretical results are illustrated via numerical simulations.

Archiving time series sewage samples as biological records of built environments

This commentary encourages the regular archiving of nucleic-acid-stabilized serial samples of wastewaters and/or sewage. Stabilized samples would facilitate retrospective reconstitution of built environments’ biological fluids. Biological time capsules would allow retrospective searches for nucleic acids from viruses such as SARS-CoV-2. Current resources for testing need not be diverted if samples are saved in case they become important in the future. Systematic storage would facilitate investigation into the origin and prevalence of viruses and other agents. Comparison of prevalence data from individual and clinical samplings with community wastewater would allow valuable comparison, contrast and correlation among different testing modalities. Current interest is focused on SARS-CoV-2, but archived samples could become valuable in many contexts including surveys for other infectious and chemical agents whose identity is not currently known. Archived time series of wastewater will take their place alongside other biological repositories and records including those from medical facilities, museums, eDNA, living cell and tissue collections. Together these will prove invaluable records of the evolving Anthropocene.

Population (Antibody) Testing for COVID-19-Technical Challenges, Application and Relevance, an English Perspective

In the UK, population virus or antibody testing using virus swabs, serum samples, blood spots or oral fluids has been performed to a limited extent for several diseases including measles, mumps, rubella and hepatitis and HIV. The collection of population-based infection and immunity data is key to the monitoring of disease prevalence and assessing the effectiveness of interventions such as behavioural modifications and vaccination. In particular, the biological properties of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its interaction with the human host have presented several challenges towards the development of population-based immunity testing. Measuring SARS-CoV-2 immunity requires the development of antibody assays of acceptable sensitivity and specificity which are capable of accurately detecting seroprevalence and differentiating protection from non-protective responses. Now that anti-COVID-19 vaccines are becoming available there is a pressing need to measure vaccine efficacy and the development of herd immunity. The unprecedented impact of the SARS-CoV-2 pandemic in the UK in terms of morbidity, mortality, and economic and social disruption has mobilized a national scientific effort to learn more about this virus. In this article, the challenges of testing for SARS-CoV-2 infection, particularly in relation to population-based immunity testing, will be considered and examples given of relevant national level studies.

Back to basics in COVID-19: Antigens and antibodies-Completing the puzzle

The outbreak of the coronavirus disease 2019 (COVID-19) has gathered 1 year of scientific/clinical information. This informational asset should be thoroughly and wisely used in the coming year colliding in a global task force to control this infection. Epidemiology of this infection shows that the available estimates of SARS-CoV-2 infection prevalence largely depended on the availability of molecular testing and the extent of tested population. Within molecular diagnosis, the viability and infectiousness of the virus in the tested samples should be further investigated. Moreover, SARS-CoV-2 has a genetic normal evolution that is a dynamic process. The immune system participates to the counterattack of the viral infection by pathogen elimination, cellular homoeostasis, tissue repair and generation of memory cells that would be reactivated upon a second encounter with the same virus. In all these stages, we still have knowledge to be gathered regarding antibody persistence, protective effects and immunological memory. Moreover, information regarding the intense pro-inflammatory action in severe cases still lacks and this is important in stratifying patients for difficult to treat cases. Without being exhaustive, the review will cover these important issues to be acknowledged to further advance in the battle against the current pandemia.

Evolution of SARS-CoV-2: Review of Mutations, Role of the Host Immune System

Since the reporting of the first cases of coronavirus in China and the publication of the first sequence of SARS-CoV-2 in December 2019, the virus has undergone numerous mutations. In Europe, the spring outbreak (March-April) was followed by a drop in the number of cases and deaths. The disease may have evolved into a milder form. The increase in PCR-positive cases in late summer 2020 did not lead to the expected increase in hospitalizations, ICU admissions, and deaths, based on the severity of the disease in the spring. This difference in disease severity could be due to factors independent of the virus or to the evolution of the virus. This review attempts to identify the mutations that have appeared since the beginning of the pandemic and their role in the temporal evolution of the pandemic. There are a cell and humoral type cross-reactivity in a large part of the population to common cold coronaviruses (HCoVs) and SARS-CoV-2. Evolutionarily important mutations and deletions have emerged in the SARS-CoV-2 genes encoding proteins that interact with the host immune system. In addition, one of the major mutations (in viral polymerase) is logically associated with a higher frequency of mutations throughout the genome. This frequency fluctuates over time and shows a peak at the time when the epidemic was most active. The rate of mutations in proteins involved in the relationship to the immune system continues to increase after the first outbreak. The cross-reactivity on the 1 hand and the viral mutations observed on the other hand could explain the evolution of the pandemic until the summer of 2020, partly due to the evolution of the virus in relation to the host immune system. The immunization campaign began in December 2020: concerns are emerging about a possible escape of the circulating variants vaccines in early 2021. These variants could also escape immunity acquired through infection with the 2020 strains.

Have artificial lighting and noise pollution caused zoonosis and the COVID-19 pandemic? A review

Where did the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) come from? Did it spread to 'patient zero' through proactive human-animal contact? Why did humans faced an increasing number of zoonotic diseases in the past few decades? In this article, we propose a new theory by which human pollution such as artificial lighting and noise accentuate pathogen shedding from bats and other wild habitants in urban environments. This theory differs from the current hypothesis that wildlife trades and bushmeat consumption largely contribute to the spillover of zoonotic pathogens to humans. As natural reservoirs, bats harbor the greatest number of zoonotic viruses among all mammalian orders, while they also have a unique immune system to maintain functioning. Some bat species roost in proximity with human settlements, including urban communities and surrounding areas that are potentially most impacted by anthropogenic activities. We review the behavioral changes of wild habitants, including bats and other species, caused by environmental pollution such as artificial lighting and noise pollution, with focus on the spillover of zoonotic pathogens to humans. We found that there is a strong positive correlation between environmental stress and the behavior and health conditions of wild species, including bats. Specifically, artificial lighting attracts insectivorous bats to congregate around streetlights, resulting in changes in their diets and improved likelihood of close contact with humans and animals. Moreover, many bat species avoid lit areas by expending more energies on commuting and foraging. Noise pollution has similar effects on bat behavior. Bats exposed to chronic noise pollution have weakened immune functions, increased viral shedding, and declined immunity during pregnancy, lactation, and vulnerable periods due to noised-induced stress. Other wild species exposed to artificial lighting and noise pollution also show stress-induced behaviors and deteriorated health. Overall, evidence supports our hypothesis that artificial lighting and noise pollution have been overlooked as long-term contributors to the spillover of zoonotic pathogens to humans in urban environments.