Showing papers in "Frontiers in virology in 2022"
TL;DR: This review unravels the complex network of interactions between SARS-CoV-2 and the host cell, highlighting the knowledge that has the potential to set the basis for the development of innovative antiviral strategies.
Abstract: The ability of a virus to spread between individuals, its replication capacity and the clinical course of the infection are macroscopic consequences of a multifaceted molecular interaction of viral components with the host cell. The heavy impact of COVID-19 on the world population, economics and sanitary systems calls for therapeutic and prophylactic solutions that require a deep characterization of the interactions occurring between virus and host cells. Unveiling how SARS-CoV-2 engages with host factors throughout its life cycle is therefore fundamental to understand the pathogenic mechanisms underlying the viral infection and to design antiviral therapies and prophylactic strategies. Two years into the SARS-CoV-2 pandemic, this review provides an overview of the interplay between SARS-CoV-2 and the host cell, with focus on the machinery and compartments pivotal for virus replication and the antiviral cellular response. Starting with the interaction with the cell surface, following the virus replicative cycle through the characterization of the entry pathways, the survival and replication in the cytoplasm, to the mechanisms of egress from the infected cell, this review unravels the complex network of interactions between SARS-CoV-2 and the host cell, highlighting the knowledge that has the potential to set the basis for the development of innovative antiviral strategies.
26 citations
TL;DR: The electrostatic potential surface of the Spike protein is mapped to show that major SARS-CoV-2 variants have accumulated positive charges in solvent-exposed regions of the spike protein, especially its ACE2-binding interface, which suggests electrostatic interactions are a major contributing factor for increased Omicron transmissibility relative to other variants.
Abstract: High transmissibility is a hallmark of the Omicron variant of SARS-CoV-2. Understanding the molecular determinants of Omicron’s transmissibility will impact development of intervention strategies. Here we map the electrostatic potential surface of the Spike protein to show that major SARS-CoV-2 variants have accumulated positive charges in solvent-exposed regions of the Spike protein, especially its ACE2-binding interface. Significantly, the Omicron Spike-ACE2 complex has complementary electrostatic surfaces. In contrast, interfaces between Omicron and neutralizing antibodies tend to have similar positively charged surfaces. Structural modeling demonstrates that the electrostatic property of Omicron’s Spike receptor binding domain (S RBD) plays a role in enhancing ACE2 recognition and destabilizing Spike-antibody complexes. Collectively, our structural analysis implies that Omicron S RBD interaction interfaces have been optimized to simultaneously promote access to human ACE2 receptors and evade antibodies. These findings suggest that electrostatic interactions are a major contributing factor for increased Omicron transmissibility relative to other variants.
24 citations
TL;DR: In this paper , the structure of the spike protein's receptor binding domain was predicted to change, which may reduce antibody interaction without completely evading existing neutralizing antibodies and therefore current vaccines.
Abstract: The genome of the SARS-CoV-2 Omicron variant (B.1.1.529) was released on November 22, 2021, which has caused a flurry of media attention due the large number of mutations it contains. These raw data have spurred questions around vaccine efficacy. Given that neither the structural information nor the experimentally-derived antibody interaction of this variant are available, we have turned to predictive computational methods to model the mutated structure of the spike protein's receptor binding domain and posit potential changes to vaccine efficacy. In this study, we predict some structural changes in the receptor-binding domain that may reduce antibody interaction without completely evading existing neutralizing antibodies (and therefore current vaccines).
16 citations
TL;DR: The symptoms reported most frequently during the early phases of the pandemic by SARS-CoV-2 infected individuals were tiredness, headache, impairment of smell or taste and dry cough; with the spread of the alpha and delta variants, the frequency of nose symptoms such as blocked or runny nose and sneezing increased to being reported by almost 60% of infected individuals.
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic and public health crisis since the beginning of 2020. First recognized for the induction of severe disease, the virus also causes asymptomatic infections or infections with mild symptoms that can resemble common colds. To provide better understanding of these mild SARS-CoV-2 infections and to monitor the development of symptoms over time, we performed a detailed analysis of self-reported symptoms of SARS-CoV-2 positive and SARS-CoV-2 negative individuals. In an online-based survey, a total of 2117 individuals provided information on symptoms associated with an acute respiratory infection, 1925 of the participants had tested positive for SARS-CoV-2 infection, and 192 had tested negative. The symptoms reported most frequently during the early phases of the pandemic by SARS-CoV-2 infected individuals were tiredness, headache, impairment of smell or taste and dry cough. With the spread of the alpha and delta variants, the frequency of nose symptoms such as blocked or runny nose and sneezing increased to being reported by almost 60% of infected individuals. Interestingly, the spread of the omicron variant brought a sharp decrease in the incidence of impaired sense of smell or taste, which was reported by only 24% in this phase of the pandemic. The constellation of symptoms should be monitored closely in the months ahead, since future SARS-CoV-2 variants are likely to bring about more changes.
13 citations
TL;DR: Emerging data indicates decreasing circulating antibody levels as well as decreases in other immune correlates in vaccinated individuals, which must be interpreted with caution taking into consideration vaccine waning and the degree of vaccine variant-mismatch resulting in adaptive immune evasion by novel emerging SARS-CoV-2 variants.
Abstract: The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, is responsible for over 400 million cases and over 5. 5 million deaths worldwide. In response to widespread SARS-CoV-2 infection, immunization of the global population has approached 60% one dose and 54% full dose vaccination status. Emerging data indicates decreasing circulating antibody levels as well as decreases in other immune correlates in vaccinated individuals. Complicating the determination of vaccine effectiveness is the concomitant emergence of novel SARS-CoV-2 variants with substantial antigenic differences from the ancestral D614G strain. The Omicron variant (B.1.1.529) spike protein has over 30 mutations compared with the D614G spike protein, which was used to design most SARS-CoV-2 vaccines in use today. Therefore, breakthrough cases of SARS-CoV-2 infections or severe disease in fully vaccinated individuals must be interpreted with caution taking into consideration vaccine waning and the degree of vaccine variant-mismatch resulting in adaptive immune evasion by novel emerging SARS-CoV-2 variants.
12 citations
TL;DR: This work considers a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among several mutations that do not individually increase viral fitness—a “fitness plateau”.
Abstract: The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, fundamental facts about the evolutionary origins of VOCs remain largely unknown. One major uncertainty is whether the VOCs evolved during transmission chains of many acute infections or during long-term infections within single individuals. We test the consistency of these two possible paths with the observed dynamics, focusing on the clustered emergence of the first three VOCs, Alpha, Beta, and Gamma, in late 2020, following a period of relative evolutionary stasis. We consider a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among multiple mutations that do not individually increase viral fitness—a “fitness plateau”. Our results suggest that the timing and dynamics of the VOC emergence, together with the observed number of mutations in VOC lineages, are in best agreement with the VOC phenotype requiring multiple mutations and VOCs having evolved within single individuals with long-term infections.
11 citations
TL;DR: Whether large under-sequenced regions were present in deposited Delta variant genome sequences was identified, to investigate the extent of the coverage dropout among all the currently available Delta sequences in six countries, and to propose simple PCR primer modifications to sequence the missing region.
Abstract: The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India in July 2020 and rapidly became dominant worldwide. The ARTIC v3 protocol for SARS-CoV-2 whole-genome sequencing, which relies on a large number of PCR primers, was among the first available early in the pandemic, but may be prone to coverage dropouts that result in incomplete genome sequences. A new set of primers (v4) was designed to circumvent this issue in June 2021. In this study, we investigated whether the sequencing community adopted the new sets of primers, especially in the context of the spread of the Delta lineage, in July 2021. Because information about protocols from individual laboratories is generally difficult to obtain, the aims of the study were to identify whether large under-sequenced regions were present in deposited Delta variant genome sequences (from April to August 2021), to investigate the extent of the coverage dropout among all the currently available Delta sequences in six countries, and to propose simple PCR primer modifications to sequence the missing region, especially for the first circulating Delta variants observed in 2021 in Switzerland. Candidate primers were tested on few clinical samples, highlighting the need to further pursue primer optimization and validation on a larger and diverse set of samples.
8 citations
TL;DR: The presence of the 19-nucleotide long RNA sequence including the FCS with 100% identity to the reverse complement of the MSH3 mRNA is highly unusual and requires further investigations.
Abstract: Among numerous point mutation differences between the SARS-CoV-2 and the bat RaTG13 coronavirus, only the 12-nucleotide furin cleavage site (FCS) exceeds 3 nucleotides. A BLAST search revealed that a 19 nucleotide portion of the SARS.Cov2 genome encompassing the furing cleavage site is a 100% complementary match to a codon-optimized proprietary sequence that is the reverse complement of the human mutS homolog (MSH3). The reverse complement sequence present in SARS-CoV-2 may occur randomly but other possibilities must be considered. Recombination in an intermediate host is an unlikely explanation. Single stranded RNA viruses such as SARS-CoV-2 utilize negative strand RNA templates in infected cells, which might lead through copy choice recombination with a negative sense SARS-CoV-2 RNA to the integration of the MSH3 negative strand, including the FCS, into the viral genome. In any case, the presence of the 19-nucleotide long RNA sequence including the FCS with 100% identity to the reverse complement of the MSH3 mRNA is highly unusual and requires further investigations.
7 citations
TL;DR: Mohapatra, Mahal, Kutikuppala, Pal, Kandi, Sarangi, Obaidullah and Mishra as mentioned in this paper have published an open-access article under the terms of the Creative Commons Attribution License (CC BY).
Abstract: COPYRIGHT © 2022 Mohapatra, Mahal, Kutikuppala, Pal, Kandi, Sarangi, Obaidullah and Mishra. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Opinion PUBLISHED 23 December 2022 DOI 10.3389/fviro.2022.1077155
7 citations
TL;DR: The immunogenicity of the SARS-CoV-2 vaccine candidate pGO-1002 is established which induces potent humoral and cellular responses to the Spike and ORF3a antigens and may provide greater protection against emerging variants.
Abstract: SARS-CoV-2 is the third pathogenic coronavirus to emerge since 2000. Experience from prior outbreaks of SARS-CoV and MERS-CoV has demonstrated the importance of both humoral and cellular immunity to clinical outcome, precepts that have been recapitulated for SARS-CoV-2. Despite the unprecedented rapid development and deployment of vaccines against SARS-CoV-2, more vaccines are needed to meet global demand and to guard against immune evasion by newly emerging SARS-CoV-2 variants. Here we describe the development of pGO-1002, a novel bi-cistronic synthetic DNA vaccine that encodes consensus sequences of two SARS-CoV-2 antigens, Spike and ORF3a. Mice immunized with pGO-1002 developed humoral and cellular responses to both antigens, including antibodies and capable of neutralizing infection by a clinical SARS-CoV-2 isolate. Rats immunized with pGO-1002 by intradermal (ID) injection followed by application of suction with our GeneDerm device also developed humoral responses that included neutralizing antibodies and RBD-ACE2 blocking antibodies as well as robust cellular responses to both antigens. Significantly, in a Syrian hamster vaccination and challenge model, ID+GeneDerm-assisted vaccination prevented viral replication in the lungs and significantly reduced viral replication in the nares of hamsters challenged with either an ancestral SARS-CoV-2 strain or the B.1.351 (Beta) variant of concern. Furthermore, vaccinated immune sera inhibited virus-mediated cytopathic effects in vitro. These data establish the immunogenicity of the SARS-CoV-2 vaccine candidate pGO-1002 which induces potent humoral and cellular responses to the Spike and ORF3a antigens and may provide greater protection against emerging variants.
6 citations
TL;DR: ZIKV infection caused profound downregulation of the transcriptional activity of genes that may underly tissue morphology, neurological development, metabolism, cell signaling and inflammation, illustrating that in utero ZIKV infections causes disruption of pathways associated with CZS in the authors' model.
Abstract: Zika virus (ZIKV) infection during pregnancy causes serious adverse outcomes to the developing fetus, including fetal loss and birth defects known as congenital Zika syndrome (CZS). The mechanism by which ZIKV infection causes these adverse outcomes, and specifically the interplay between the maternal immune response and ZIKV replication has yet to be fully elucidated. Using an immunocompetent mouse model of transplacental ZIKV transmission and adverse pregnancy outcomes, we have previously shown that Asian lineage ZIKV disrupts placental morphology and induces elevated secretion of IL-1β. In the current manuscript, we characterized placental damage and inflammation during in utero African lineage ZIKV infection. Within 48 h after ZIKV infection at embryonic day 10, viral RNA was detected in placentas and fetuses from ZIKA infected dams, which corresponded with placental damage and reduced fetal viability as compared with mock infected dams. Dams infected with ZIKV had reduced proportions of trophoblasts and endothelial cells and disrupted placental morphology compared to mock infected dams. While placental IL-1β was increased in the placenta, but not the spleen, within 3 h post infection, this was not caused by activation of the NLRP3 inflammasome. Using bulk mRNAseq from placentas of ZIKV and mock infected dams, ZIKV infection caused profound downregulation of the transcriptional activity of genes that may underly tissue morphology, neurological development, metabolism, cell signaling and inflammation, illustrating that in utero ZIKV infections causes disruption of pathways associated with CZS in our model.
TL;DR: Lack of VS was frequently observed in this Harare cohort of pregnant women, mainly due to new HIV diagnosis, hence not being on ART and suboptimal duration of ART exposure, and eliminating HIV-MTCT will require timely screening and commencing women together with their spouses/intimate partners on ART before pregnancy or early after conception.
Abstract: Background Achieving and maintaining viral suppression (VS) in people living with HIV/AIDS on antiretroviral therapy (ART) remains a crucial clinical goal, more so in pregnancy to prevent mother-to-child-transmission (MTCT). There is a need to understand VS kinetics and barriers to achieving it in order to meet the target of eliminating HIV-MTCT by 2030. Methods HIV-infected pregnant women ≥20 weeks of gestation with different durations of Tenofovir/Lamivudine/Efavirenz exposures seeking antenatal care services at four primary health centres in high-density residential areas in Harare, Zimbabwe were enrolled in the University of Zimbabwe Birth Cohort Study. Plasma viral load (VL) was quantified by reverse transcriptase–polymerase chain reaction. Demographic, clinical, socio-economic and HIV- and ART-related factors were tested in multivariable logistic regression analyses as potential predictors for VS and undetectable VL. Results From March 2016 to June 2019, 608 HIV-infected pregnant women were enrolled. 63 (10.4%) were self-reported-ART-naïve; 324 (53.3%) and 221 (36.3%) initiated ART pre- and post-conception, respectively. Time from ART initiation to VS (VL ≤ 1,000 copies/ml) in 95% of the women was 126 days. Overall lack of VS (VL > 1,000 copies/ml) was observed in 133 (21.9%) women being 76.2, 27.4 and 7.7% in self-reported-ART-naïve, post-conception and pre-conception groups, respectively. Undetectable VL (≤ 50 copies/ml) was observed in 371 (61.2%) and low-level viremia (51–1,000 copies/ml) in 102 (16.8%) women. In multivariable models for all participants regardless of ART exposure, being on ART was the strongest predictor for both VS and undetectable VL (odds ratio 95% confidence interval, OR (CI): 8.9(4.2–19.5) and 8.1(3.2–24.4), respectively). For women on ART, duration of ART use >126 days was the strongest predictor with OR (CI): 6.7(3.3–14.0) for VS and 8.5(5.6–13.1) for undetectable VL. Other relevant predictors for favourable virological outcomes were older maternal age, HIV-status disclosure, absence of ART side effects and self-reported depression. Having a spouse/intimate partner on ART predicted a 4 times higher likelihood for VS. Discussion Lack of VS was frequently observed in this Harare cohort of pregnant women, mainly due to new HIV diagnosis, hence not being on ART and suboptimal duration of ART exposure. Since VS for 95% of women needed about 4 months of ART exposure, eliminating HIV-MTCT will require timely screening and commencing women together with their spouses/intimate partners on ART before pregnancy or early after conception. Clinical Trial Registration www.ClinicalTrials.gov, identifier: NCT04087239.
TL;DR: The findings show the evolution of the intra-host variability during the course of a long-lasting infection with severe acute respiratory syndrome coronavirus 2.
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. Several cases of persistent infection have been described, but there are few reports that compared the genetic variability among samples collected from the patient during infection. In the current study, we reported a viral genetic analysis of a diabetic male patient with Non-Hodgkin Lymphoma affected by persistent SARS-CoV-2 infection. We sequenced the patient-derived viral isolated both from oro/nasopharyngeal swab and VeroE6 cell line, collected from the same patient at different points of the infection. Due to the insufficient material of the second swab received, in order to obtain a complete coverage of the viral genome, it was convenient to perform a virus isolation after cell culture. Both genomes belonged to Pangolin Lineage B.1, Nextstrain clade 20A and GISAID clade G. The mutation spectrum predicted for the two viral genomes reveal three additionally mutations in the sequence of second sample when compared with mutations set identified in the first sample. Our findings show the evolution of the intra-host variability during the course of a long-lasting infection.
TL;DR: The quickly spreading in Campania of new variants of SARS-CoV-2 and the strict surveillance of the occurrence of genetic variants of the disease are suggested.
Abstract: Coronavirus disease 2019 (COVID-19) emerged in December 2019 when the first case was reported in Wuhan, China, and turned into a pandemic. Whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in understanding the disease. For this reason, we performed WGS of 101 SARS-CoV-2 strains obtained from individuals from two districts of Campania (Italy) from January to May 2021. The phylogenetic analysis of sequence data identified five types of clades including 10 different Pango lineages: 20A (Lineages B.1.258.17, B.1.258.14, and B.1.160) (n = 10; 9.9%), 20B (Lineages B.1.1.351 and B.1.374) (n = 5; 4.9%), 20E (EU1) (Lineages B.1.177.53, B.1.177.75, and B.1.177) (n = 5; 4.9%), 20I (Alpha.V1) (B.1.1.7) (n = 60; 59.4%), and 20J (Gamma.V3) (Lineage P.1.1) (n = 21; 20.7%). In the early time of the epidemic (January and February 2021), B.1.1.7 lineage was in 62% of samples only in Benevento district, while this lineage appears in Avellino later in 64% of samples from March to May. The occurrence of P.1.1 lineage spreading from March to the end of the study was recorded in all districts with the same frequencies of ~21%. The highest genomic distance was observed in Lineage P.1.1. Moreover, we identified 219 “known” missense mutations with different frequencies (114 in ORF1a/1b; 12 in ORF3a; 29 in S; 5 in M; 29 in N; and 5 each in ORF7a and ORF8). This report suggests the quickly spreading in Campania of new variants of SARS-CoV-2 and the strict surveillance of the occurrence of genetic variants of SARS-CoV-2.
TL;DR: A 43 amino acid peptide based on the N-term of Neck-domain could block the ACE2 dimerization and the interaction between RBD and ACE2, and mitigate the SARS-COV-2/host cell interaction.
Abstract: The coronavirus disease 2019 (COVID-19) pandemic has caused over 6 million death and 460 million reported cases globally. More effective antiviral medications are needed to curb the continued spread of this disease. The infection by SARS-COV-2 virus is initiated via the interaction between the receptor binding domain (RBD) of the viral glycoprotein Spike (S protein) and the N-term peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2) expressed on host cell membrane. ACE2 forms protein homodimer primarily through its ferredoxin-like fold domain (aka. Neck-domain). We investigated whether the dimerization of ACE2 receptor plays a role in SARS-COV-2 virus infection. We report here that the ACE2 receptor dimerization enhances the recognition of SARS-COV-2 S protein. A 43 amino acid peptide based on the N-term of Neck-domain could block the ACE2 dimerization and the interaction between RBD and ACE2, and mitigate the SARS-COV-2/host cell interaction. Our study illustrated a new route to develop potential therapeutics for the prevention and treatment of SARS-COV-2 viral infection.
TL;DR: Mice intoxicated and infected with ricin and SARS-CoV-2 demonstrated a marked stimulation of essential immunity genes and biological pathways involved in the activation of natural-killer response, cell death receptors, cytotoxic T-cells, Toll-like receptor signaling and the NLRP3 inflammasome pathway, which predicts clinical manifestations that are consistent with severe COVID-19 in humans.
Abstract: Severe manifestations of coronavirus disease 2019 (COVID-19) are mostly restricted to distinct groups of people who have preexisting morbidities. Most COVID-19 animal models develop a mild pathology that resolves within a relatively short period of time, reflecting the more prevalent asymptomatic-to-mild performance of the disease observed in humans. Mice are normally unaffected by SARS coronavirus-2 infection, because of the inability of the virus to bind effectively to the murine angiotensin-converting enzyme 2 (ACE2) receptor. We have previously demonstrated that induction of mild and transient pulmonary morbidity, by application of low doses of ricin, rendered CD1 mice to be susceptible to this virus, which was displayed by sustained body weight loss and mortality rates >50%. In the present study, we performed transcriptomic analyses charting the major alterations in gene expression of mice that were pre-exposed to low doses of ricin and then subjected to SARS-CoV-2 infection compared to mice that were solely exposed to ricin or infected with SARS-CoV-2. Mice intoxicated and infected with ricin and SARS-CoV-2 demonstrated a marked stimulation of essential immunity genes and biological pathways involved in the activation of natural-killer response, cell death receptors, cytotoxic T-cells, Toll-like receptor signaling and the NLRP3 inflammasome pathway. At the protein level, an induced early and transient interferon response was recorded which was subsequently suppressed. The activation of this array of genes predicts clinical manifestations that are consistent with severe COVID-19 in humans, thereby establishing the suitability of this unique animal model for the study of severe COVID-19 disease.
TL;DR: The specific pathogenesis of TTV has not been fully established, and it is believed that it may be a virus that benefits humans, and the TTV genome in the water is considered an indicator of viral contamination due to its high prevalence in water bodies.
Abstract: Torque teno virus (TTV) is a single-stranded, circular DNA virus, named after a patient (TT), formerly known as transfusion-transmitted virus (TTV), and the naming was just an accidental coincidence. The first TTV genome was detected by Nishizawa et al. in human serum (1). Due to the presence of TTV DNA in the fraction of 1.26 g/cm3 at the sucrose density gradient, DNase I did not digest this; therefore, it was considered a virus (1). Subsequently, numerous TTV and TTVrelated genomes were detected in humans and animals (2–4). According to the ICTV 2020 report, the Anelloviridae family contains 31 genera and 155 species. Among these 31 genera, the genus Alphatorquevirus has 26 species; other genera include Betatorquevirus (TTMV [torque teno mini virus] with 38 species) and Gammatorquevirus (TTMDV [torque teno midi virus] with 15 species), which contain TTV that could infect most humans. The TTV infects almost all humans globally with a high prevalence rate/omnipresence (2–5), co-infection of different genotypes of TTVs in an individual is also documented (6, 7), and it could persist in the infected individual for a long time (8). Furthermore, the TTV DNA has been detected in blood, semen, breast milk, saliva, nasal secretions, tears, bile, urine, and feces (3–5). The TTV is likely to transmit through blood, semen, breast milk, saliva, and feces (9–12). Next, the TTV DNA levels in the blood are considered a potential marker for immunological status in solid organ transplantation and immunosuppression drug treatment (13–15). The correlation of TTV DNA levels in pathological conditions like hepatitis, gastroenteritis, periodontitis, multiple sclerosis, and cancer was also documented (16–19). However, the specific pathogenesis of TTV has not been fully established, and it is also believed that it may be a virus that benefits humans (5). Interestingly, the TTV genome in the water is considered an indicator of viral contamination due to its high prevalence in water bodies (20, 21).
TL;DR: It is suggested that high IL-10 expression at the fetal-maternal interface following LCMV-Arm infection prevents clearance of viral load by impairing CD8 T cell activation and poses a significant threat to successful pregnancy outcome.
Abstract: Pregnant mice infected with Lymphocytic Choriomeningitis Virus (Armstrong) (LCMV-Arm) experience high viral loads in the placenta and uterine tissue by 5–8 days post-infection, a time when the virus is nearly completely cleared from the spleen and blood. Interleukin 10 (IL-10) plays a crucial role in T cell responses associated with systemic viral clearance. Using the LCMV-arm model of infection, we examined first, whether IL-10 is involved in viral clearance in the placenta and uterine tissue and secondly, the potential mechanisms underlying this phenomenon. C57BL/6 (WT) and mice deficient in IL-10 (IL-10 KO) were infected with LCMV-Arm on day 10 of pregnancy. Placenta and uterine tissue, collected 2 and 8 days later, were analyzed using real time RT-PCR, plaque assays for viral load, and flow cytometry. In WT mice placenta and uterine tissue expression of IL-10 was elevated with LCMV-Arm infection. Fetus resorption was elevated in WT on days 2 and 8 post-infection as compared to IL-10 KO, and by day 19 of gestation delivery was greater. Viral loads in the placenta and uterine tissue were resolved early in IL-10 KO mice, but persistent in tissues of WT mice. Levels of NRF2 and FAS were equivalent, but BCL2L11 was higher in IL-10 KO uterus. IL-6, Interferon-β (IFN-β), CCL2, and IL-17 levels were also equivalent. IL-10 KO tissues tended toward higher expression of interferon-γ (IFN-γ) and had significantly lower expression of Transforming growth factor beta (TGF-β). The proportion of placenta and uterine tissue CD8 T cells expressing the activation markers CD44hi and PD1 were elevated in IL-10 KO mice. These data suggest that high IL-10 expression at the fetal-maternal interface following LCMV-Arm infection prevents clearance of viral load by impairing CD8 T cell activation and poses a significant threat to successful pregnancy outcome. The ability to modulate IL-10 expression at the maternal-fetal interface may help overcome negative pregnancy outcomes arising during acute LCMV and other viral infections in humans.
TL;DR: Results denote a mostly cellular immune response of vampire bats to CoV infection and identify putative biomarkers that could provide new insights into CoV pathogenesis in wild and experimental populations.
Abstract: The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune mechanisms of viral tolerance is restricted to a small number of bat–virus relationships and remains poor for coronaviruses (CoVs), despite their relevance to human health. Proteomics holds particular promise for illuminating the immune factors involved in bat responses to infection, because it can accommodate especially low sample volumes (e.g., sera) and thus can be applied to both large and small bat species as well as in longitudinal studies where lethal sampling is necessarily limited. Further, as the serum proteome includes proteins secreted from not only blood cells but also proximal organs, it provides a more general characterization of immune proteins. Here, we expand our recent work on the serum proteome of wild vampire bats (Desmodus rotundus) to better understand CoV pathogenesis. Across 19 bats sampled in 2019 in northern Belize with available sera, we detected CoVs in oral or rectal swabs from four individuals (21.1% positivity). Phylogenetic analyses identified all vampire bat sequences as novel α-CoVs most closely related to known human CoVs. Across 586 identified serum proteins, we found no strong differences in protein composition nor abundance between uninfected and infected bats. However, receiver operating characteristic curve analyses identified seven to 32 candidate biomarkers of CoV infection, including AHSG, C4A, F12, GPI, DSG2, GSTO1, and RNH1. Enrichment analyses using these protein classifiers identified downregulation of complement, regulation of proteolysis, immune effector processes, and humoral immunity in CoV-infected bats alongside upregulation of neutrophil immunity, overall granulocyte activation, myeloid cell responses, and glutathione processes. Such results denote a mostly cellular immune response of vampire bats to CoV infection and identify putative biomarkers that could provide new insights into CoV pathogenesis in wild and experimental populations. More broadly, applying a similar proteomic approach across diverse bat species and to distinct life history stages in target species could improve our understanding of the immune mechanisms by which wild bats tolerate viruses.
TL;DR: Sustained elevation of type I interferon signaling, here reflected by elevated IFI27 expression in the chronic infection phase, is a key pathogenic feature of both HIV-1 and HIV-2.
Abstract: Disease progression is slower in HIV-2, as compared with HIV-1 infection, in accordance with low or undetectable plasma viremia at viral setpoint. However, it is unclear why most HIV-2 infected individuals are still at risk of developing AIDS. To explore if specific host responses are linked to HIV disease severity, we have compared blood gene expression profiles between HIV seronegative and HIV-1, HIV-2 or dually HIV-1/HIV-2 infected individuals. In this study the gene encoding Interferon alpha-inducible protein 27 (IFI27) was found to be the most differentially expressed. Detailed expression analysis revealed significantly higher IFI27 expression in HIV infected individuals compared with seronegative individuals, irrespectively of HIV type. Moreover, IFI27 expression was higher in HIV-1 than in HIV-2 infected individuals. Multiple linear regression analysis, adjusting for age and sex, showed also that plasma viral load was the strongest predictor of IFI27 expression, followed by CD4% and HIV type. In line with this, IFI27 expression was found to be higher in HIV-2 viremic, compared with HIV-2 aviremic individuals. Still, HIV-2 aviremic individuals displayed elevated IFI27 expression compared with seronegative individuals. Furthermore, in HIV-2 infected individuals, IFI27 expression was also correlated with plasma markers previously linked to inflammation and disease progression in HIV infection. Taken together, our findings suggest that sustained elevation of type I interferon signaling, here reflected by elevated IFI27 expression in the chronic infection phase, is a key pathogenic feature of both HIV-1 and HIV-2.
TL;DR: Results indicate that active anti-SARS-CoV-2 molecules exist within the repertoire of antiviral, antiparasitic and antimicrobial compounds available to date and holds promise not only for the discovery of new therapeutic targets, but also for the development of novel antiviral medicines against COVID-19.
Abstract: Until December 2021, the COVID-19 pandemic has caused more than 5.5 million deaths. Vaccines are being deployed worldwide to mitigate severe disease and death, but continued transmission and the emergence of SARS-CoV-2 variants indicate that specific treatments against COVID-19 are still necessary. We screened 400 compounds from the Medicines for Malaria Venture (MMV) Pathogen Box seeking for molecules with antiviral activity against SARS-CoV-2 by using a high-throughput screening (HTS) infection assay in Vero CCL81 cells. On resupply of 15 selected hit compounds, we confirmed that 7 of them presented a dose-dependent cytoprotective activity against SARS-CoV-2-induced cytopathic effect (CPE) in the micromolar range. They were validated in low-throughput infection assays using four different cell lines, including the human lung Calu-3 cell line. MMV000063, MMV024937, MMV688279, and MMV688991 reduced viral load in cell culture, assessed by RT-qPCR and viral plaque assay, while MMV688279 and MMV688991 (also known as nitazoxanide) were the most promising, reducing SARS-CoV-2 load by at least 100-fold at 20 µM in almost all cell types tested. Our results indicate that active anti-SARS-CoV-2 molecules exist within the repertoire of antiviral, antiparasitic and antimicrobial compounds available to date. Although the mode of action by which MMV688279 and MMV688991 reduce SARS-CoV-2 replication is yet unknown, the fact that they were active in different cell types holds promise not only for the discovery of new therapeutic targets, but also for the development of novel antiviral medicines against COVID-19.
TL;DR: Current insights on disparities in the replication of pathogenic human retroviruses are examined, with a particular focus on the determinants of structural and genetic diversity amongst HIVs and HTLV.
Abstract: Studies of retroviruses have led to many extraordinary discoveries that have advanced our understanding of not only human diseases, but also molecular biology as a whole. The most recognizable human retrovirus, human immunodeficiency virus type 1 (HIV-1), is the causative agent of the global AIDS epidemic and has been extensively studied. Other human retroviruses, such as human immunodeficiency virus type 2 (HIV-2) and human T-cell leukemia virus type 1 (HTLV-1), have received less attention, and many of the assumptions about the replication and biology of these viruses are based on knowledge of HIV-1. Existing comparative studies on human retroviruses, however, have revealed that key differences between these viruses exist that affect evolution, diversification, and potentially pathogenicity. In this review, we examine current insights on disparities in the replication of pathogenic human retroviruses, with a particular focus on the determinants of structural and genetic diversity amongst HIVs and HTLV.
TL;DR: This mini review provides an overview of HCV infection, including details on the virological aspects, infection of the immune cells, and its impact on the immune system.
Abstract: Hepatitis C is a worldwide liver disease caused by hepatitis C virus (HCV) infection. The virus causes acute and chronic liver inflammation, and it is transmitted mainly by exposure to contaminated blood. HCV is capable of infecting hepatocytes and peripheral blood mononuclear cells, causing complications and disease progression. This mini review provides an overview of HCV infection, including details on the virological aspects, infection of the immune cells, and its impact on the immune system.
TL;DR: In this article , a sylvatic dengue strain was detected in a febrile patient living in Saré Yoba in the Kolda region of southern Senegal.
Abstract: Dengue virus 2 (DENV-2) was detected in a febrile patient living in Saré Yoba in the Kolda region of southern Senegal. Phylogenetic analysis based on the full coding region revealed that the virus belongs to the DENV-2 sylvatic genotype and is closely related to a strain (JF260983/99.66% identity) detected in Spain in a tourist who traveled to Guinea-Bissau (which borders the Kolda region) in 2009. This highlights a potential recent under-reported circulation of sylvatic dengue in the southern part of Senegal and calls for reinforced integrated surveillance among humans, non-human primates, and arboreal mosquitoes through a one-health approach.
TL;DR: It is shown that one or two specific amino acid changes in the N-protein can negatively impact the analytical sensitivity of RATs, and antibodies used in such lateral flow assays should be optimized and target preferentially more conserved regions of N- protein.
Abstract: Rapid antigen tests (RATs) are used as convenient SARS-CoV-2 tests to minimize infection risks in the private and public domain (e.g., access to shops, concerts, sports, and other social events). RATs are: however, less sensitive than quantitative reverse transcription Polymerase chain reaction (RT-qPCR) assays; hence, samples with low viral loads may be misdiagnosed. Reports on the ability of RATs to detect SARS-CoV-2 variants of concern (VOCs) Delta and Omicron are often only qualitative. We, therefore, examined the analytical sensitivities of four different RATs for the detection of both full virus and recombinant proteins of relevant VOCs. Since most RATs are based on the detection of the SARS-CoV-2 nucleocapsid protein (N-protein), we constructed multiple N-protein mutants (mirroring specific amino acid exchanges of VOC N-proteins) using prokaryotic expression plasmids and site-directed PCR mutagenesis. Testing of recombinant proteins by four RATs revealed amino acid substitutions R203K and R203M, are critical for the sensitivity of some RATs. Interestingly, R203M mutation completely abrogated antigen detection even at high protein concentrations in the Delta variant. As a proof-of-concept study, we show that one or two specific amino acid changes in the N-protein can negatively impact the analytical sensitivity of RATs. Hence, antibodies used in such lateral flow assays should be optimized and target preferentially more conserved regions of N-protein.
TL;DR: Decidual and placental immunity during maternal viral (co)-infection with HIV-1, human cytomegalovirus (HCMV), and Zika virus is characterized, highlighting the importance of antiviral and immunomodulatory therapies during maternal mono-and co-infection.
Abstract: In humans, the hemochorial placenta is a unique temporary organ that forms during pregnancy to support fetal development, gaseous exchange, delivery of nutrition, removal of waste products, and provides immune protection, while maintaining tolerance to the HLA-haploidentical fetus. In this review, we characterize decidual and placental immunity during maternal viral (co)-infection with HIV-1, human cytomegalovirus (HCMV), and Zika virus. We discuss placental immunology, clinical presentation, and epidemiology, before characterizing host susceptibility and cellular tropism, and how the three viruses gain access into specific placental target cells. We describe current knowledge on host-viral interactions with decidual and stromal human placental macrophages or Hofbauer cells, trophoblasts including extra villous trophoblasts, T cells, and decidual natural killer (dNK) cells. These clinically significant viral infections elicit both innate and adaptive immune responses to control replication. However, the three viruses either during mono- or co-infection (HIV-1 and HCMV) escape detection to initiate placental inflammation associated with viral transmission to the developing fetus. Aside from congenital or perinatal infection, other adverse pregnancy outcomes include preterm labor and spontaneous abortion. In addition, maternal HIV-1 and HCMV co-infection are associated with impaired fetal and infant immunity in postnatal life and poor clinical outcomes during childhood in exposed infants, even in the absence of vertical transmission of HIV-1. Given the rapidly expanding numbers of HIV-1-exposed uninfected infants and children globally, further research is urgently needed on neonatal immune programming during maternal mono-and co-infection. This review therefore includes sections on current knowledge gaps that may prompt future research directions. These gaps reflect an emerging but poorly characterized field. Their significance and potential investigation is underscored by the fact that although viral infections result in adverse consequences in both mother and developing fetus/newborn, antiviral and immunomodulatory therapies can improve clinical outcomes in the dyad.
TL;DR: In this article , the role of egg adapted mutants in IBV vaccines on the reactivity of serum from vaccinated or IBV infected individuals was evaluated using neutralizing antibody assays and the results showed that there is a significant difference in neutralization antibody titers between the egg adapted vaccine for the B/Yamagata lineage compared to representative clinical isolates from that season and the cell cultured vaccine.
Abstract: Influenza B Viruses (IBV) have caused an increasing number of cases over the last 15 years. The focus of this study was to assess the role of egg adapted mutants in IBV vaccines on the reactivity of serum from vaccinated or IBV infected individuals. We focused on the 2017-2018 IBV season as this was a significant influenza year with reported low vaccine effectiveness by the CDC. Patient samples were obtained from Johns Hopkins Adult Emergency Room for virus isolation and antigenic characterization. Antigenic characterization was evaluated using neutralizing antibody assays. Viral characterization was carried out using viral genome sequencing and structural modeling, MDCK-SIAT1 growth curves, MDCK Plaque assays and human primary nasal epithelial cell (hNEC) growth curves. In our analysis, we found that in the vaccine strains of both IBV lineages, there was an amino acid change at position 197 (B/Brisbane HA Numbering) that leads to a loss of glycosylation. Our antigenic evaluation shows that there is a significant difference in neutralizing antibody titers between the egg adapted vaccine for the B/Yamagata lineage compared to representative clinical isolates from that season and the cell cultured vaccine. We propose that this loss of a glycosylation site is an important site for propagation in the allantois and that this common site change may play a role in antigenic recognition and therefore immune protection from circulating viruses. Screening egg cultured vaccine viruses for egg adapted mutants, further transitioning vaccine production to mammalian culture models (MDCK) or investigating new models of influenza vaccination may be necessary to improve efficacy of the seasonal influenza vaccine for protection from IBV.
TL;DR: Historic context regarding the roles of reservoir and intermediate hosts in coronavirus circulation is provided and current knowledge of these for SARS-CoV-2 is discussed to help control the global health and economic impacts of COVID-19.
Abstract: The emergence of SARS-CoV-2 in 2019 has resulted in a global pandemic with devastating human health and economic consequences. The development of multiple vaccines, antivirals and supportive care modalities have aided in our efforts to gain control of the pandemic. However, the emergence of multiple variants of concern and spillover into numerous nonhuman animal species could protract the pandemic. Further, these events also increase the difficulty in simultaneously monitoring viral evolution across multiple species and predicting future spillback potential into the human population. Here, we provide historic context regarding the roles of reservoir and intermediate hosts in coronavirus circulation and discuss current knowledge of these for SARS-CoV-2. Increased understanding of SARS-CoV-2 zoonoses are fundamental for efforts to control the global health and economic impacts of COVID-19.
TL;DR: ATA is a potent inhibitor of HBV replication by disrupting the RNase H activity of the viral polymerase.
Abstract: Background Chronic hepatitis B virus (HBV) infection is a global health threat for which there is an urgent need to develop novel therapeutics. Methods Aurintricarboxylic acid (ATA) has been demonstrated with broad-spectrum antimicrobial and antiviral activities. In this study, we implemented ATA treatment in HBV-infected and HBV-transfected hepatocytes to uncover whether ATA inhibits HBV replication and its underlying mechanism. Results HBV DNA levels were significantly reduced, while viral proteins or transcripts were not altered. In contrast, ATA treatment did not further deteriorate HBV DNAs, viral proteins, and transcripts in hepatocytes transfected by an HBV RNase H dead mutant. Moreover, ATA showed an inhibitory effect on DNA synthesis in hepatocytes transfected with lamivudine-resistant HBV mutants. Conclusions ATA is a potent inhibitor of HBV replication by disrupting the RNase H activity of the viral polymerase.
TL;DR: A tight regulation of HERV expression during human T cell development is found, with possible implications for the process of T cell selection, as well as the interplay with host restriction factors and potential underlying pathways.
Abstract: Human Endogenous Retroviruses (HERVs) constitute up to 8% of the human genome and have been emerging as important modulators of the immune system, being associated with cancer, autoimmunity and infectious diseases. Here, we investigated the expression of three HERV families in the human thymus. HERV-K, -W, and -R envelope (env) and HERV-K gag transcriptional levels were quantified in the main thymocyte subsets, thymic epithelial cells (TECs), B cells and myeloid populations, and Env protein expression was studied in thymic tissue. We found that HERV mRNA decreased with T cell development, which was in agreement with the identification of HERV-K Env protein in CD3 negative cortical cells. These results suggest a distinct regulation of HERV expression along T cell development, prompting us to evaluate the interplay with host restriction factors and potential underlying pathways. The transcriptional levels of some HERVs were found to positively correlate with the expression of the host restriction factors APOBEC3G and SLFN11, and, conversely, a negative correlation was found with SAMHD1. Moreover, IFN-α and IFN-γ induced the upregulation of HERV-K env and gag in purified CD4 single-positive thymocytes. Additionally, we found high levels of HERV mRNAs in TECs. Overall, our data support a tight regulation of HERV expression during human T cell development, with possible implications for the process of T cell selection.