Search

Molecular virology tools are critical for basic studies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and for developing new therapeutics. Experimental systems that do not rely on viruses capable of spread are needed for potential use in lower-containment settings. In this work, we use a yeast-based reverse genetics system to develop spike-deleted SARS-CoV-2 self-replicating RNAs. These noninfectious self-replicating RNAs, or replicons, can be trans-complemented with viral glycoproteins to generate replicon delivery particles for single-cycle delivery into a range of cell types. This SARS-CoV-2 replicon system represents a convenient and versatile platform for antiviral drug screening, neutralization assays, host factor validation, and viral variant characterization. [ABSTRACT FROM AUTHOR]

While RNAi is often heralded as a promising new strategy for insect pest control, a major obstacle that still remains is the efficient delivery of dsRNA molecules within the cells of the targeted insects. However, it seems overlooked that dsRNA viruses already have developed efficient strategies for transport of dsRNA molecules across tissue barriers and cellular membranes. Besides protecting their dsRNA genomes in a protective shell, dsRNA viruses also display outer capsid layers that incorporate sophisticated mechanisms to disrupt the plasma membrane layer and to translocate core particles (with linear dsRNA genome fragments) within the cytoplasm. Because of the perceived efficiency of the translocation mechanism, it is well worth analyzing in detail the molecular processes that are used to achieve this feat. In this review, the mechanism of cell entry by dsRNA viruses belonging to the Reoviridae family is discussed in detail. Because of the large amount of progress in mammalian versus insect models, the mechanism of infections of reoviruses in mammals (orthoreoviruses, rotaviruses, orbiviruses) will be treated as a point of reference against which infections of reoviruses in insects (orbiviruses in midges, plant viruses in hemipterans, insect-specific cypoviruses in lepidopterans) will be compared. The goal of this discussion is to uncover the basic principles by which dsRNA viruses cross tissue barriers and translocate their cargo to the cellular cytoplasm; such knowledge subsequently can be incorporated into the design of dsRNA virus-based viral-like particles for optimal delivery of RNAi triggers in targeted insect pests. [ABSTRACT FROM AUTHOR]

This paper aimed to investigate, analyze and visualize the scientific output of global virology research by examining the collaborative pattern and co-authorship network. A total of 80220 records were extracted from the web of science database after searching 'Virology' as a research area. Multi-authored papers are more than single-authored papers with 85% of the whole. The degree of collaboration was 0.994 in the field of Virology. Wang Y is the most active author with 429 papers, 5621 total citations, and 37 h-index. To understand the trend of evolution pattern and proximity of efficiency, we investigate a co-authorship network of a relatively new and emerging academic field. The approach and potential applications of co-authorship network analysis in virology research are discussed in this article. [ABSTRACT FROM AUTHOR]

Viral infections are posing a great threat to humanity for the last few years. Among these, Chikungunya which is a mosquito-borne viral infection has produced enormous epidemics around the world after been rebounded. Although this infection shows a low mortality rate, patients suffer from fever, arthralgia, and maculopapular rashes, which reduce the quality of life for several weeks to years. The currently available treatments only provide symptomatic relief based on analgesics, antipyretics, and anti-inflammatory drugs which are nonspecific without satisfactory results. Medicinal plants are a widely accepted source of new molecules for the treatment of infectious diseases including viral infections. The scientific reports, primarily focusing on the anti-chikungunya activity of plant extracts, natural origin pure compounds, and their synthetic analog published from 2011 to 2021, were selected from PubMed, Google Scholar, and Scopus by using related keywords like anti-chikungunya plants, natural antivirals for Chikungunya. The present review decodes scientific reports on medicinal plants against chikungunya virus (CHIKV) infection and demystifies the potential phytoconstituents which reveals that the screening of flavonoids containing plants and phytochemicals showing efficacy against other arbovirus infections, may prove as a potential lead for drug development against CHIKV. The present article also outlines pathogenesis, clinical aspects, molecular virology, and diagnostic approaches of CHIKV infection. [ABSTRACT FROM AUTHOR]

Copyright of Avian Diseases is the property of American Association of Avian Pathologists, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This document is a correction notice for an article titled "Selective targeting and clustering of phosphatidylserine lipids by RSV M protein is critical for virus particle production" published in the Journal of Biological Chemistry. The correction addresses an error in the author affiliation, stating that the correct affiliation for Jitendriya Swain, Laura Veyrié, and Delphine Muriaux is the Institut de Recherche en Infectiologie de Montpellier (IRIM), UMR 9004 CNRS, University of Montpellier, in Montpellier, France. The correction is published by Elsevier Inc on behalf of the American Society for Biochemistry and Molecular Biology. [Extracted from the article]

The Third International Conference on Crimean-Congo Hemorrhagic Fever (CCHF) was held in Thessaloniki, Greece, September 19–21, 2023, bringing together a diverse group of international partners, including public health professionals, clinicians, ecologists, epidemiologists, immunologists, and virologists. The conference was attended by 118 participants representing 24 countries and the World Health Organization (WHO). Meeting sessions covered the epidemiology of CCHF in humans; Crimean-Congo hemorrhagic fever virus (CCHFV) in ticks; wild and domestic animal hosts; molecular virology; pathogenesis and animal models; immune response related to therapeutics; and CCHF prevention in humans. The concluding session focused on recent WHO recommendations regarding disease prevention, control strategies, and innovations against CCHFV outbreaks. This meeting report summarizes lectures by the invited speakers and highlights advances in the field. [ABSTRACT FROM AUTHOR]

• The implementation of the quality management software (UnityRT) in molecular virology/microbiology was evaluated. • UnityRT consolidated the capture, analysis, monitoring, and tracking of QC data, along with corrective actions. • Real-time QC monitoring can have a significant clinical impact. Quality control (QC) is one component of an overarching quality management system (QMS) that aims at assuring laboratory quality and patient safety. QC data must be acceptable prior to reporting patients' results. Traditionally, QC statistics, records, and corrective actions were tracked at the Johns Hopkins Molecular Virology Laboratory using Microsoft Excel. Unity Real-Time (UnityRT), a QMS software (Bio-Rad Laboratories), which captures and analyzes QC data by instrument and control lot per assay, was implemented and its impact on the workflow was evaluated. The clinical utility of real-time QC monitoring using UnityRT is highlighted with a case of subtle QC trending of HIV-1 quantitative control results. A comprehensive workflow analysis was performed, with a focus on Epstein Barr Virus (EBV) and BKV quantitative viral load testing (Roche cobas 6800). The number of QC steps and time to complete each step were assessed before and after implementing UnityRT. Our assessment of monthly QC data review revealed a total of 10 steps over 57 min when using Microsoft Excel, versus 6 steps over 11 min when using UnityRT. HIV-1 QC monitoring revealed subtle trending of the low positive control above the mean from November to December 2022, correlating with a change in the reagent kit lot. This associated with a shift in patients' results from positives below the lower limit of quantification to positives between 20 and 100 copies/mL. UnityRT consolidated QC analyses, monitoring, and tracking corrective actions. UnityRT was associated with significant time savings, which along with the interfaced feature of the QC capture and data analysis, have improved the workflow and reduced the risk of laboratory errors. The HIV-1 case revealed the value of the real-time monitoring of QC. [ABSTRACT FROM AUTHOR]

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonosis with a high case fatality rate in humans. Although the disease is widely found in Africa, Europe, and Asia, the distribution and genetic diversity of CCHF virus (CCHFV) are poorly understood in African countries. To assess the risks of CCHF in Zambia, where CCHF has never been reported, epidemiologic studies in cattle and ticks were conducted. Through an indirect immunofluorescence assay, CCHFV nucleoprotein-specific serum IgG was detected in 8.4% (88/1,047) of cattle. Among 290 Hyalomma ticks, the principal vector of CCHFV, the viral genome was detected in 11 ticks. Phylogenetic analyses of the CCHFV S and M genome segments revealed that one of the detected viruses was a genetic reassortant between African and Asian strains. This study provides compelling evidence for the presence of CCHFV in Zambia and its transmission to vertebrate hosts. Author summary: Crimean-Congo hemorrhagic fever (CCHF) is a severe viral disease mainly transmitted by ticks. Effective prophylactics and therapeutics have not been established for this disease yet. While CCHF is endemic in Africa, information on the distribution and genetic diversity of CCHF virus (CCHFV) is quite limited in many Sub-Saharan African countries. In this study, we conducted serologic and molecular epidemiologic investigations for CCHFV infection in cattle and ticks in Zambia. Serologic screening revealed that 8.4% of cattle were tested positive for CCHFV-specific IgG. Hyalomma ticks infected with CCHFV were also identified by genetic screening. Phylogenetic analyses showed that one of the CCHFVs detected in Zambia was a genetic reassortant between African and Asian CCHFV strains. Currently, Zambia is considered CCHF-free country because CCHF cases have never been reported. However, the findings in this study indicate that CCHFV is maintained in Hyalomma ticks and occasionally transmitted to vertebrate hosts such as cattle in Zambia. Further epidemiologic studies and continuous monitoring of CCHFV infection should be implemented in the southern African region. [ABSTRACT FROM AUTHOR]

Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals suspected of being infected with rabies virus from different regions of Jordan were collected during 2019. Seven of them tested positive using the fluorescent antibody test and real-time SYBR RT-PCR assay. Five specimens were from stray dogs and two from foxes. The whole genome sequences were obtained from the positive samples. Sequence analysis showed that one dog virus from Al Quwaysimah city located in Amman governorate, was closely related to an Israeli strain belonging to a Cosmopolitan ME1a clade. The genomes of the remaining six viruses (four from dogs and two from foxes) collected from different areas of Jordan were genetically-related to each other and clustered together with sequences from Iran and Turkey; all belong to Cosmopolitan ME2 clade. These sequences were analyzed with six other Jordanian rabies virus nucleoprotein (N) gene sequences available in the public database, five of them belong to ME1a clade and one belongs to ME1b clade. Rabies virus whole genome data is scarce across the Middle East. This study provides a better understanding of the molecular epidemiology of rabies virus in the region. Author summary: In this study, we performed whole genome sequencing (WGS) for rabies virus (RABV) isolates from seven samples, five of which were of stray dogs, and the other two were from foxes. Specimens were collected from animals across Jordan, including Balqa, Amman, Irbid, Tafilah, and Madaba governorates. Six out of the seven isolates were belonging to the Cosmopolitan ME2 clade, which related to the Iranian and Turkish sequences. This is not the case previously, where the majority of the Jordanian isolates belong to Cosmopolitan ME1a clade and closely related to the sequences from Israel. This shift might be due to the applied regulations across borders between Jordan and Israel. Besides the growth in travel and trade movement between Jordan and Turkey, where the latter is a border country with Iran. These collected data, where such studies are not common in the Middle East countries, will enhance our understanding of the RABV evolution and epidemiology in the region for rapid and effective response for rabies virus outbreaks. [ABSTRACT FROM AUTHOR]

A growing body of evidence addressing the involvement of human cytomegalovirus (HCMV) in malignancies had directed attention to the oncomodulation paradigm. HCMV-DB infected human mammary epithelial cells (HMECs) in culture showed the emergence of clusters of rapidly proliferating, spheroid-shaped transformed cells named CTH (CMV-Transformed HMECs) cells. CTH cells assessment suggests a direct contribution of HCMV to oncogenesis, from key latent and lytic genes activating oncogenic pathways to fueling tumor evolution. We hypothesized that the presence of HCMV genome in CTH cells is of pivotal importance for determining its oncogenic potential. We previously reported the detection of a long non-coding (lnc) RNA4.9 gene in CTH cells. Therefore, we assessed here the presence of UL69 gene, located nearby and downstream of the lncRNA4.9 gene, in CTH cells. The HCMV UL69 gene in CTH cells was detected using polymerase chain reaction (PCR) and sequencing of UL69 gene was performed using Sanger method. The corresponding amino acid sequence was then blasted against the UL69 sequence derived from HCMV-DB genome using NCBI Protein BLAST tool. A 99% identity was present between the nucleotide sequence present in CTH cells and HCMV-DB genome. UL69 transcript was detected in RNA extracts of CTH cells, using a reverse transcription polymerase chain reaction (RT-PCR) assay, and pUL69 protein was identified in CTH lysates using western blotting. Ganciclovir-treated CTH cells showed a decrease in UL69 gene detection and cellular proliferation. In CTH cells, the knockdown of UL69 with siRNA was assessed by RT-qPCR and western blot to reveal the impact of pUL69 on HCMV replication and CTH cell proliferation. Finally, UL69 gene was detected in breast cancer biopsies. Our results indicate a close link between the UL69 gene detected in the HCMV-DB isolate used to infect HMECs, and the UL69 gene present in transformed CTH cells and tumor biopsies, further highlighting a direct role for HCMV in breast tumor development. [ABSTRACT FROM AUTHOR]

Background and Aim: The peste des petits ruminants (PPR) is a highly contagious disease of small ruminants which negatively affects animal production and the socioeconomic status of farmers. Peste des petits ruminants virus (PPRV) encodes eight proteins, with the viral fusion protein (F) playing a role in virus virulence and stimulating an effective protective immune response. This study aimed to isolate and complete the identification of PPRV circulating in goats in different Egyptian governorates and perform molecular characterization of the PPRV F gene. Materials and Methods: Samples were collected from unvaccinated animals with clinical signs suggestive of PPR. A total of 256 sera were tested for the detection of PPRV antibodies using a competitive enzyme-linked immunosorbent assay (c-ELISA) kit, while 214 samples of blood buffy coat preparation, animal swabs (nasal, ocular, and saliva), and fecal and tissue samples were tested for the detection of the PPRV antigen using an antigen-capture ELISA kit. Molecular diagnosis, gene cloning, blast analysis, and phylogenetic analysis were performed for the molecular characterization of PPRV. Results: The seroprevalence results of PPRV antibodies in the tested sera showed a total of 67.9% positive samples. The rates of PPR antigen recorded by the antigen-capture ELISA in the swabs (nasal and ocular) and tissue samples were 44.3%, 46.8%, and 43.5%, respectively, with saliva swabs having the highest rate of PPRV positivity (76.4%) and fecal samples having the lowest (33.3%). Molecular characterization of the PPRV Vero cell culture revealed that the circulating PPRV strain belongs to the IV lineage. Blast analysis of the PPRV F gene showed 96.7% identity with the PPRV strain Egypt-2014 fusion protein (F) gene, KT006589.1, differing by 43 single-nucleotide polymorphisms. Conclusion: The results of this study indicate that the emerging PPRV belongs to the IV lineage among small ruminant animals. The findings also indicate the need for an innovative strategy to control and eliminate this disease based on a regularly administered and effective vaccine, a test to distinguish between infected and vaccinated animals, and the need for further study on the protein structure and PPRV F gene expression, which should help us to understand the molecular evolution of the virus and control and eliminate PPR disease. [ABSTRACT FROM AUTHOR]

The hepatitis E virus (HEV) capsid protein pORF2 comprises three potential N-linked glycosylation sites. One site, N562, is located at the cell attachment and neutralizing antigenic regions. The present study performed detailed analyses of the effects of specific amino acid substitutions at position 562 in the homodimerization, glycosylation, antigenicity, immunogenicity and neutralization activities of HEV pORF2. Recombinant HEV pORF2 glycoprotein E1 (amino acids 439-617) and three mutant variants (N562L, N562C and N562K) were expressed in Pichia pastoris (P. pastoris) and SDS-PAGE, Western blot analysis, tunicamycin assay, double-antibody sandwich ELISA and in vitro PCR-based neutralization assay were performed to characterize the different constructs. All proteins were indicated to be secreted by P. pastoris and formed homodimers. Tunicamycin assay revealed the glycosylated status of the wild-type protein, but the mutants were indicated to be non-glycosylated. All proteins were immunoreactive with a neutralizing monoclonal antibody but were not recognized by the antibody after denaturation into monomers. An in vitro PCR-based neutralization assay using mouse antibodies indicated efficient neutralization against N562L, whereas antibodies against N562C and N562K were revealed to be non-neutralizing. Collectively, the present study indicated that specific amino acid substitutions at position 562 serve crucial roles in the activity of the HEV neutralizing epitope. [ABSTRACT FROM AUTHOR]

In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology. [ABSTRACT FROM AUTHOR]

Background: Molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is at the forefront of the global response to the coronavirus disease 2019 (COVID-19) pandemic. However, molecular diagnostic capabilities are poorly developed in many African countries. Efforts by the Nigeria Centre for Disease Control and other public health agencies to scale up facilities for molecular testing across the continent are well documented, but there are few accounts from the laboratories at the frontline. Intervention: As part of an institutional response to the COVID-19 pandemic, the University of Benin Teaching Hospital, Benin City, Nigeria, signed a memorandum of understanding with a World Bank-supported institution to obtain a non-proprietary testing platform, renovated an existing molecular virology laboratory and validated the test process to make SARS-CoV-2 testing readily available for decision-making by frontline health workers. These efforts resulted in the University of Benin Teaching Hospital's inclusion in the Nigeria Centre for Disease Control COVID-19 molecular laboratory network. The laboratory achieved a turnover of 12 123 tests within 7 months of operation. Challenges faced and dealt with include incompatible equipment, limited skilled manpower, unstable (unreliable) electric power supply, disrupted procurement and supply chain, and significant overhead costs. Lessons learnt: Molecular diagnostic capability is essential in laboratory preparedness for pandemic response and can be achieved by establishing collaborative networks in low-resource settings. Recommendations: Molecular diagnostic capabilities attained during the COVID-19 pandemic should be maintained by governmental support of the local biotechnology sector, collaboration with partners and stakeholders and the expansion of diagnostics to include other diseases of public health importance. [ABSTRACT FROM AUTHOR]

Annual seasonal influenza vaccines are composed of two influenza A strains representing the H1N1 and H3N2 subtypes, and two influenza B strains representing the Victoria and Yamagata lineages. Strains from these Influenza A and Influenza B viruses currently co-circulate in humans. Of these, strains associated with the H3N2 subtype are affiliated with severe influenza seasons. H3N2 influenza viruses pre-dominated during 3 of the last 5 quite severe influenza seasons. During the 2016/2017 flu season, the H3N2 component of the influenza vaccine exhibited a poor protective efficacy (∼28–42%) against preventing infection of co-circulating strains. Since their introduction to the human population in 1968, H3N2 Influenza viruses have rapidly evolved both genetically and antigenically in an attempt to escape host immune pressures. As a result, these viruses have added numerous N-linked glycans to the viral hemagglutinin (HA), increased the overall net charge of the HA molecule, changed their preferences in receptor binding, and altered the ability of neuraminidase (NA) to agglutinate red blood cells prior to host entry. Over time, these adaptations have made characterizing these viruses increasingly difficult. This review investigates these recent changes in modern H3N2 influenza viruses and explores the methods that researchers are currently developing in order to study these viruses.

The incidence of Kaposi's sarcoma-associated herpesvirus (KSHV)-associated Kaposi Sarcoma has declined precipitously in the present era of effective HIV treatment. However, KSHV-associated lymphoproliferative disorders although rare, have not seen a similar decline. Lymphoma is now a leading cause of death in people living with HIV (PLWH), indicating that the immune reconstitution provided by antiretroviral therapy is not sufficient to fully correct the lymphomagenic immune dysregulation perpetrated by HIV infection. As such, novel insights into the mechanisms of KSHV-mediated pathogenesis in the immune compartment are urgently needed in order to develop novel therapeutics aimed at prevention and treatment of KSHV-associated lymphoproliferations. In this review, we will discuss our current understanding of KSHV molecular virology in the lymphocyte compartment, concentrating on studies which explore mechanisms unique to infection in B lymphocytes. [ABSTRACT FROM AUTHOR]

Alphaviruses (genus Alphavirus ; family Togaviridae) are a medically relevant family of viruses that include chikungunya virus and Mayaro virus. Infectious cDNA clones of these viruses are necessary molecular tools to understand viral biology. Traditionally, rescuing virus from an infectious cDNA clone requires propagating plasmids in bacteria, which can result in mutations in the viral genome due to bacterial toxicity or recombination and requires specialized equipment and knowledge to propagate the bacteria. Here, we present an alternative- rolling circle amplification (RCA), an in vitro technology. We demonstrate that the viral yield of transfected RCA product is comparable to midiprepped plasmid, albeit with a slight delay in kinetics. RCA, however, is cheaper and less time-consuming. Further, sequential RCA did not introduce mutations into the viral genome, subverting the need for glycerol stocks and retransformation. These results indicate that RCA is a viable alternative to traditional plasmid-based approaches to viral rescue. [ABSTRACT FROM AUTHOR]

Problem: We investigated if the PROGINS mutation increases the risk of hepatitis E virus (HEV) infection in liver transplant recipients. PROGINS was analyzed through KASP assay; HEV serologies assessed via enzyme‐linked immunosorbent assay and multiplex cytokine assays were evaluated in plasma with the ProcartaPlex human immunoassay. Seventy liver transplant recipients were evaluated, of which 23 (33%) were HEV immunoglobuln G (IgG)‐positive (HEV+). The frequency of PROGINS in the HEV+ group was 34%, compared with 14% in those that were HEV IgG negative (HEV−). Cytokine measurements in a sub‐set of samples from HEV+/PROGINS+ individuals showed decreased plasma levels of monokine induced by gamma interferon, a proliferation‐inducing ligand, and stem cell factor, as well as increased levels of eotaxin‐3 and interleukin‐31 compared with those HEV−/PROGINS− samples. Our findings suggest an association between the PROGINS mutation and seropositivity for HEV in liver transplant recipients with consequent distorted cytokine levels. Highlights: It is unclear why transplant recipients have an increased risk of HEV infection. We found an increased rate the PROGINS mutations liver transplant in HEV‐positive individuals. [ABSTRACT FROM AUTHOR]

The presence of a quasispecies in hepatitis E virus (HEV) infection has been documented, however, the implications of a quasispecies in HEV‐host interaction are poorly understood. Here, we analyzed the whole genome sequences of a HEV 4d from the feces and liver biopsy of a patient during the icteric and convalescent phases in an acute hepatitis E infection. Viral RNAs were extracted, reversely transcribed and seven fragments encompassing the entire viral genome were amplified and cloned. By sequencing multiple colonies of each cloned viral genome amplicon with Sanger sequencing, we verified the existence of the HEV quasispecies or intra‐host genetic variations within the fecal and liver biopsy samples. There were broader genetic variations in the HEV ORF1 region including the PCP, HPX, and RdRp regions during the convalescent phase whereas more genetic variations in the ORF2 P domain during the icteric phase. The quasispecies dynamics might reflect host immune pressure during viral clearance. Highlights: Verify the presence of viral quasispecies in an acute hepatitis E virus (HEV) infection.Different pattern of quasispecies during the icteric phase and convalescent phase.Identification of hot spot genetic variations in the P domain of ORF2. [ABSTRACT FROM AUTHOR]

The pandemic caused by novel severe acute respiratory syndrome coronavirus (SARS‐CoV‐2) has resulted in over 452 822 deaths in the first 20 days of June 2020 due to the coronavirus virus disease 2019 (COVID‐19). The SARS‐CoV‐2 uses the host angiotensin‐converting enzyme 2 (ACE2) receptor to gain entry inside the human cells where it replicates by using the cell protein synthesis mechanisms. The knowledge of the tissue distribution of ACE2 in human organs is therefore important to predict the clinical course of the COVID‐19. Also important is the understanding of the viral receptor‐binding domain (RBD), a region within the spike (S) proteins, that enables the entry of the virus into the host cells to synthesize vaccine and monoclonal antibodies (mAbs). We performed an exhaustive search of human protein databases to establish the tissues that express ACE2 and performed an in‐depth analysis like sequence alignments and homology modeling of the spike protein (S) of the SARS‐CoV‐2 to identify antigenic regions in the RBD that can be exploited to synthesize vaccine and mAbs. Our results show that ACE2 is widely expressed in human organs that may explain the pulmonary, systemic, and neurological deficits seen in COVID‐19 patients. We show that though the S protein of the SARS‐CoV‐2 is a homolog of S protein of SARS‐CoV‐1, it has regions of dissimilarities in the RBD and transmembrane segments. We show peptide sequences in the RBD of SARS‐CoV‐2 that can bind to the major histocompatibility complex alleles and serve as effective epitopes for vaccine and mAbs synthesis. Highlights: On the basis of our results in the present study, the distribution and density of ACE2 receptor can be computed to understand the multisystem and specific organ attacks as seen clinically in COVID‐19 caused by SARS‐CoV‐2. The expression of ACE2 in the brain provides and explanation to the neurological deficits seen in COVID‐19 as has been widely reported now. We show the emergence of mutation (99.97% sequence identities) between the SARS‐CoV‐2 (Wuhan‐Hu‐1 virus) compared with the recently deposited genomes of diverse clinical isolates (May 2020). By the homology modeling of receptor‐binding domain (RBD) of SARS‐CoV‐1 and SARS‐CoV‐2, we show the structural similarities between both the proteins. For vaccine and monoclonal antibody synthesis against SARS‐CoV‐2 we identified peptides sequences in the receptor‐binding domain (RBD) of SARS‐CoV‐2 with strong binding predictions to the MHC class I and class II allele with log‐transformed binding affinity, nM affinity, and ranks. As the amino acids in the RBD sequences predicted in this study are known to interact with human ACE2 receptors, synthesis of monoclonal antibodies against them can prove to be of translational value. Our results could be useful for designing effective prevention and treatment strategies in COVID‐19. [ABSTRACT FROM AUTHOR]

The resurgence of Bordetella pertussis infections leading to whooping cough is a concern in many parts of the world. The number of pertussis cases in China has increased significantly since 2013. In this study, whole-genome sequencing analysis was performed for 388 B. pertussis strains isolated in China from the 1970s to 2018, combining 594 published strains from around the world. This study revealed that lineage V diverged about 50 years ago in China, while lineage IV is dominant in the other countries. It also revealed that the erythromycin-resistant sub-lineages Va, Vb, and Vc with limited genomic variation emerged 11 ~ 12 years ago. These three sub-lineages were identified after the co-purified acellular vaccines (cp-ACVs) completely replaced the previous whole cell vaccines (WCVs) after the national immunization program of 2012. It suggests that the cp-ACVs cannot induce immunity that is potent enough to restrict the spread of the lineage V, antibiotic abuse further favors the spread of this lineage in China. These findings demand a reassessment of the immunization strategy and development of new vaccines in China to stop the resurgence and drug resistance of B. pertussis. [ABSTRACT FROM AUTHOR]

Despite 25 years of research, the basic virology of Kaposi Sarcoma Herpesviruses (KSHV) in B lymphocytes remains poorly understood. This study seeks to fill critical gaps in our understanding by characterizing the B lymphocyte lineage-specific tropism of KSHV. Here, we use lymphocytes derived from 40 human tonsil specimens to determine the B lymphocyte lineages targeted by KSHV early during de novo infection in our ex vivo model system. We characterize the immunological diversity of our tonsil specimens and determine that overall susceptibility of tonsil lymphocytes to KSHV infection varies substantially between donors. We demonstrate that a variety of B lymphocyte subtypes are susceptible to KSHV infection and identify CD138+ plasma cells as a highly targeted cell type for de novo KSHV infection. We determine that infection of tonsil B cell lineages is primarily latent with few lineages contributing to lytic replication. We explore the use of CD138 and heparin sulfate proteoglycans as attachment factors for the infection of B lymphocytes and conclude that they do not play a substantial role. Finally, we determine that the host T cell microenvironment influences the course of de novo infection in B lymphocytes. These results improve our understanding of KSHV transmission and the biology of early KSHV infection in a naïve human host, and lay a foundation for further characterization of KSHV molecular virology in B lymphocyte lineages. Author summary: KSHV infection is associated with cancer in B cells and endothelial cells, particularly in the context of immune suppression. Very little is known about how KSHV is transmitted and how it initially establishes infection in a new host. Saliva is thought to be the primary route of person-to-person transmission for KSHV, making the tonsil a likely first site for KSHV replication in a new human host. Our study examines KSHV infection in B cells extracted from the tonsils of 40 human donors in order to determine what types of B cells are initially targeted for infection and examine how the presence (or absence) of other immune cells influence the initial stages of KSHV infection. We found that a variety of B cell subtypes derived from tonsils can be infected with KSHV. Interestingly, plasma cells (mature antibody-secreting B cells) were a highly targeted cell type. These results lay the foundation for further studies into the specific biology of KSHV in different types of B cells, an effort that may help us ultimately discover how to prevent the establishment of infection in these cells or reveal new ways to halt the progression of B cell cancers associated with KSHV infection. [ABSTRACT FROM AUTHOR]