Investigating host-virus interaction mechanism and phylogenetic analysis of viral proteins involved in the pathogenesis

Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics against them. However, the complex molecular and cellular processes that these viruses use to infect and multiply in human cells have been a source of great concern for the scientific community since the discovery of the first human infecting virus. Viral disease outbreaks, such as the recent COVID-19 pandemic caused by a novel coronavirus, have claimed millions of lives and caused significant economic damage worldwide. In this study, we investigated the mechanisms of host-virus interaction and the molecular machinery involved in the pathogenesis of some common human viruses. We also performed a phylogenetic analysis of viral proteins involved in host-virus interaction to understand the changes in the sequence organization of these proteins during evolution for various strains of viruses to gain insights into the viral origin’s evolutionary perspectives.

Virus Yellows in sugar beet – possibilities to achieve virus resistance

Virus yellows in sugar beet is caused by different virus species. Monitoring has shown that Beet yellows virus (BYV), Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV) are common and widespread, while Beet mosaic virus (BtMV) is less prevalent. The green peach aphid (Myzus persicae) is considered the main vector of these viruses. Sugar beet varieties with resistance or tolerance traits are currently not available to practical growers, therefore it is imperative to support breeding efforts with improved strategies to achieve virus resistance. For this purpose, a field test was established in which yield differences between susceptible and tolerant varieties can be generated by a 3% inoculation with BMYV-carrying aphids. A greenhouse bioassay has also been developed to distinguish susceptible and tolerant genotypes following BYV infection. Both assays pave the way for future use of natural resources such as wild forms and other breeding material to screen for virus resistance. In addition, molecular biology approaches are used to identify plant susceptibility factors of the plant-virus interaction, which will be knocked out via modern precision breeding methods to generate recessive virus resistance. Consequently, genotypes with naturally occurring mutations in the appropriate factors can be used for crossbreeding processes into elite breeding material.

Identification of diverse viruses associated with grasshoppers unveils phylogenetic congruence between hosts and viruses

Locusts and grasshoppers are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling locust outbreaks in fragile ecosystems. Here we use metagenomic sequencing to profile the rich viral communities in 34 grasshopper species and report 322 viruses, including 202 novel species. Most of the identified viruses are related to other insect viruses and some are targeted by antiviral RNAi pathway, indicating they infect grasshoppers. Some plant/fungi/vertebrate associated viruses are also abundant in our samples. Our analysis of relationships between host and virus phylogenies suggests that the composition of viromes is closely allied with host evolution, and there is significant phylogenetic relatedness between grasshoppers and viruses from Lispiviridae, Partitiviridae, Orthomyxoviridae, Virgaviridae and Flaviviridae. Overall, this study is a thorough exploration of viruses in grasshoppers and provide an essential evolutionary and ecological context for host-virus interaction in Acridoidea.

Seroprevalence of Cytomegalovirus Antibodies Among COVID-19 Patients

One of the biggest infectious diseases for humans in modern history is the COVID-19 pandemic. The disease mechanisms of human viral infections have been modified by virus-virus interaction. This study was carried out to detect the seroprevalence of CMV in COVID-19 patients. A total of 105 cases (58 females and 47 males) with an age range of 17-65 years (mean age 39.52±11.02 years) were included in this study. HCMV-IgG and IgM were determined in subjects' cases. Sixty-five out of 105 (62%) were positive for SARS-CoV-2, while 40 (38%) had negative SARS-CoV-2. Forty-seven (72.3%) and 11 (16.9%) cases out of 65 SARS-CoV-2 positive patients were positive for CMV-IgG and IgM antibodies, respectively. No significant differences were noted between females and males in terms of seroprevalence rates. A high rate of positive CMV-IgG was observed among 40-64 years COVID-19 patients. It is concluded that the seroprevalence of CMV antibodies amongst COVID-19 cases is high in relation to findings in cases without SARSCoV-2.

Host Antiviral Responses against Avian Infectious Bronchitis Virus (IBV): Focus on Innate Immunity

Avian infectious bronchitis virus (IBV) is an important gammacoronavirus. The virus is highly contagious, can infect chickens of all ages, and causes considerable economic losses in the poultry industry worldwide. In the last few decades, numerous studies have been published regarding pathogenicity, vaccination, and host immunity-virus interaction. In particular, innate immunity serves as the first line of defense against invasive pathogens and plays an important role in the pathogenetic process of IBV infection. This review focuses on fundamental aspects of host innate immune responses after IBV infection, including identification of conserved viral structures and different components of host with antiviral activity, which could provide useful information for novel vaccine development, vaccination strategies, and intervention programs.

Binding Strength and Hydrogen Bond Numbers between COVID-19 RBD and HVR of Antibody

The global battle against the COVID-19 pandemic relies strongly on the human defense of antibody, which is assumed to bind the antigen’s receptor binding domain (RBD) with its hypervariable region (HVR). Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been largely limited to the genomic sequencing, which poses serious challenges to containment and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, the real cause of the antibody-virus specificity at the molecular level, which is inconceivable to be investigated otherwise. Temperature dependence was discovered in the absorption value from the 1550 cm−1 absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27 °C and 31 °C, with the relative absorbance matching the hydrogen bonding numbers of the two antibody types (19 vs. 12) at 37 °C. Meanwhile, the ratio of bonds at 27 °C, calculated by thermodynamic exponentials, produces at least 5% inaccuracy. Beyond genomic sequencing, the temperature dependence, as well as the bond number match at 37 °C between relative absorbance and the hydrogen bonding numbers of the two antibody types, is not only of clinical significance in particular but also as a sample for the physical/chemical understanding of vaccine–antibody interactions in general.

Antiviral Filtering Capacity of GO-Coated Textiles

Background. New antiviral textiles for the protection and prevention of life-threatening viral diseases are needed. Graphene oxide derivatives are versatile substances that can be combined with fabrics by different green electrochemistry methods. Methods In this study, graphene oxide (GO) nanosheets were combined with textile samples to study GO antiviral potential. GO synthesized in the Chemistry laboratories at the University of Rome Tor Vergata (Italy) and characterized with TEM/EDX, XRD, TGA, Raman spectroscopy, and FTIR, was applied at three different concentrations to linen textiles with the hot-dip and dry method to obtain filters. The GO-treated textiles were tested to prevent infection of a human glioblastoma cell line (U373) with human herpesvirus 6A (HHV-6A). Green electrochemical exfoliation of graphite into the oxidized graphene nanosheets provides a final GO-based product suitable for a virus interaction, mainly depending on the double layer of nanosheets, their corresponding nanometric sizes, and Z-potential value. Results Since GO-treated filters were able to prevent infection of cells in a dose-dependent fashion, our results suggest that GO may exert antiviral properties that can be exploited for medical devices and general use fabrics.

Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces

COVID-19 is detected using reverse transcription polymerase chain reaction (RT-PCR) of nasal swabs. A very sensitive and rapid detection technique using easily-collected fluids like saliva must be developed for safe and precise mass testing. Here, we introduce a metasurface platform for direct sensing of COVID-19 from unprocessed saliva. We computationally screen gold metasurfaces out of a pattern space of 2100 combinations for strongly-enhanced light-virus interaction with machine learning and use it to investigate the presence and concentration of the SARS-CoV-2. We use machine learning to identify the virus from Raman spectra with 95.2% sensitivity and specificity on 36 PCR positive and 33 negative clinical samples and to distinguish wild-type, alpha, and beta variants. Our results could pave the way for effective, safe and quantitative preventive screening and identification of variants.